U.S. patent application number 17/463597 was filed with the patent office on 2022-01-13 for flow through electroporation modules and instrumentation.
The applicant listed for this patent is Inscripta, Inc.. Invention is credited to Nathan Bade, Phillip Belgrader, Jorge Bernate, Don Masquelier.
Application Number | 20220010256 17/463597 |
Document ID | / |
Family ID | |
Filed Date | 2022-01-13 |
United States Patent
Application |
20220010256 |
Kind Code |
A1 |
Bade; Nathan ; et
al. |
January 13, 2022 |
FLOW THROUGH ELECTROPORATION MODULES AND INSTRUMENTATION
Abstract
The present disclosure provides a flow-through electroporation
device configured for use in an automated multi-module cell
processing environment and configured to decrease cell processing
time and the risk of clogging.
Inventors: |
Bade; Nathan; (Boulder,
CO) ; Bernate; Jorge; (Boulder, CO) ;
Belgrader; Phillip; (Pleasanton, CA) ; Masquelier;
Don; (Boulder, CO) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Inscripta, Inc. |
Boulder |
CO |
US |
|
|
Appl. No.: |
17/463597 |
Filed: |
September 1, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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17230196 |
Apr 14, 2021 |
11118153 |
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17463597 |
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17140057 |
Jan 2, 2021 |
11015162 |
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17230196 |
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16904386 |
Jun 17, 2020 |
10907125 |
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17140057 |
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62864368 |
Jun 20, 2019 |
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62964203 |
Jan 22, 2020 |
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International
Class: |
C12M 1/42 20060101
C12M001/42; C12M 1/00 20060101 C12M001/00; C12N 13/00 20060101
C12N013/00 |
Claims
1. A method of introducing exogenous material into live cells
comprising: providing a flow-through electroporation (FTEP) device
for introducing an exogenous material into cells in a fluid, the
FTEP device comprising: a. an inlet and ant inlet channel for
receiving a fluid comprising cells and/or exogenous material into
the FTEP device; b. an outlet and an outlet channel for removing a
fluid comprising transformed cells and exogenous material from the
FTEP device; c. a flow channel intersecting and positioned between
the inlet channel and the outlet channel, wherein the flow channel
has, moving from the inlet channel toward the outlet channel, an
inlet-filter region, an inlet-proximal region, a central region, an
outlet-proximal region, and an outlet-filter region; d. a plurality
of parallel-configured obstructions defining flow lanes disposed
within the central region of the flow channel, wherein the
parallel-configured obstructions are selected from elongated oval-,
triangular-, rectangular-, and elliptical-shaped obstructions; and
wherein the number of obstructions in the central region of the
flow channel increases from the inlet proximal region to the
central region, then decreases from the central region to in the
outlet proximal region; and e. a first and a second electrode
positioned in electrode channels, wherein the first electrode is
positioned in the inlet proximal region of the flow channel and the
second electrode is positioned in the outlet proximal region of the
flow channel; wherein the electrodes are positioned perpendicularly
to the flow channel, are in fluid and electrical communication with
fluid in the flow channel, wherein the electrodes apply one or more
electric pulses to the cells in the fluid as they pass through the
flow channel, thereby introducing exogenous material into the cells
in the fluid, and wherein the device is formed by injection molding
in one piece with the exception of the electrodes; introducing the
live cells in fluid into the inlet of the FTEP device; introducing
the exogenous material into the inlet of the FTEP device; and
applying one or more electric pulses to the live cells in the fluid
as the live cells pass through the flow channel, thereby
introducing exogenous material into the cells.
2. The method of claim 1, wherein there are three or more
parallel-configured obstructions.
3. The method of claim 1, further comprising an inlet filter
comprising filter elements disposed in the inlet-filter region of
the flow channel and an outlet filter comprising filter elements
disposed in the outlet-filter region of the flow channel.
4. The method of claim 1, further comprising a reservoir coupled to
the inlet for introducing the cells in fluid into the FTEP device
and a reservoir coupled to the outlet for removing transformed
cells from the FTEP device.
5. The method of claim 1, wherein the FTEP device comprises a
second inlet and a second inlet channel and further comprising a
reservoir coupled to the second inlet for introducing exogenous
material into the FTEP device.
6. The method of claim 5, wherein the second inlet and second inlet
channel are located between the inlet channel and the first
electrode.
7. The method of claim 5, wherein the second inlet and second inlet
channel are located between the second electrode and the outlet
channel.
8. The method of claim 1, wherein the device is configured for use
with bacterial, yeast and mammalian cells.
9. The method device of claim 8, wherein the device is configured
for use with bacterial cells.
10. The method device of claim 8, wherein the device is configured
for use with yeast cells.
11. The method device of claim 8, wherein the device is configured
for use with mammalian cells.
12. The method device of claim 1, wherein the number of
obstructions in the central region of the flow channel is from 3 to
15.
13. The method of claim 1, wherein the number of obstructions in
the central region of the flow channel increases from 3-5
obstructions at the inlet proximal region to 9-15 obstructions in
the central region, then decreases from 9-15 obstructions in the
central region to 3-5 obstructions in the outlet proximal
region.
14. The method of claim 1, wherein the narrowest flow lane between
obstructions is from 10 to 350 .mu.m wide.
15. The method of claim 14, wherein the narrowest flow lane between
obstructions is from 30 to 250 .mu.m wide.
16. The method of claim 1, the FTEP device demonstrates optimal
uptake at 6.8 psi and 3 kV.
17. The method of claim 1, wherein the electrodes supply a voltage
of 1-60 kV/cm.
18. The method of claim 17, wherein the electrodes supply a voltage
of 5-60 kV/cm.
19. The method of claim 18, wherein the electrodes supply a voltage
of 5-40 kV/cm.
20. The method of claim 1, wherein the flow through the FTEP device
is from 0.01 mL/min to 7.5 mL/min.
21. The method of claim 1, wherein the pressure in the FTEP is from
1-30 psi.
22. The method of claim 21, wherein the pressure in the FTEP is
from 2-10 psi.
23. The method of claim 1, wherein the FTEP is from 3-15 cm
long.
24. The method of claim 1, wherein the FTEP is from 4-12 cm
long.
25. The method of claim 1, wherein the FTEP is from 0.5 to 5 cm
wide.
26. The method of claim 1, further comprising a ramp in the central
region proximal to the inlet-proximal region of the flow channel to
a central portion of the central region decreasing the flow channel
height, and a ramp from the central portion of the central region
to the central region proximal to the outlet-proximal region of the
flow channel increasing the flow channel height.
27. The method of claim 1, wherein the number of obstructions in
the central region of the flow channel is from 5 to 100.
28. The method of claim 27, wherein the number of obstructions in
the central region of the flow channel is from 6 to 80.
29. The method of claim 28, wherein the number of obstructions in
the central region of the flow channel is from 7 to 60.
30. The method of claim 29, wherein the number of obstructions in
the central region of the flow channel is from 8 to 40.
Description
RELATED CASES
[0001] The present application is a continuation of U.S. Ser. No.
17/230,196, filed 14 Apr. 2021, now allowed; which is a
continuation of U.S. Ser. No. 17/140,057, filed 2 Jan. 2021,
entitled "Flow Through Electroporation Modules and
Instrumentation", now U.S. Pat. No. 11,015,162; which is a
continuation of U.S. Ser. No. 16/904,386, filed 17 Jun. 2020,
entitled "Flow Through Electroporation Modules and
Instrumentation", now U.S. Pat. No. 10,907,125; which claims
priority to U.S. Ser. No. 62/864,368, filed 20 Jun. 2019, entitled
"Flow Through Electroporation Modules and Instrumentation"; and
U.S. Ser. No. 62/964,203, filed 22 Jan. 2020, entitled "Flow
Through Electroporation Modules and Instrumentation", both of which
are incorporated herein in their entirety.
FIELD OF THE INVENTION
[0002] The present disclosure relates to flow-through
electroporation devices configured as stand-alone electroporation
modules or as one module in automated multi-module cell processing
instruments.
BACKGROUND OF THE INVENTION
[0003] In the following discussion certain articles and methods
will be described for background and introductory purposes. Nothing
contained herein is to be construed as an "admission" of prior art.
Applicant expressly reserves the right to demonstrate, where
appropriate, that the articles and methods referenced herein do not
constitute prior art under the applicable statutory provisions.
[0004] The cell membrane constitutes the primary barrier for the
transport of molecules and ions between the interior and the
exterior of a cell. Electroporation, also known as
electropermeabilization, substantially increases cell membrane
permeability in the presence of a pulsed electric field.
Traditional electroporation systems have been widely used; however,
traditional systems require high current input and suffer from
adverse environmental conditions such as electric field distortion,
local pH variation, metal ion dissolution and excess heat
generation, all of which may contribute to low electroporation
efficiency and/or cell viability. Further, traditional
electroporation systems are not easily automated or incorporated
into automated cell processing systems where electroporation is but
one process of many processes performed. There is thus a need for
automated multi-module cell processing systems and components
thereof capable of transforming multiple cells in an efficient and
automated fashion. The present invention addresses this need.
SUMMARY OF THE INVENTION
[0005] This Summary is provided to introduce a selection of
concepts in a simplified form that are further described below in
the Detailed Description. This Summary is not intended to identify
key or essential features of the claimed subject matter, nor is it
intended to be used to limit the scope of the claimed subject
matter. Other features, details, utilities, and advantages of the
claimed subject matter will be apparent from the following written
Detailed Description including those aspects illustrated in the
accompanying drawings and defined in the appended claims.
[0006] The present disclosure provides an electroporation device
configured both for use as a stand-alone electroporation device and
for use in an automated multi-module cell processing environment.
The electroporation device utilizes a microfluidic flow-through
configuration that facilitates continuous processing of cell
suspensions. By decreasing the cross-sectional area of paths or
lanes of fluid flow in the flow channel between electrodes and
adjusting the pressure driving the fluid flow through the device,
the electric field strength experienced by cells can be made
sufficiently high with a desired duration of poration to porate the
plasma membrane. The narrow flow channels are parallelized to
decrease processing time and reduce the chance of catastrophic
failure due to clogging.
[0007] In certain embodiments, there is provided a flow-through
electroporation (FTEP) device for introducing an exogenous material
into cells in a fluid, the FTEP device comprising: an inlet and an
inlet channel for receiving a fluid comprising cells and/or
exogenous material into the FTEP device; an outlet and an outlet
channel for removing a fluid comprising transformed cells and
exogenous material from the FTEP device; a flow channel
intersecting and positioned between the inlet channel and the
outlet channel, wherein the flow channel has, moving from the inlet
channel toward the outlet channel, an inlet-filter region, an
inlet-proximal region, a central region, an outlet-proximal region,
and an outlet-filter region; an inlet filter comprising filter
elements disposed in the inlet-filter region of the flow channel
and an outlet filter comprising filter elements disposed in the
outlet-filter region of the flow channel; a plurality of
obstructions defining flow paths disposed within the central region
of the flow channel; and a first and a second electrode positioned
in electrode channels, wherein the first electrode is positioned in
the inlet proximal region of the flow channel and the second
electrode is positioned in the outlet proximal region of the flow
channel; wherein the electrodes are positioned perpendicularly to
the flow channel, are in fluid and electrical communication with
fluid in the flow channel, and wherein the electrodes apply one or
more electric pulses to the cells in the fluid as they pass through
the flow channel, thereby introducing exogenous material into the
cells in the fluid.
[0008] In some aspects of this embodiment, the plurality of
obstructions defining flow paths disposed within the central region
of the flow channel increase in density from the inlet proximal
region of the flow channel to a central portion of the central
region and decrease in density from the central portion of the
central region to the outlet proximal region of the flow
channel.
[0009] In some aspects of this embodiment, the FTEP device further
comprises a reservoir coupled to the inlet for introducing the
cells in fluid into the FTEP device and a reservoir coupled to the
outlet for removing transformed cells from the FTEP device, and in
some aspects, the FTEP device comprises a second inlet and a second
inlet channel and further comprises a reservoir coupled to the
second inlet for introducing exogenous material into the FTEP
device. In some configurations, the second inlet and second inlet
channel are located between the inlet channel and the first
electrode, and in alternative configurations the second inlet and
second inlet channel are located between the first electrode and
the central region.
[0010] In some aspects, elongated obstructions may be arranged in a
parallel configuration, and in some aspects, peg-like obstructions
may be arranged in rows.
[0011] The FTEP devices described herein are configured for use
with bacterial, yeast and mammalian cells.
[0012] In some aspects, the number of obstructions in the central
region of the flow channel is from 5 to 100, and in other aspects,
the number of obstructions in the central region of the flow
channel is from 6 to 80, 7 to 60 or 8 to 40.
[0013] In some aspects, the inlet filter region comprises an inlet
filter comprising filter elements disposed in the inlet-filter
region of the flow channel, wherein the inlet filter elements
comprise triangular-, square-, rectangular-, pentagonal-,
hexagonal-, oval-, or elliptical-shaped elements.
[0014] In some aspects, the outlet filter region comprises an
outlet filter comprising filter elements disposed in the
outlet-filter region of the flow channel, wherein the outlet filter
elements comprise elongated oval-, triangular-, square-,
rectangular-, pentagonal-, hexagonal-, oval-, or elliptical-shaped
elements.
[0015] In some aspects, the narrowest flow path between
obstructions is from 10 .mu.m to 350 .mu.m wide, and in other
aspects, narrowest flow path between obstructions is from 30 .mu.m
to 250 .mu.m wide.
[0016] In some aspects, the obstructions are triangular-, square-,
rectangular-, pentagonal-, hexagonal-, oval-, or elliptical-shaped
obstructions, or a combination of two or more shaped
obstructions.
[0017] In many aspects, there is presented herein an automated
multi-module cell processing instrument comprising the FTEP devices
described herein.
[0018] In some aspects, the FTEP device demonstrates optimal uptake
at 6.8 psi and 3 kV and recapitulates a rectangular pulse and
residence time similar to a cuvette system.
[0019] In some aspects of the FTEP device, the electrodes supply a
voltage of 1-25 kV/cm, and in some aspects, the electrodes supply a
voltage of 5-60 kV/cm, or 10-50 kV/cm, or 20-40 kV/cm.
[0020] In some aspects, the flow through the FTEP device is from
0.01 mL/min to 7.5 mL/min and the pressure in the FTEP is from 1-30
psi, or from 2-10 psi. In some aspects, the FTEP is from 3-15 cm
long, or from 4-12 cm long, and from 0.5 to 5 cm wide.
[0021] In some aspects, the FTEP device further comprises a ramp in
the central region proximal to the inlet-proximal region of the
flow channel extending to a central portion of the central region,
wherein the flow channel height decreases at the central portion,
and a ramp from the central portion of the central region to the
central region proximal to the outlet-proximal region of the flow
channel wherein the flow channel height increases at the
outlet-proximal region. In some aspects, the FTEP device further
comprises steps instead of ramps wherein the decrease in channel
height from the inlet-proximal region to the central region and the
increase in channel height from the central region to the
outlet-proximal region is an abrupt step rather than a ramp.
[0022] These aspects and other features and advantages of the
invention are described below in more detail.
BRIEF DESCRIPTION OF THE DRAWINGS
[0023] The foregoing and other features and advantages of the
present disclosure will be more fully understood from the following
detailed description of illustrative embodiments taken in
conjunction with the accompanying drawings in which:
[0024] FIGS. 1A through 1C are top perspective, bottom perspective,
and bottom views, respectively, of a flow-through electroporation
device assembly. FIG. 1D depicts one embodiment of a bottom view of
an FTEP, and FIG. 1E is a blow up of the circled region of FIG. 1D.
FIGS. 1F-1H are representations of an obstruction array and
individual obstruction structures. FIGS. 1I-1K are representations
of an obstruction array and individual obstruction structures.
FIGS. 1L-1N are representations of an alternative embodiment of an
obstruction array and individual obstruction structures. FIG. 10
depicts (i) electrodes arrayed on an electrode platform before
insertion into an FTEP assembly; (ii) an electrode; and (iii) the
electrode inserted into an electrode channel with the electrode and
electrode channel adjacent to the flow channel. FIG. 1P shows
scanning electromicrographs of an inlet-filter region of a flow
channel comprising a filter, as well as an inlet.
[0025] FIGS. 2A and 2B depict the structure and components of an
exemplary embodiment of a reagent cartridge comprising an FTEP
device.
[0026] FIGS. 3A-3F depict the structure and components of an
exemplary FTEP device that is configured to reside within, e.g.,
the exemplary reagent cartridge shown in FIG. 2A.
[0027] FIGS. 4A-4C depict an automated multi-module instrument and
modules and components thereof with which to generate the edited
cells.
[0028] FIG. 5A depicts one embodiment of a rotating growth vial for
use with a cell growth module. FIG. 5B illustrates a perspective
view of one embodiment of a rotating growth vial in a cell growth
module. FIG. 5C depicts a cut-away view of the cell growth module
from FIG. 5B. FIG. 5D illustrates the cell growth module of FIG. 5B
coupled to LED, detector, and temperature regulating
components.
[0029] FIG. 6A depicts retentate (top) and permeate (bottom)
members for use in a tangential flow filtration module (e.g., cell
growth and/or concentration module), as well as the retentate and
permeate members assembled into a tangential flow assembly
(bottom). FIG. 6B depicts two side perspective views of a reservoir
assembly of a tangential flow filtration module. FIGS. 6C-6E depict
an exemplary top, with fluidic and pneumatic ports and gasket
suitable for the reservoir assemblies shown in FIG. 6B.
[0030] FIG. 7A depicts a simplified graphic of a workflow for
singulating, editing and normalizing cells. FIGS. 7B-7D depict an
embodiment of a solid wall isolation incubation and normalization
(SWIIN) module. FIG. 7E depicts the embodiment of the SWIIN module
in FIGS. 7B-7D further comprising a heater and a heated cover.
[0031] FIG. 8 is a flow chart of an exemplary method for automated
multi-module cell editing to produce the cell libraries as
described herein.
[0032] FIG. 9 is a simplified block diagram of an embodiment of an
exemplary automated multi-module cell processing instrument
comprising a solid wall singulation/growth/editing/normalization
module.
[0033] FIG. 10 is a simplified block diagram of an alternative
embodiment of an exemplary automated multi-module cell processing
instrument comprising a solid wall
singulation/growth/editing/normalization module, in this case, used
for recursive editing.
[0034] FIG. 11 is a simplified process diagram of yet another
embodiment of an exemplary automated multi-module cell processing
instrument, in this case without a singulation module.
[0035] FIG. 12A depicts an FTEP with a constricted flow channel
with obstructions at the ends of the flow channel proximate to the
inlet and outlet (at right), and an obstruction array as described
herein (at left). FIG. 12B-12D are bar graphs depicting the number
of cells that were input (far left bar), the number of cells that
survived electroporation (left bar for each datapoint), and the
number of cells that were transformed (right bar for each
datapoint) at varying kV and pressures. The obstruction arrays
described herein were benchmarked against a NEPA device and a
single constriction device.
[0036] FIG. 13 shows two graphs, at left shows simulated electric
field strength experienced by cells vs. time for cells passing
through a single constriction FTEP (such as shown in FIG. 12A, top)
and at right shows simulated electric field strength experienced by
cells vs. time for cells passing through a parallel-constriction
FTEP (such as shown in FIGS. 1M and 1N).
[0037] FIG. 14 shows the results of electric field strength and
residence time sweeps for the parallel-constriction FTEP as shown
in FIGS. 1L-IN where the obstructions in the center region define a
1 mm length, which confirms optimal uptake at 6.8 psi, 3 kV.
[0038] FIG. 15 shows the results of electric field strength and
residence time sweeps for the parallel-constriction FTEP as shown
in FIGS. 1L-IN where the obstructions in the center region define a
0.5 mm length. Note that the parallel-constriction FTEP allows one
to control the magnitude of a constant, high electric field
strength and the amount of time cells are exposed to the electric
field by simply adjusting the applied voltage and pressure.
[0039] It should be understood that the drawings are not
necessarily to scale, and that like reference numbers refer to like
features.
DETAILED DESCRIPTION
[0040] All of the functionalities described in connection with one
embodiment of the methods, devices or instruments described herein
are intended to be applicable to the additional embodiments of the
methods, devices and instruments described herein except where
expressly stated or where the feature or function is incompatible
with the additional embodiments. For example, where a given feature
or function is expressly described in connection with one
embodiment but not expressly mentioned in connection with an
alternative embodiment, it should be understood that the feature or
function may be deployed, utilized, or implemented in connection
with the alternative embodiment unless the feature or function is
incompatible with the alternative embodiment.
[0041] The practice of the techniques described herein may employ,
unless otherwise indicated, conventional techniques and
descriptions of molecular biology (including recombinant
techniques), cell biology, biochemistry, and genetic engineering
technology, which are within the skill of those who practice in the
art. Such conventional techniques and descriptions can be found in
standard laboratory manuals such as Green and Sambrook, Molecular
Cloning: A Laboratory Manual. 4th, ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y., (2014); Current
Protocols in Molecular Biology, Ausubel, et al. eds., (2017);
Neumann, et al., Electroporation and Electrofusion in Cell Biology,
Plenum Press, N.Y., 1989; and Chang, et al., Guide to
Electroporation and Electrofusion, Academic Press, Calif. (1992),
all of which are herein incorporated in their entirety by reference
for all purposes. Nucleic acid-guided nuclease techniques can be
found in, e.g., Genome Editing and Engineering from TALENs and
CRISPRs to Molecular Surgery, Appasani and Church (2018); and
CRISPR: Methods and Protocols, Lindgren and Charpentier (2015);
both of which are herein incorporated in their entirety by
reference for all purposes.
[0042] Note that as used herein and in the appended claims, the
singular forms "a," "an," and "the" include plural referents unless
the context clearly dictates otherwise. Thus, for example,
reference to "a cell" refers to one or more cells, and reference to
"the system" includes reference to equivalent steps, methods and
devices known to those skilled in the art, and so forth.
Additionally, it is to be understood that terms such as "left,"
"right," "top," "bottom," "front," "rear," "side," "height,"
"length," "width," "upper," "lower," "interior," "exterior,"
"inner," and/or "outer" that may be used herein merely describe
points of reference and do not necessarily limit embodiments of the
present disclosure to any particular orientation or configuration.
Furthermore, terms such as "first," "second," "third," etc., merely
identify one of a number of portions, components, steps,
operations, functions, and/or points of reference as disclosed
herein, and likewise do not necessarily limit embodiments of the
present disclosure to any particular configuration or
orientation.
[0043] Additionally, the terms "approximately," "proximate,"
"minor," and similar terms generally refer to ranges that include
the identified value within a margin of 20%, 10% or preferably 5%
in certain embodiments, and any values therebetween.
[0044] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. All
publications mentioned herein are incorporated by reference for the
purpose of describing and disclosing devices, formulations and
methodologies that may be used in connection with the presently
described invention.
[0045] Where a range of values is provided, it is understood that
each intervening value, between the upper and lower limit of that
range and any other stated or intervening value in that stated
range is encompassed within the invention. The upper and lower
limits of these smaller ranges may independently be included in
smaller ranges, and are also encompassed within the invention,
subject to any specifically excluded limit in the stated range.
Where the stated range includes one or both of the limits, ranges
excluding either or both of those included limits are also included
in the invention.
[0046] In the following description, numerous specific details are
set forth to provide a more thorough understanding of the present
invention. However, it will be apparent to one of skill in the art
that the present invention may be practiced without one or more of
these specific details. In other instances, features and procedures
well known to those skilled in the art have not been described in
order to avoid obscuring the invention. The terms used herein are
intended to have the plain and ordinary meaning as understood by
those of ordinary skill in the art.
[0047] The term "complementary" as used herein refers to
Watson-Crick base pairing between nucleotides and specifically
refers to nucleotides hydrogen-bonded to one another with thymine
or uracil residues linked to adenine residues by two hydrogen bonds
and cytosine and guanine residues linked by three hydrogen bonds.
In general, a nucleic acid includes a nucleotide sequence described
as having a "percent complementarity" or "percent homology" to a
specified second nucleotide sequence. For example, a nucleotide
sequence may have 80%, 90%, or 100% complementarity to a specified
second nucleotide sequence, indicating that 8 of 10, 9 of 10 or 10
of 10 nucleotides of a sequence are complementary to the specified
second nucleotide sequence. For instance, the nucleotide sequence
3'-TCGA-5' is 100% complementary to the nucleotide sequence
5'-AGCT-3'; and the nucleotide sequence 3'-TCGA-5' is 100%
complementary to a region of the nucleotide sequence
5'-TAGCTG-3'.
[0048] The term DNA "control sequences" refers collectively to
promoter sequences, polyadenylation signals, transcription
termination sequences, upstream regulatory domains, origins of
replication, internal ribosome entry sites, nuclear localization
sequences, enhancers, and the like, which collectively provide for
the replication, transcription and translation of a coding sequence
in a recipient cell. Not all of these types of control sequences
need to be present so long as a selected coding sequence is capable
of being replicated, transcribed and--for some
components--translated in an appropriate host cell.
[0049] As used herein the term "donor DNA" or "donor nucleic acid"
refers to nucleic acid that is designed to introduce a DNA sequence
modification (insertion, deletion, substitution) into a locus by
homologous recombination using nucleic acid-guided nucleases. For
homology-directed repair, the donor DNA must have sufficient
homology to the regions flanking the "cut site" or site to be
edited in the genomic target sequence. The length of the homology
arm(s) will depend on, e.g., the type and size of the modification
being made. In many instances and preferably, the donor DNA will
have two regions of sequence homology (e.g., two homology arms) to
the genomic target locus. Preferably, an "insert" region or "DNA
sequence modification" region--the nucleic acid modification that
one desires to be introduced into a genome target locus in a
cell-will be located between two regions of homology. The DNA
sequence modification may change one or more bases of the target
genomic DNA sequence at one specific site or multiple specific
sites. A change may include changing 1, 2, 3, 4, 5, 10, 15, 20, 25,
30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more base
pairs of the target sequence. A deletion or insertion may be a
deletion or insertion of 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50,
75, 100, 150, 200, 300, 400, or 500 or more base pairs of the
target sequence.
[0050] As used herein, "enrichment" refers to enriching for edited
cells by singulation, optionally inducing editing, and growth of
singulated or substantially singulated cells into terminal-sized
colonies (e.g., saturation or normalization of colony growth).
Alternatively, "enrichment" may be performed on a bulk liquid
culture, by inducing editing when the cells are at the end of the
logarithmic stage of growth or just after the cells enter growth
senescence. Inducing editing entails inducing transcription of the
nuclease, gRNA or both.
[0051] The terms "guide nucleic acid" or "guide RNA" or "gRNA"
refer to a polynucleotide comprising 1) a guide sequence capable of
hybridizing to a genomic target locus, and 2) a scaffold sequence
capable of interacting or complexing with a nucleic acid-guided
nuclease.
[0052] "Homology" or "identity" or "similarity" refers to sequence
similarity between two peptides or, more often in the context of
the present disclosure, between two nucleic acid molecules. The
term "homologous region" or "homology arm" refers to a region on
the donor DNA with a certain degree of homology with the target
genomic DNA sequence. Homology can be determined by comparing a
position in each sequence which may be aligned for purposes of
comparison. When a position in the compared sequence is occupied by
the same base or amino acid, then the molecules are homologous at
that position. A degree of homology between sequences is a function
of the number of matching or homologous positions shared by the
sequences.
[0053] "Operably linked" refers to an arrangement of elements where
the components so described are configured so as to perform their
usual function. Thus, control sequences operably linked to a coding
sequence are capable of effecting the transcription, and in some
cases, the translation, of a coding sequence. The control sequences
need not be contiguous with the coding sequence so long as they
function to direct the expression of the coding sequence. Thus, for
example, intervening untranslated yet transcribed sequences can be
present between a promoter sequence and the coding sequence and the
promoter sequence can still be considered "operably linked" to the
coding sequence. In fact, such sequences need not reside on the
same contiguous DNA molecule (i.e. chromosome) and may still have
interactions resulting in altered regulation.
[0054] A "promoter" or "promoter sequence" is a DNA regulatory
region capable of binding RNA polymerase and initiating
transcription of a polynucleotide or polypeptide coding sequence
such as messenger RNA, ribosomal RNA, small nuclear or nucleolar
RNA, guide RNA, or any kind of RNA transcribed by any class of any
RNA polymerase I, II or III. Promoters may be constitutive or
inducible, and in some embodiments--particularly many embodiments
in which enrichment is employed--the transcription of at least one
component of the nucleic acid-guided nuclease editing system is
under the control of an inducible promoter.
[0055] As used herein the term "selectable marker" refers to a gene
introduced into a cell, which confers a trait suitable for
artificial selection. General use selectable markers are well-known
to those of ordinary skill in the art. Drug selectable markers such
as ampicillin/carbenicillin, kanamycin, chloramphenicol,
erythromycin, tetracycline, gentamicin, bleomycin, streptomycin,
rifampicin, puromycin, hygromycin, blasticidin, and G418 may be
employed. In other embodiments, selectable markers include, but are
not limited to sugars such as rhamnose, human nerve growth factor
receptor (detected with a MAb, such as described in U.S. Pat. No.
6,365,373); truncated human growth factor receptor (detected with
MAb); mutant human dihydrofolate reductase (DHFR; fluorescent MTX
substrate available); secreted alkaline phosphatase (SEAP;
fluorescent substrate available); human thymidylate synthase (TS;
confers resistance to anti-cancer agent fluorodeoxyuridine); human
glutathione S-transferase alpha (GSTA1; conjugates glutathione to
the stem cell selective alkylator busulfan; chemoprotective
selectable marker in CD34+cells); CD24 cell surface antigen in
hematopoietic stem cells; human CAD gene to confer resistance to
N-phosphonacetyl-L-aspartate (PALA); human multi-drug resistance-1
(MDR-1; P-glycoprotein surface protein selectable by increased drug
resistance or enriched by FACS); human CD25 (IL-2.alpha.;
detectable by Mab-FITC); Methylguanine-DNA methyltransferase (MGMT;
selectable by carmustine); and Cytidine deaminase (CD; selectable
by Ara-C). "Selective medium" as used herein refers to cell growth
medium to which has been added a chemical compound or biological
moiety that selects for or against selectable markers.
[0056] The terms "target genomic DNA sequence", "target sequence",
or "genomic target locus" refer to any locus in vitro or in vivo,
in a nucleic acid (e.g., genome) of a cell or population of cells,
in which a change of at least one nucleotide is desired using a
nucleic acid-guided nuclease editing system. The target sequence
can be a genomic locus or extrachromosomal locus.
[0057] A "vector" is any of a variety of nucleic acids that
comprise a desired sequence or sequences to be delivered to and/or
expressed in a cell. Vectors are typically composed of DNA,
although RNA vectors are also available. Vectors include, but are
not limited to, plasmids, fosmids, phagemids, virus genomes, YACs,
BACs, synthetic chromosomes, and the like. As used herein, the
phrase "engine vector" comprises a coding sequence for a nuclease
to be used in the nucleic acid-guided nuclease systems and methods
of the present disclosure. The engine vector may also comprise, in
a bacterial system, the .lamda. Red recombineering system or an
equivalent thereto. Engine vectors also typically comprise a
selectable marker. As used herein the phrase "editing vector"
comprises a donor nucleic acid, optionally including an alteration
to the target sequence that prevents nuclease binding at a PAM or
spacer in the target sequence after editing has taken place, and a
coding sequence for a gRNA. The editing vector may also comprise a
selectable marker and/or a barcode. In some embodiments, the engine
vector and editing vector may be combined; that is, all editing and
selection components may be found on a single vector. Further, the
engine and editing vectors comprise control sequences operably
linked to, e.g., the nuclease coding sequence, recombineering
system coding sequences (if present), donor nucleic acid, guide
nucleic acid, and selectable marker(s).
The Invention Generally
[0058] Electroporation is a widely-used method for permeabilization
of cell membranes that works by temporarily generating pores in the
cell membranes with electrical stimulation. The applications of
electroporation include the delivery of DNA, RNA, siRNA, peptides,
proteins, antibodies, drugs or other substances to a variety of
cells such as mammalian cells (including human cells), plant cells,
archaea, yeasts, other eukaryotic cells, bacteria, and other cell
types. Further, mixtures of cell types can also be electroporated
in a single run; e.g., mixtures of E. coli strains, mixtures of
bacterial strains, mixtures of yeast strains, mixtures of mammalian
cells. Electrical stimulation may also be used for cell fusion in
the production of hybridomas or other fused cells. During a typical
electroporation procedure, cells are suspended in a buffer or
medium that is favorable for cell survival. For bacterial cell
electroporation, low conductance mediums, such as water, glycerol
solutions and the like, are often used to reduce the heat
production by transient high current. The cells and material to be
electroporated into the cells (collectively "the cell sample") is
then placed in a cuvette embedded with two flat electrodes for an
electrical discharge. For example, Bio-Rad (Hercules, Calif.) makes
the GENE PULSER XCELL.TM. line of products to electroporate cells
in cuvettes. Traditionally, electroporation requires high field
strength.
[0059] Generally speaking, microfluidic flow-through
electroporation (FTEP)--using cell suspension volumes of less than
approximately 10 ml and as low as 1 l--allows for more precise
control over the transfection or transformation process and permits
flexible integration with other cell processing tools compared to
bench-scale electroporation devices. Microfluidic flow-through
electroporation thus provides unique advantages for, e.g., single
cell transformation, processing, and analysis; microfluidic
electroporation may be used for multi-unit FTEP device
configurations; and microfluidic electroporation devices may be
integrated into automated multi-module cell processing
instruments.
[0060] A particular characteristic of the FTEP devices disclosed
herein is that rather than having a single flow path for the cells
to be porated, the FTEP devices described herein have a single flow
channel but many flow paths. The flow channel comprises
obstructions or flow diverters such that the single flow channel is
separated or parallelized into many flow paths. Configuring the
flow channel into many flow paths provides the advantage that if
one flow path becomes clogged, there are several to many
alternative flow paths that may be taken. That is, if only a single
flow path is present and this single flow path is clogged or
obstructed, the result is a catastrophic failure of the
electroporation device. Further, at constant applied voltage,
electric field strength can be increased by reducing the spacing
between the obstructions in the obstruction array. Thus, as the
spacing between obstructions gets smaller, the electric field
increases and thus the efficiency of electroporation of the cells
increases.
[0061] The present disclosure provides FTEP devices, automated
multi-module instruments and methods of using FTEP devices that
achieve high efficiency cell electroporation with low toxicity
where the electroporation devices and systems can be integrated
with other automated cell processing tools. Further, the
electroporation device of the disclosure allows for multiplexing
where two to many electroporation units are constructed and used in
parallel, which allows for particularly easy integration with
robotic liquid handling instrumentation. Such automated
instrumentation includes, but is not limited to, off-the-shelf
automated liquid handling systems from Tecan (Mannedorf,
Switzerland), Hamilton (Reno, Nev.), Beckman Coulter (Fort Collins,
Colo.), etc.
[0062] During the electroporation process, it is important to use
voltage sufficient for achieving electroporation of material into
the cells, but not too much voltage as too much power will decrease
cell viability. For example, to electroporate a suspension of a
human cell line, 200 volts is needed for a 0.2 ml sample in a 4
mm-gap cuvette with exponential discharge from a capacitor of about
1000 g. However, if the same 0.2 ml cell suspension is placed in a
longer container with 2 cm electrode distance (5 times of cuvette
gap distance), the voltage required would be 1000 volts, but a
capacitor of only 40 .mu.F (1/25 of 1000 g) is needed because the
electric energy from a capacitor follows the equation of:
E=0.5U.sup.2C
where E is electric energy, U is voltage and C is capacitance.
Therefore, a high voltage pulse generator is easy to manufacture
because it needs a much smaller capacitor to store a similar amount
of energy. Similarly, it would not be difficult to generate other
wave forms of higher voltages.
[0063] The electroporation devices of the disclosure allow for a
high rate of cell transformation in a relatively short amount of
time. The rate of cell transformation is dependent on the cell type
and the number of cells being transformed. For example, for E.
coli, the electroporation devices can provide a cell transformation
rate of 10.sup.3 to 10.sup.12 cells per minute, 10.sup.4 to
10.sup.10 per minute, 10.sup.5 to 10.sup.9 per minute, or 10.sup.6
to 10.sup.8 per minute. Typically, 10.sup.7 to 10.sup.8 yeast cells
are subjected to transformation and 10.sup.4 to 10.sup.5 are
transformed per round of transformation, and 10.sup.9-10.sup.10
bacterial are subjected to transformation and 10.sup.6 to 10.sup.7
are transformed per round of transformation. The electroporation
devices also allow transformation of batches of cells ranging from
1 cell to 10.sup.11 cells in a single transformation procedure
using parallel devices.
Exemplary FTEP Embodiments
[0064] An FTEP assembly is illustrated in FIGS. 1A-1C. FIGS. 1A
through 1C are top perspective, bottom perspective, and bottom
views, respectively, of an FTEP assembly 1500 comprising six
co-joined FTEP devices 150. FIG. 1A depicts six FTEP units 150
arranged on a single, integrally-formed injection molded substrate
156. Each of the six FTEP units 150 have wells 152 that define
inlets and wells 154 that define outlets. Further, on each FTEP
unit one of two electrode channels 178 can be seen. FIG. 1B is a
bottom perspective view of the FTEP assembly 1500 with the six
co-joined FTEP devices 150 of FIG. 15A arranged on a single
substrate 156. Six inlet wells 152 can be seen, one for each
flow-through electroporation unit 150, and one outlet well 154 can
be seen on the left-most FTEP unit. Also seen in FIG. 1B for each
FTEP unit 150 are an inlet 102, an outlet 104, a flow channel 106
comprising five regions: an inlet-filter region 106a, an
inlet-proximal region 106b, a central region 106c, an
outlet-proximal region 106d, and an outlet-filter region 106e (only
central region 106c is labeled in this FIG. 1B, but see FIG. 1C).
Each FTEP unit further comprises two electrodes 108 flanking
central region 106c of flow channel 106. Central region 106c of
flow channel 106 comprises a central portion (not labeled)
comprising an obstruction array 176 that includes a plurality of
obstructions (not seen clearly in this FIG. 1B) which provide
several to many paths for cells to travel through flow channel 106.
Additionally seen are filters 172 and 170 included in the
inlet-filter region 106a and outlet-filter region 106e,
respectively, of flow channel 106 to prevent clogging in flow
channel 106.
[0065] FIG. 1C is a bottom view of the FTEP assembly 1500 of the
six co-joined FTEP devices 150 of FIGS. 1A and 1B. Depicted in FIG.
1C are six FTEP units 150 arranged on a single substrate 156, where
each FTEP unit 150 comprises an inlet 102, an outlet 104, a flow
channel 106 comprising five regions: an inlet-filter region 106a,
an inlet-proximal region 106b, a central region 106c, an
outlet-proximal region 106d, and an outlet-filter region 106e. Each
FTEP unit further comprises two electrodes 108 flanking the central
region 106c of flow channel 106. Central region 106c of flow
channel 106 comprises a central portion comprising an obstruction
array 176 that includes a plurality of obstructions (not seen
clearly in this FIG. 1C) which provide a number of flow paths for
cells travelling through flow channel 106. Additionally seen are
filters 172 and 170 included in the inlet-filter region 106a and
outlet-filter region 106e, respectively, of flow channel 106 to
prevent clogging of the channel. Once the six FTEP units 150 are
fabricated, they can be separated from one another (e.g., "snapped
apart") upon the depicted score lines and used one at a time;
alternatively, the FTEP units may be used in embodiments where two
or more FTEP units 150 are used in parallel.
[0066] The FTEP described herein comprises a filter 172 in the
inlet-filter region 106a of flow channel 106 and a filter 170 in
the outlet-filter region 106e of flow channel 106, as well as the
obstruction array 176 comprising a plurality of obstructions. The
filters serve the purpose of filtering the fluid containing the
cells and DNA (or other material to be porated into the cells)
before the fluid encounters either the inlet-proximal region 106b
or outlet-proximal region 106d of flow channel 106. In this
embodiment, there are filters both at the inlet-filter region 106a
and outlet-filter region 106e of flow channel 106 because the FTEP
devices may utilize a push-pull pneumatic means to flow liquids
from inlet 102 to outlet 104, then from outlet 104 back to inlet
102 for another round of electroporation. The filter, like the
obstruction array, decreases the likelihood that cells or other
matter will clog the flow channel. Instead, if there is particulate
matter that poses a threat to clogging the flow channel, the filter
will catch the particulate matter leaving other pores or flow paths
through which the rest of the cell/DNA/fluid can pass. Note that in
this embodiment, the filter has a gradient flow path size, from
large flow paths at the inlet to smaller flow paths toward the
inlet proximal region 106b of the flow channel 106, and from large
flow paths at the outlet 104 to small flow paths toward the
outlet-proximal region 106d of flow channel 106; however, in
alternative embodiments the flow paths may be the same size (e.g.,
not gradiated) or have an alternative gradient configuration.
[0067] The obstruction array 176 provides a number of flow paths
for the cells and the material to be porated into the cells that
travel through flow channel 106. Such a configuration reduces the
likelihood of catastrophic failure of the FTEP device from clogging
compared to devices with a single flow path. If one of the flow
paths becomes clogged, the cells and material to be porated into
the cells can flow through an alternative flow path. Again, a
particular characteristic of the FTEP devices disclosed herein is
that rather than having a single flow path for the cells to be
porated, the FTEP devices have a single flow channel with many flow
paths. In the devices described herein, the flow channel comprises
obstructions of flow diverters such that the flow channel is
separated or parallelized into many flow paths. Configuring the
flow channel into many flow paths provides the advantage that if
one flow path becomes clogged, there are several to many
alternative flow paths that may be taken. That is, if only a single
flow path is present and this single flow path is clogged or
obstructed, the result is a catastrophic failure of the
electroporation device.
[0068] The substrate, inlet wells, outlet wells, filters and
obstruction arrays of the FTEP device can be made from many
materials depending on whether the FTEP device is to be reused,
autoclaved, or is disposable, including stainless steel, silicon,
glass, resin, polyvinyl chloride, polyethylene, polyamide,
polystyrene, polyethylene, polypropylene, acrylonitrile butadiene,
polycarbonate, polyetheretheketone (PEEK), polysulfone and
polyurethane, co-polymers of these and other polymers. Similarly,
the walls of the channels in the device can be made of any suitable
material including silicone, resin, glass, glass fiber, polyvinyl
chloride, polyethylene, polyamide, polyethylene, polypropylene,
acrylonitrile butadiene, polycarbonate, polyetheretheketone (PEEK),
polysulfone and polyurethane, co-polymers of these and other
polymers. Preferred materials include crystal styrene, cyclo-olefin
polymer (COP) and cyclic olefin co-polymers (COC), which allow the
FTEP device to be formed entirely by injection molding in one piece
with the exception of the electrodes and, e.g., a bottom and/or top
sealing film if present.
[0069] The FTEP devices described herein (or portions of the FTEP
devices) can be created or fabricated via various techniques, e.g.,
as entire devices or by creation of structural layers that are
fused or otherwise coupled. For example, for metal FTEP devices,
fabrication may include precision mechanical machining or laser
machining; for silicon FTEP devices, fabrication may include dry or
wet etching; for glass FTEP devices, fabrication may include dry or
wet etching, powderblasting, sandblasting, or photostructuring; and
for plastic FTEP devices, fabrication may include thermoforming,
injection molding, hot embossing, or laser machining. The
components of the FTEP devices may be manufactured separately and
then assembled, or certain components of the FTEP devices (or even
the entire FTEP device except for the electrodes) may be
manufactured (e.g., using 3D printing) or molded (e.g., using
injection molding) as a single entity, with other components added
after molding. For example, housing and channels may be
manufactured or molded as a single entity, with the electrodes
later added to form the FTEP unit. In some embodiments, a film or a
flat substrate may be used to seal the bottom of the device. The
film, in some embodiments, is made from the same material as the
FTEP device, in this case, e.g., crystal styrene, cyclo-olefin
polymer (COP) or cyclic olefin co-polymers (COC). The FTEP device
may also be formed in two or more parallel layers, e.g., a layer
with the horizontal channel and filter, a layer with the vertical
channels, and a layer with the inlet and outlet ports, which are
manufactured and/or molded individually and assembled following
manufacture.
[0070] In specific aspects, the FTEP device can be manufactured
using a circuit board as a base, with the electrodes, filter and/or
the flow channel formed in the desired configuration on the circuit
board, and the remaining housing of the device containing, e.g.,
the one or more inlet and outlet channels and/or the flow channel
formed as a separate layer that is then sealed onto the circuit
board. The sealing of the top of the housing onto the circuit board
provides the desired configuration of the different elements of the
FTEP devices of the disclosure. Also, two to many FTEP devices (up
to 48 or more) may be manufactured in parallel on a single
substrate, then separated from one another thereafter or used in
parallel. In certain embodiments, the FTEP devices are reusable
and, in some embodiments, the FTEP devices are disposable. In
additional embodiments, the FTEP devices may be autoclavable.
[0071] The electrodes 108 can be formed from any suitable metal,
such as copper, stainless steel, titanium, aluminum, brass, silver,
rhodium, gold or platinum, or graphite. One preferred electrode
material is alloy 303 (UNS330300) austenitic stainless steel. An
applied electric field can destroy electrodes made from of metals
like aluminum. If a multiple-use (e.g., non-disposable) FTEP device
is desired--as opposed to a disposable, one-use FTEP device--the
electrode plates can be coated with metals resistant to
electrochemical corrosion. Conductive coatings like noble metals,
e.g., gold, can be used to protect the electrode plates.
[0072] The overall size of the FTEP device may be from 3 cm to 15
cm in length, or 4 cm to 12 cm in length, or 4.5 cm to 10 cm in
length. The overall width of the FTEP device may be from 0.5 cm to
5 cm, or from 0.75 cm to 3 cm, or from 1 cm to 2.5 cm, or from 1 cm
to 1.5 cm.
[0073] In embodiments of the FTEP device where reservoirs are used
to introduce cells and exogenous material into the FTEP device, the
reservoirs range in volume from 100 .mu.L to 10 mL, or from 500
.mu.L to 7.5 mL, or from 1 mL to 5 mL. The flow rate in the FTEP
ranges from 0.01 mL to 5.0 mL per minute, or from 0.05 mL to 3.0 mL
per minute, or from 0.1 mL to 2.5 mL per minute or from 0.2 to 2.0
mL per minute. The pressure in the FTEP device ranges from 1-30
psi, or from 2-10 psi, or from 3-5 psi.
[0074] To avoid different field intensities between the electrodes,
the electrodes should be arranged in parallel. Furthermore, the
surface of the electrodes should be as smooth as possible without
pin holes or peaks. Electrodes having a roughness Rz of 1 to 10
.mu.m are preferred. In another embodiment of the invention, the
flow-through electroporation device comprises at least one
additional electrode which applies a ground potential to the FTEP
device.
[0075] The electrodes are configured to deliver 1-50 kV/cm, or 5-40
kV/cm, or 10-25 kV/cm. The further apart the electrodes are, the
more voltage needs to be supplied; in addition, the voltage
delivered of course depends on the types of cells being porated,
the medium in which the cells are suspended, the size of the
electroporation channel, and the length and diameter of the
electrodes. There are many different pulse forms that may be
employed with the FTEP device, including exponential decay waves,
square or rectangular waves, arbitrary wave forms, or a selected
combination of wave forms. One type of common pulse form is the
exponential decay wave, typically made by discharging a loaded
capacitor to the cell sample. The exponential decay wave can be
made less steep by linking an inductor to the cell sample so that
the initial peak current can be attenuated. When multiple waveforms
in a specified sequence are used, they can be in the same direction
(direct current) or different directions (alternating current).
Using alternating current can be beneficial in that two topical
surfaces of a cell instead of just one can be used for molecular
transport, and alternating current can prevent electrolysis. The
pulse generator can be controlled by a digital or analog panel. In
some embodiments, square wave forms are preferred, and in other
embodiments, an initial wave spike before the square wave is
preferred.
[0076] The FTEP device may be configured to electroporate cell
sample volumes between 1 .mu.L to 5 ml, 25 .mu.L to 2.5 ml, 50
.mu.L to 2 ml, 100 .mu.L to 1 .mu.L, or 200 .mu.L to 750 .mu.L. The
medium or buffer used to suspend the cells and material (reagent)
to be electroporated into the cells for the electroporation process
may be any suitable medium or buffer for the type of cells being
transformed or transfected, such as SOC, MEM, DMEM, IMDM, RPMI,
Hanks', PBS and Ringer's solution, where the media may be provided,
e.g., in a reagent cartridge as part of a kit. Further, because the
cells must be made electrocompetent prior to transformation or
transfection, the buffer also may comprise glycerol or sorbitol,
and may also comprise a surfactant. For electroporation of most
eukaryotic cells the medium or buffer usually contains salts to
maintain a proper osmotic pressure. The salts in the medium or
buffer also render the medium conductive. For electroporation of
very small prokaryotic cells such as bacteria, sometimes water or
10% glycerol is used as a low conductance medium to allow a very
high electric field strength. In that case, the charged molecules
to be delivered still render water-based medium more conductive
than the lipid-based cell membranes and the medium may still be
roughly considered as conductive particularly in comparison to cell
membranes.
[0077] The compound to be electroporated into the cells can be any
compound known in the art to be useful for electroporation, such as
nucleic acids, oligonucleotides, polynucleotides, DNA, RNA,
peptides, proteins and small molecules like hormones, cytokines,
chemokines, drugs, or drug precursors. In addition, the FTEP
devices may comprise push-pull pneumatic means to allow multi-pass
electroporation procedures; that is, cells to be electroporated may
be "pulled" from the inlet toward the outlet for one pass of
electroporation, then be "pushed" from the outlet end of the
flow-through FTEP device toward the inlet end to pass between the
electrodes again for another pass of electroporation. This process
may be repeated one to many times. Alternatively, the FTEP may be
used to porate sequential aliquots of cells; for example, a first
volume of cells is porated in a first pass with the first volume
then transferred to recovery, then a second volume of cells is
porated in a second pass with the second volume then transferred to
recovery, and so on with third, fourth and fifth volumes or
more.
[0078] FIG. 1D is an enlarged bottom view of an FTEP device 150
with the regions of the flow channel labeled. The FTEP device 150
comprises an inlet 102, an outlet 104, a flow channel 106
comprising five regions: an inlet-filter region 106a, an
inlet-proximal region 106b, a central region 106c, an
outlet-proximal region 106d, and an outlet-filter region 106e. Two
electrodes 108 flank the central region 106c of flow channel 106
which comprises the obstruction array. Also seen are ramps 174a and
174b. Ramp 174a proximal to inlet 102 decreases the cross-sectional
area of flow channel 106 from the region of ramp 174a proximal to
electrode 108 traveling toward the region of ramp 174a proximal to
the central region 106c of flow channel 106. Ramp 174b proximal to
outlet 104 increases the cross-sectional area of flow channel 106
from the region of ramp 174b proximal to central region 106c of
flow channel 106 traveling toward electrode 108. Channel height is
a parameter that can be used to tune electric field strength. At
constant applied voltage, the electric field strength can be
increased by reducing the cross-sectional area of the flow channel
through which the cells pass. For example, as the height of the
flow channel decreases, the electric field strength increases.
Similarly, as described above, when the spacing between the
obstructions in the obstruction array gets smaller, the electric
field strength increases. Thus, the optional ramps serve the
purpose of increasing electric field strength to achieve enhanced
electroporation efficiency. Ramps 174a and 174b may be configured
similarly (though in mirror image) or may have different
configurations. The ramps can range in length from 0.3 mm to 4.0
mm, or from 0.5 mm to 3.0 mm, or from 0.8 mm to 2.4 mm. Width W of
the ramp 174 is preferably equal to that of the channel, such as
approximately 0.5 mm to 10 mm, or from 1 mm to 5 mm, or from 1.5 mm
to 4 mm. Ramp 174a decreases the cross-sectional height of central
region 106c of flow channel 106--and ramp 174b increases the
cross-sectional height of central region 106c of flow channel 106
to electrode 108--from 250 .mu.m to 25 .mu.m, or from 200 .mu.m to
50 .mu.m, or from 100 .mu.m to 25 .mu.m. Additionally, the
configuration of ramps 174a and 174b may be a smooth transition of
flow channel height from larger cross-sectional height to smaller
cross-sectional height, or the configuration of ramps 174a and 174b
may be stepped. For example for ramp 174a, a first step may
decrease the cross-sectional height of central region 106c by 25 mm
for a length X of central region 106c, then a next step may
decrease the cross-sectional height of central region 106c by
another 25 mm for length Y of central region 106c. Again, the
configuration of ramp 174b may match (mirror image) the
configuration of ramp 174 a or may be different than that of
174a.
[0079] Obstruction array 176 includes a plurality (e.g., several to
many) of obstructions (not seen clearly in this FIG. 1D) which
provide a number of flow paths for cells to travel through flow
channel 106. Additionally seen are filters 172 and 170 included in
the inlet-filter region 106a and outlet-filter region 106e,
respectively, of flow channel 106 to prevent clogging of flow
channel 106. FIG. 1E is a blow up of the circled portion 182 of
FIG. 1D showing detail of central region 106c of flow channel 106.
Seen in FIG. 1E are two electrodes 108, disposed in electrode
channels 178, which flank central region 106c of flow channel 106.
The detail of obstruction array 176 is seen, with individual
obstructions 180. In addition, optional ramp regions 174a and 174b
are seen. The ramp regions ramp up (e.g. creates vertical
cross-sectional narrowing of flow channel 106) from the
inlet-proximal region 106b (not seen) of flow channel 106 toward
central region 106c, and ramp down (e.g., creates a vertical
widening of flow channel 106) from central region 106c toward
outlet proximal region 106d (not shown) of flow channel 106 as
described above.
[0080] Depending on the type of cells to be electroporated (e.g.,
bacterial, yeast, mammalian) and the configuration of the
electrodes, the distance between the electrodes in the flow channel
can vary widely. The length LI from the mid-point of each electrode
108 is approximately 1 to 15 mm, or 2 to 12 mm, 3 to 10 mm, or 4 mm
to 8 mm.
[0081] FIGS. 1F-1K show different views of obstruction arrays 176,
with individual obstructions 180. FIG. 1F depicts a top view of
central region 106c of the flow channel (not labeled), with a
central portion 110 of central region 106c, ramps 174a and 174b,
obstruction array 176, and electrodes 108 disposed in electrode
channels 178. FIG. 1G is a top perspective view of the central
region (not labeled) of the flow channel (also not labeled),
depicting central portion 110 of the central region, obstruction
array 176, ramps 174, and electrodes 108 disposed within electrode
channels 178. FIG. 1H is a close up of an obstruction array (not
labeled) showing obstructions 180 and flow paths 182 between
obstructions 180. Although the obstructions are shown in this
embodiment as oval-shaped, flat-topped elements, it should be
understood that the obstructions may be triangular-, square-,
rectangular-, pentagonal-, hexagonal-, rounded peg-, elliptical-,
elongated oval- (see, e.g., FIGS. 1L-1N), or other faceted-shaped
elements, and may be a combination of shapes and configurations of
obstruction elements.
[0082] In this embodiment, there are 40 total obstructions, and the
size of the flow paths moving from the inlet-proximal region of the
flow channel (not labeled) to the center region of the central
region 106c of the flow channel decreases; that is, the number of
obstructions in a row moving from the inlet-proximal region of the
flow channel to the center portion 110 of the central region 106c
of the flow channel increases from 3 to 5 to 7 to 10. Similarly,
the size of the flow paths moving from the center portion 110 of
the central region 106c to the outlet-proximal region of the flow
channel (not labeled) increases; that is, the number of
obstructions in a row moving from the center portion 110 of the
central region 106c to the outlet-proximal region of the flow
channel (not labeled) decreases from 10 to 7 to 5 to 3. At the
mid-point of the obstruction array (e.g., the center portion 110 of
center region of the flow path (not labeled) there are 10
obstructions 180 defining 11 flow paths. The number of obstructions
can range from 4 to 150, from 6 to 120, from 8 to 100, or from 10
to 90. The pattern or configuration of the obstructions can be
symmetrical (as in FIGS. 1F-1K) or random. In this embodiment, the
oval-shaped or elongated obstructions are approximately 220 .mu.m
long and 100 .mu.m wide, and the obstructions are at least about
100 .mu.m apart, thus forming minimal flow path widths of 100
.mu.m. However, in alternative embodiments the obstructions can be
from 50 .mu.m long to 20 .mu.m wide, from 100 .mu.m long to 50
.mu.m wide, or from 250 .mu.m long to 150 .mu.m wide. Round
obstructions may be used instead or in combination with elongated
obstructions or with other configurations of obstructions. Round
obstructions may be approximately between 25 .mu.m-200 .mu.m in
diameter, or between 50 .mu.m to 150 .mu.m in diameter, or 75 .mu.m
to 125 .mu.m in diameter. The flow paths or distance between
obstructions can range from 10 .mu.m to 350 .mu.m, from 20 .mu.m to
300 .mu.m, or from 30 .mu.m to 250 .mu.m.
[0083] FIGS. 1I-1K are similar to FIGS. 1F-1H, showing views of an
alternately-configured obstruction array 176 and individual
obstruction 180s. FIG. 1I shows a top view of central region 106c
of flow channel (not labeled), with central portion 110, ramps 174,
and electrodes 108 in electrode channels (not labeled). FIG. 1J is
a top view of an area of an obstruction array (not labeled) showing
individual obstructions 180 and central portion 110 of the central
region (not labeled) of the flow channel (also not labeled). Note
that the outer margin of the FTEP device in central region (not
labeled) coincident to the obstruction array is contoured to
provide flow paths 182 similar to the flow channels between
obstructions 180. FIG. 1K is a close-up view of obstructions 180
and flow paths 182. Again the obstructions are shown in this
embodiment as oval-shaped, flat-topped elements; however, it should
be understood that the obstructions may be triangular-, square-,
rectangular-, pentagonal-, hexagonal-, rounded peg-, elliptical-,
elongated oval- or other faceted-shaped elements, and may be a
combination of shapes and configurations of obstruction elements.
In this embodiment, there are 33 total obstructions in a
3-5-5-7-5-5-3 pattern moving from the inlet-proximal region of the
flow channel to the center portion of the center region of the flow
channel to the outlet-proximal region of the flow channel (regions
not labeled).
[0084] FIG. 1L is a bottom view of an alternative embodiment of an
obstruction FTEP device 190, here a parallel-obstruction device,
with the regions of the flow channel labeled. The
parallel-obstruction FTEP device 190 comprises an inlet 102, an
outlet 104, a flow channel 106 comprising five regions: an
inlet-filter region 106a, an inlet-proximal region 106b, a central
region 106c, an outlet-proximal region 106d, and an outlet-filter
region 106e. Two electrodes 108 flank the central region 106c of
flow channel 106 which comprises the obstruction array 177. Also
seen are steps 174c and 174d. Steps 174c and 174d are much like
ramps 174a and 174b seen in FIGS. 1D, 1E, 1G and 1I; however,
instead of a "ramp" or gradual decreasing of channel height (with
ramp 174a) or gradual increasing of channel height (as with ramp
174b), steps 174c and 174d are true steps--that is, the decrease or
increase in channel height to and from the central channel region
106c is abrupt. Step 174c proximal to inlet 102 decreases the
cross-sectional area of flow channel 106 from the region of step
174c proximal to electrode 108 traveling toward the region of step
174c proximal to the central region 106c of flow channel 106. Step
174d proximal to outlet 104 increases the cross-sectional area of
flow channel 106 from the region of step 174d proximal to central
region 106c of flow channel 106 traveling toward electrode 108 and
outlet 104. As described above, channel height is a parameter that
can be used to tune electric field strength. At constant applied
voltage, the electric field strength can be increased by reducing
the cross-sectional area of the flow channel through which the
cells pass. For example, as the height of the flow channel
decreases, the electric field strength increases. The steps serve
the purpose of increasing electric field strength to achieve
enhanced electroporation efficiency. As with ramps 174a and 174b,
steps 174c and 174d may be configured similarly (though in mirror
image) or may have different configurations. For an exemplary
channel height of 100 .mu.m, the step can range in height from 10
.mu.m to 80 .mu.m, or from 20 .mu.m to 70 .mu.m, or from 20 .mu.m
to 60 .mu.m. Width W of the steps 174c and 174d is preferably equal
to that of the channel, such as approximately 0.5 mm to 3.0 mm, or
from 1.0 mm to 2.0 mm, or from 1.25 mm to 1.75 mm. For other
channel heights, the steps would be of the same proportion. Again,
the configuration of step 174c may match (mirror image) the
configuration of step 174d or may be different than that of 174d.
Parallel-obstruction array 177 includes a plurality (e.g., several
to many) of obstructions in central region 106c (not seen clearly
in this FIG. 1L) which provide a number of flow paths for cells to
travel through flow channel 106. Additionally seen are filters 172
and 170 included in the inlet-filter region 106a and outlet-filter
region 106e, respectively, of flow channel 106 to prevent clogging
of flow channel 106.
[0085] FIGS. 1M and 1N show different views of parallel-obstruction
arrays 177 (e.g., obstructions with a different configuration than
shown in FIGS. 1D-1K), with individual obstructions 180. In FIGS.
1M and 1N, the obstructions or flow diverters are elongated oval
structures that are arranged parallel to one another forming
"lanes" for cell flow. That is, instead of a plurality of
obstructions arranged in a pattern such as in rows (see, e.g., the
3-5-5-7-5-5-3 pattern in FIGS. 1I-1K), the present
parallel-obstruction embodiment comprises elongated obstructions
that form flow "lanes." FIG. 1M depicts a top view of central
region 106c of the flow channel (not labeled), with a central
portion 110 of central region 106c, steps 174c and 174d,
obstruction array 177, and electrodes 108 disposed in electrode
channels 178. Note that the length of the obstruction array 177 in
channel 106 is denoted here as 1.0 mm in length with the length of
the "shelf" formed by the steps approximately 1.1 mm in length.
FIG. 1N is a top perspective view of the central region (not
labeled) of the flow channel (also not labeled), depicting
parallel-obstruction array 177 in channel 106 (not labeled) and
step 174c, obstructions 180 and flow paths 182 between obstructions
180. Although the obstructions are shown in this embodiment as long
oval-shaped, flat-topped elements, it should be understood that the
obstructions may be triangular-, square-, rectangular-,
pentagonal-, hexagonal-, rounded peg-, elliptical- or other
faceted-shaped elements, and may be a combination of shapes and
configurations of obstruction elements. Note that step 174c
decreases the channel height in this exemplary embodiment from 100
.mu.m to 50 .mu.m, and the height of obstructions 180 is 50
.mu.m.
[0086] In this embodiment, there are 7 total obstructions in
parallel, resulting in 8 parallel paths for cell flow. In this
embodiment, the elongated obstructions are approximately 1000 .mu.m
long and 100 .mu.m wide, and the obstructions are at least about
200 .mu.m apart center-to-center of the obstructions, thus forming
minimal flow path widths of approximately 100 .mu.m. However, in
alternative embodiments the obstructions can be from 200 .mu.m long
to 25 .mu.m wide, from 500 .mu.m long to 50 .mu.m wide, or from
4000 .mu.m long to 100 .mu.m wide, with the length of the
obstructions limited only by the distance between electrodes. The
flow lanes between obstructions can range from 2 .mu.m to 300
.mu.m, from 10 .mu.m to 200 .mu.m, or from 25 .mu.m to 100 .mu.m in
width.
[0087] FIG. 10 depicts (i) the electrodes 108 positioned on an
electrode platform 158 before insertion into the FTEP array 1500;
here an FTEP array comprising six FTEP devices (not labeled), where
each FTEP device has an inlet well 152 and an outlet well 154. In
use, the FTEP devices are used in an orientation inverted relative
to that shown in FIG. 10 (i). FIG. 10 (ii) depicts an electrode 108
contained within and projecting from an electrode sheath 184. FIG.
10 (iii) depicts the electrode 108 within electrode sheath 184 and
inserted into an electrode channel 178 with the electrode channel
178 (and electrode 108) adjacent to flow channel 106. In the
embodiment shown in FIG. 10 (iii), electrode 108 is even/flush with
the wall of flow channel 106; that is, electrode 108 is not in the
path of the cells/DNA/fluid flowing through flow channel 106;
however, neither is the electrode recessed within the electrode
channel 178. In alternative embodiments, electrode 108 may be
recessed within electrode channel 178. The configuration of the
electrode channel 178 and the flow channel 106 help prevent
trapping air and reduce discontinuities in the electric field.
[0088] FIG. 1P shows scanning electron micrographs of filter 172.
Note in this embodiment, the porosity of filter 172 varies from
large flow paths near the inlet 102 to small flow paths near inlet
proximal region 106b (not shown). When a second filter is present
at the outlet-filter region 106e (not shown), the second filter may
also vary in porosity. In the case of a second filter between the
outlet and the outlet-proximal region 106d, the filter can vary
from large flow paths near the outlet proximal region to small flow
paths toward the outlet-proximal region 106d. Scale information is
shown in each micrograph. Moreover, as with the configuration of
the obstructions, though the scanning electron micrographs in FIG.
1P show the filter elements as rounded "pegs", it should be
understood that the filter elements may be triangular-, square-,
rectangular-, pentagonal-, hexagonal-, oval-, elliptical- or other
faceted-shaped pegs, or a combination of differently-configured and
differently-sized filter elements.
Reagent Cartridges Comprising FTEPs
[0089] FIG. 2A depicts an exemplary combination reagent cartridge
200 comprising an FTEP device 206 ("cartridge" or "reagent
cartridge") that may be used in an automated multi-module cell
processing instrument. Cartridge 200 comprises a body 202, and
reagent receptacles or reservoirs 204 along with an FTEP device 206
(exemplary embodiments of which are described in detail in relation
to FIGS. 1A-1P). Cartridge 200 may be disposable or may be
configured to be reused. Cartridge 200 may be made from any
suitable material, including stainless steel, aluminum, paper or
other fiber, or plastics including polyvinyl chloride, cyclic
olefin copolymer (COC), polyethylene, polyamide, polypropylene,
acrylonitrile butadiene, polycarbonate, polyetheretheketone (PEEK),
poly(methyl methylacrylate) (PMMA), polysulfone, and polyurethane,
and co-polymers of these and other polymers. If the cartridge is
disposable, preferably it is made of plastic or paper. Preferably
the material used to fabricate the cartridge is
thermally-conductive, as in certain embodiments the cartridge 200
contacts a thermal device (not shown) that heats or cools reagents
in the reagent receptacles or reservoirs 204. In some embodiments,
the thermal device is a Peltier device or thermoelectric cooler.
Reagent receptacles or reservoirs 204 may be receptacles into which
individual tubes of reagents are inserted as shown in FIG. 2A,
receptacles into which one or more multiple co-joined tubes are
inserted (e.g., a row of four tubes that are co-joined are inserted
into the reagent receptacles), or the reagent receptacles may hold
the reagents without inserted tubes with the reagents dispensed
directly into the receptacles or reservoirs. Additionally, the
receptacles 204 in a reagent cartridge 200 may be configured for
any combination of tubes, co-joined tubes, and direct-fill of
reagents.
[0090] In one embodiment, the reagent receptacles or reservoirs 204
of reagent cartridge 200 are configured to hold various size tubes,
including, e.g., 250 ml tubes, 25 ml tubes, 10 ml tubes, 5 ml
tubes, and Eppendorf (e.g., microcentrifuge) tubes. In yet another
embodiment, all receptacles may be configured to hold the same size
tube, e.g., 5 ml tubes, and reservoir inserts may be used to
accommodate smaller tubes in the reagent reservoir. In yet another
embodiment--particularly in an embodiment where the reagent
cartridge 200 is disposable--the reagent reservoirs 204 hold
reagents without inserted tubes. In this disposable embodiment, the
reagent cartridge may be part of a kit, where the reagent cartridge
is pre-filled with reagents and the receptacles or reservoirs
sealed with, e.g., foil, film, heat seal acrylic or the like and
presented to a consumer where the reagent cartridge can then be
used in an automated multi-module cell processing instrument. The
reagents contained in the reagent cartridge 200 will vary depending
on work flow; that is, the reagents will vary depending on the
processes to which the cells are subjected in the automated
multi-module cell processing instrument. For various embodiments of
reagent cartridges of particular use in automated multi-module cell
processing instruments, see U.S. Pat. Nos. 10,376,889, issued 13
Aug. 2019; U.S. Pat. No. ,406,525, issued 10 Sep. 2019; and U.S.
Pat. No. ,478,822, issued 19 Nov. 2019.
[0091] FIG. 2B depicts an exemplary matrix configuration 240 for
the reagents contained in the reagent cartridges of FIG. 2A, where
this matrix embodiment is a 4.times.4 reagent matrix. Through a
matrix configuration, a user (or programmed processor) can locate
the proper reagent for a given process. That is, reagents such as
cell samples, enzymes, buffers, nucleic acid vectors, expression
cassettes, reaction components (such as, e.g., MgCl.sub.2, dNTPs,
isothermal nucleic acid assembly reagents, Gap Repair reagents, and
the like), wash solutions, ethanol, and magnetic beads for nucleic
acid purification and isolation, etc., are positioned in the matrix
240 at a known position. For example, reagents are located at
positions A1 (210), A2 (211), A3 (212), A4 (213), B1 (214), B2
(215) and so on through, in this embodiment, to position D4 (225).
FIG. 2A is labeled to show where several reservoirs 204 correspond
to matrix 240; see receptacles 210, 211, 212, 213, 221 and 225.
Although the reagent cartridge 200 of FIG. 2A and the matrix
configuration 240 of FIG. 2B shows a 4.times.4 matrix, matrices of
the reagent cartridge and electroporation devices can be any
configuration, such as, e.g., 2.times.2, 2.times.3, 2.times.4,
2.times.5, 2.times.6, 3.times.3, 3.times.5, 4.times.6, 6.times.7,
or any other configuration, including asymmetric configurations, or
two or more different matrices depending on the reagents needed for
the intended workflow.
[0092] In preferred embodiments of reagent cartridge 200 shown in
FIG. 2A, the reagent cartridge comprises a script (not shown)
readable by a processor (not shown) for dispensing the reagents via
a liquid handling device (ADP head shown at 432 of FIG. 4A) and
controlling the electroporation device contained within reagent
cartridge 200. Also, the reagent cartridge 200 as one component in
an automated multi-module cell processing instrument may comprise a
script specifying two, three, four, five, ten or more processes
performed by the automated multi-module cell processing instrument,
or even specify all processes performed by the automated
multi-module cell processing instrument. In certain embodiments,
the reagent cartridge is disposable and is pre-packaged with
reagents tailored to performing specific cell processing protocols,
e.g., genome editing or protein production. Because the reagent
cartridge contents vary while components of the automated
multi-module cell processing instrument may not, the script
associated with a particular reagent cartridge matches the reagents
used and cell processes performed. Thus, e.g., reagent cartridges
may be pre-packaged with reagents for genome editing and a script
that specifies the process steps (or a script that modifies the
steps of a pre-programmed script based on, e.g., an updated reagent
in the reagent cartridge) for performing genome editing in an
automated multi-module cell processing instrument such as described
in relation to FIGS. 4A-4C.
[0093] For example, the reagent cartridge 200 of FIG. 2A may
comprise a script to pipette electrocompetent cells from reservoir
A2 (211), transfer the cells to the electroporation device 206,
pipette a nucleic acid solution comprising an editing vector from
reservoir C3 (220), transfer the nucleic acid solution to the
electroporation device, initiate the electroporation process for a
specified time, then move the porated cells to a reservoir D4 (225)
in the reagent cassette or to another module such as the rotating
growth vial (see, e.g., 418 of FIG. 4A) in the automated
multi-module cell processing instrument in FIG. 4A. In another
example, the reagent cartridge may comprise a script to pipette
transfer of a nucleic acid solution comprising a vector from
reservoir C3 (220), nucleic acid solution comprising editing
oligonucleotide cassettes in reservoir C4 (221), and isothermal
nucleic acid assembly reaction mix from Al (210) to an isothermal
nucleic acid assembly/desalting reservoir. The script may also
specify process steps performed by other modules in the automated
multi-module cell processing instrument. For example, the script
may specify that the isothermal nucleic acid assembly/desalting
module be heated to 50.degree. C. for 30 min to generate an
assembled isothermal nucleic acid product; and desalting of the
assembled isothermal nucleic acid product via magnetic bead-based
nucleic acid purification involving a series of pipette transfers
and mixing of magnetic beads in reservoir B2 (215), ethanol wash in
reservoir B3 (216), and water in reservoir Cl (218) to the
isothermal nucleic acid assembly/desalting reservoir (not seen in
FIG. 4A).
[0094] FIGS. 3A-3C depict three side perspective views of a
flow-through electroporation device insert 308 configured to be
inserted into, e.g., a reagent cartridge. In the embodiment of
reagent cartridge 200 depicted in FIG. 2A, the flow-through
electroporation device 206 (in FIGS. 3A-3F, FTEP 306) is located in
the reagent cartridge 200 (also see reagent cartridge 410 with
flow-through electroporation device 430 as one component of an
automated multi-module cell processing instrument 400 in FIG. 4A);
although in alternative embodiments, the FTEP module may be
separate from the reagent cartridge. The FTEP comprises an inlet
well 352 (covered in FIGS. 3A and 3B), and outlet well 354 (also
covered in FIGS. 3A and 3B), and the exterior of the electrode
channels 378. The FTEP device insert 308 comprises both a tab 317,
and an outer flange 307. FIG. 3C depicts the FTEP device insert 308
with a cover 305 for, e.g., shipping and to keep the FTEP device
306 sterile until use. The FTEP inserts may be made of any
appropriate material; however, the inserts are in most embodiments
disposable, so typically are fabricated from biocompatible
plastics, including polyvinyl chloride, cyclic olefin copolymer
(COC), polyethylene, polyamide, polypropylene, acrylonitrile
butadiene, polycarbonate, polyetheretheketone (PEEK), poly(methyl
methylacrylate) (PMMA), polysulfone, and polyurethane, and
co-polymers of these and other polymers.
[0095] FIGS. 3D-3F offer additional views of an FTEP insert 308.
FIG. 3D is a cross section of the FTEP insert 308, housing FTEP 306
with inlet well 352, outlet well 354, and electrode channels 378.
FTEP insert 308 comprises an outer flange 307, an FTEP cover 305,
and tab 317, which is configured to engage with, e.g., a tab
engagement member (not shown) in a reagent cartridge when inserted
into a reagent cartridge. Also shown is FTEP cover 305, which in
this embodiment is a tear-off foil, film or other type seal that is
used to maintain the sterility of the FTEP until ready for use.
FIG. 3E is a top view of the FTEP insert 308 shown in FIG. 3D. Seen
are FTEP insert cover or seal 305, which protects and keeps sterile
the FTEP device before use and is removable by a user, data 373,
and machine-readable indicia 375. Data 373 may include information
such as a lot number, a serial number, a product number, an
expiration date, or other data pertinent to FTEP insert 308.
Machine-readable indicia 375 may be a barcode, QR code, a Data
Matrix code (error correction-type barcode), RFID or other type of
machine-readable indicia, detected by one or more imaging sensors
(e.g., barcode scanners, cameras, etc.) (not shown) located in an
automated multi-module cell processing instrument to, e.g., confirm
the contents of and optionally to control the operation of FTEP
insert 308. FIG. 3F is a top view of FTEP insert 308 with FTEP
insert cover 305 (seen in FIG. 3E) removed. Again, data 373,
machine-readable indicia 375, and FTEP 306 can be seen. Also,
electrodes channels 378 of FTEP 306 are seen.
Nucleic Acid-Directed Nuclease Genome Editing Generally
[0096] The FTEP device of the present invention may be a
stand-alone device or module or may be one module in an automated
multi-module cell processing instrument. In one embodiment, the
FTEP device is used in an automated cell processing instrument
designed for creating genome edits in live cells. A recent
discovery for editing live cells involves nucleic acid-guided
nuclease (e.g., RNA-guided nuclease) editing. A nucleic acid-guided
nuclease complexed with an appropriate synthetic guide nucleic acid
in a cell can cut the genome of the cell at a desired location. The
guide nucleic acid helps the nucleic acid-guided nuclease recognize
and cut the DNA at a specific target sequence. By manipulating the
nucleotide sequence of the guide nucleic acid, the nucleic
acid-guided nuclease may be programmed to target any DNA sequence
for cleavage as long as an appropriate protospacer adjacent motif
(PAM) is nearby. In certain aspects, the nucleic acid-guided
nuclease editing system may use two separate guide nucleic acid
molecules that combine to function as a guide nucleic acid, e.g., a
CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA). In
other aspects, the guide nucleic acid may be a single guide nucleic
acid that includes both the crRNA and tracrRNA sequences.
[0097] In general, a guide nucleic acid (e.g., gRNA) complexes with
a compatible nucleic acid-guided nuclease and can then hybridize
with a target sequence, thereby directing the nuclease to the
target sequence. A guide nucleic acid can be DNA or RNA;
alternatively, a guide nucleic acid may comprise both DNA and RNA.
In some embodiments, a guide nucleic acid may comprise modified or
non-naturally occurring nucleotides. In cases where the guide
nucleic acid comprises RNA, the gRNA may be encoded by a DNA
sequence on a polynucleotide molecule such as a plasmid, linear
construct, or the coding sequence may reside within an editing
cassette. The sequence for the gRNA may be under the control of a
constitutive promoter, or, in some embodiments and preferably, an
inducible promoter as described below.
[0098] A guide nucleic acid comprises a guide sequence, where the
guide sequence is a polynucleotide sequence having sufficient
complementarity with a target sequence to hybridize with the target
sequence and direct sequence-specific binding of a complexed
nucleic acid-guided nuclease to the target sequence. The degree of
complementarity between a guide sequence and the corresponding
target sequence, when optimally aligned using a suitable alignment
algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%,
90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined
with the use of any suitable algorithm for aligning sequences. In
some embodiments, a guide sequence is about or more than about 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In
some embodiments, a guide sequence is less than about 75, 50, 45,
40, 35, 30, 25, 20 nucleotides in length. Preferably the guide
sequence is 10-30 or 15-20 nucleotides long, or 15, 16, 17, 18, 19,
or 20 nucleotides in length.
[0099] In the present methods and compositions, the guide nucleic
acid is provided as a sequence to be expressed from a plasmid or
vector and comprises both the guide sequence and the scaffold
sequence as a single transcript under the control of a promoter,
and in some embodiments, an inducible promoter. The guide nucleic
acid can be engineered to target a desired target sequence by
altering the guide sequence so that the guide sequence is
complementary to a desired target sequence, thereby allowing
hybridization between the guide sequence and the target sequence.
In general, to generate an edit in the target sequence, the
gRNA/nuclease complex binds to a target sequence as determined by
the guide RNA, and the nuclease recognizes a protospacer adjacent
motif (PAM) sequence adjacent to the target sequence. The target
sequence can be any polynucleotide endogenous or exogenous to a
prokaryotic or eukaryotic cell, or in vitro. For example, the
target sequence can be a polynucleotide residing in the nucleus of
a eukaryotic cell. The target sequence can be a sequence encoding a
gene product (e.g., a protein) or a non-coding sequence (e.g., a
regulatory polynucleotide, an intron, a PAM, or "junk" DNA).
[0100] The guide nucleic acid may be part of an editing cassette
that encodes the donor nucleic acid. Alternatively, the guide
nucleic acid may not be part of the editing cassette and instead
may be encoded on the engine or editing vector backbone. For
example, a sequence coding for a guide nucleic acid can be
assembled or inserted into a vector backbone first, followed by
insertion of the donor nucleic acid in, e.g., the editing cassette.
In other cases, the donor nucleic acid in, e.g., an editing
cassette can be inserted or assembled into a vector backbone first,
followed by insertion of the sequence coding for the guide nucleic
acid. In yet other cases, the sequence encoding the guide nucleic
acid and the donor nucleic acid (inserted, for example, in an
editing cassette) are simultaneously but separately inserted or
assembled into a vector. In yet other embodiments, the sequence
encoding the guide nucleic acid and the sequence encoding the donor
nucleic acid are both included in the editing cassette.
[0101] The target sequence is associated with a proto-spacer
mutation (PAM), which is a short nucleotide sequence recognized by
the gRNA/nuclease complex. The precise preferred PAM sequence and
length requirements for different nucleic acid-guided nucleases
vary; however, PAMs typically are 2-7 base-pair sequences adjacent
or in proximity to the target sequence and, depending on the
nuclease, can be 5' or 3' to the target sequence. Engineering of
the PAM-interacting domain of a nucleic acid-guided nuclease may
allow for alteration of PAM specificity, improve target site
recognition fidelity, decrease target site recognition fidelity, or
increase the versatility of a nucleic acid-guided nuclease. In
certain embodiments, the genome editing of a target sequence both
introduces a desired DNA change to a target sequence, e.g., the
genomic DNA of a cell, and removes, mutates, or renders inactive a
proto-spacer mutation (PAM) region in the target sequence.
Rendering the PAM at the target sequence inactive precludes
additional editing of the cell genome at that target sequence,
e.g., upon subsequent exposure to a nucleic acid-guided nuclease
complexed with a synthetic guide nucleic acid in later rounds of
editing. Thus, cells having the desired target sequence edit and an
altered PAM can be selected using a nucleic acid-guided nuclease
complexed with a synthetic guide nucleic acid complementary to the
target sequence. The genome of the cells that did not undergo the
first editing event will be cut rendering a double-stranded DNA
break, and thus these cells will not continue to be viable. The
genome of the cells containing the desired target sequence edit and
PAM alteration will not be cut, as these edited cells no longer
contain the necessary PAM site and will thus continue to grow and
propagate.
[0102] The range of target sequences that nucleic acid-guided
nucleases can recognize is constrained by the need for a specific
PAM to be located near the desired target sequence. As a result, it
often can be difficult to target edits with the precision that is
necessary for genome editing. It has been found that nucleases can
recognize some PAMs very well (e.g., canonical PAMs), and other
PAMs less well or poorly (e.g., non-canonical PAMs). Because
certain of the methods disclosed herein allow for identification of
edited cells in a background of unedited cells (see, e.g., FIGS.
7A-7E and the descriptions thereof), the methods allow for
identification of edited cells where the PAM is less than optimal;
that is, the methods for identifying edited cells herein allow for
identification of edited cells even if editing efficiency is very
low. Additionally, the present methods expand the scope of target
sequences that may be edited since edits are more readily
identified, including cells where the genome edits are associated
with less functional PAMs.
[0103] As for the nuclease component of the nucleic acid-guided
nuclease editing system, a polynucleotide sequence encoding the
nucleic acid-guided nuclease can be codon optimized for expression
in particular cell types, such as archaeal, prokaryotic or
eukaryotic cells. Eukaryotic cells can be yeast, fungi, algae,
plant, animal, or human cells. Eukaryotic cells may be those of or
derived from a particular organism, such as a mammal, including but
not limited to human, mouse, rat, rabbit, dog, or non-human mammals
including non-human primates. The choice of nucleic acid-guided
nuclease to be employed depends on many factors, such as what type
of edit is to be made in the target sequence and whether an
appropriate PAM is located close to the desired target sequence.
Nucleases of use in the methods described herein include but are
not limited to Cas 9, Cas 12/CpfIl, MAD2, or MAD7 or other
MADzymes. As with the guide nucleic acid, the nuclease may be
encoded by a DNA sequence on a vector (e.g., the engine vector) and
be under the control of a constitutive or inducible promoter. In
some embodiments, the sequence encoding the nuclease is under the
control of an inducible promoter, and the inducible promoter may be
separate from but the same as the inducible promoter controlling
transcription of the guide nucleic acid; that is, a separate
inducible promoter drives the transcription of the nuclease and
guide nucleic acid sequences but the two inducible promoters may be
the same type of inducible promoter (e.g., both are pL promoters).
Alternatively, the inducible promoter controlling expression of the
nuclease may be different from the inducible promoter controlling
transcription of the guide nucleic acid; that is, e.g., the
nuclease may be under the control of the pBAD inducible promoter,
and the guide nucleic acid may be under the control of the pL
inducible promoter.
[0104] Another component of the nucleic acid-guided nuclease system
is the donor nucleic acid. In some embodiments, the donor nucleic
acid is on the same polynucleotide (e.g., editing vector or editing
cassette) as the guide nucleic acid and may be (but not
necessarily) under the control of the same promoter as the guide
nucleic acid (e.g., a single promoter driving the transcription of
both the guide nucleic acid and the donor nucleic acid). The donor
nucleic acid is designed to serve as a template for homologous
recombination with a target sequence nicked or cleaved by the
nucleic acid-guided nuclease as a part of the gRNA/nuclease
complex. A donor nucleic acid polynucleotide may be of any suitable
length, such as about or more than about 20, 25, 50, 75, 100, 150,
200, 500, or 1000 nucleotides in length. In certain preferred
aspects, the donor nucleic acid can be provided as an
oligonucleotide of between 20-300 nucleotides, more preferably
between 50-250 nucleotides. The donor nucleic acid comprises a
region that is complementary to a portion of the target sequence
(e.g., a homology arm). When optimally aligned, the donor nucleic
acid overlaps with (is complementary to) the target sequence by,
e.g., about 20, 25, 30, 35, 40, 50, 60, 70, 80, 90 or more
nucleotides. In many embodiments, the donor nucleic acid comprises
two homology arms (regions complementary to the target sequence)
flanking the mutation or difference between the donor nucleic acid
and the target template. The donor nucleic acid comprises at least
one mutation or alteration compared to the target sequence, such as
an insertion, deletion, modification, or any combination thereof
compared to the target sequence.
[0105] Often the donor nucleic acid is provided as an editing
cassette, which is inserted into a vector backbone where the vector
backbone may comprise a promoter driving transcription of the gRNA
and the coding sequence of the gRNA, or the vector backbone may
comprise a promoter driving the transcription of the gRNA but not
the gRNA itself. Moreover, there may be more than one, e.g., two,
three, four, or more guide nucleic acid/donor nucleic acid
cassettes inserted into an editing vector, where each guide nucleic
acid is under the control of separate different promoters, separate
like promoters, or where all guide nucleic acid/donor nucleic acid
pairs are under the control of a single promoter. In some
embodiments, the promoter driving transcription of the gRNA and the
donor nucleic acid (or driving more than one gRNA/donor nucleic
acid pair) is an inducible promoter and the promoter driving
transcription of the nuclease is an inducible promoter as well. For
additional information regarding editing cassettes, see U.S. Pat.
Nos. 9,982,278; 10,240,167; 10,266,849; 10,351,877; 10,364,442; and
10,435,715; and U.S. Ser. Nos. 16/275,465 and U.S. Ser. No.
16/551,517.
[0106] In addition to the donor nucleic acid, an editing cassette
may comprise one or more primer sites. The primer sites can be used
to amplify the editing cassette by using oligonucleotide primers;
for example, if the primer sites flank one or more of the other
components of the editing cassette.
[0107] Also, as described above, the donor nucleic acid may
optionally comprise--in addition to the at least one mutation
relative to a target sequence--one or more PAM sequence alterations
that mutate, delete or render inactive the PAM site in the target
sequence. The PAM sequence alteration in the target sequence
renders the PAM site "immune" to the nucleic acid-guided nuclease
and protects the target sequence from further editing in subsequent
rounds of editing if the same nuclease is used.
[0108] In addition, the editing cassette may comprise a barcode. A
barcode is a unique DNA sequence that corresponds to the donor DNA
sequence such that the barcode can identify the edit made to the
corresponding target sequence. The barcode typically comprises four
or more nucleotides. In some embodiments, the editing cassettes
comprise a collection of donor nucleic acids representing, e.g.,
gene-wide or genome-wide libraries of donor nucleic acids. The
library of editing cassettes is cloned into vector backbones where,
e.g., each different donor nucleic acid is associated with a
different barcode.
[0109] Additionally, in some embodiments, an expression vector or
cassette encoding components of the nucleic acid-guided nuclease
system further encodes a nucleic acid-guided nuclease comprising
one or more nuclear localization sequences (NLSs), such as about or
more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs. In
some embodiments, the engineered nuclease comprises NLSs at or near
the amino-terminus, NLSs at or near the carboxy-terminus, or a
combination thereof.
[0110] The engine and editing vectors comprise control sequences
operably linked to the component sequences to be transcribed. As
stated above, the promoters driving transcription of one or more
components of the nucleic acid-guided nuclease editing system may
be inducible such as one or both of the gRNA and the nuclease. A
number of gene regulation control systems have been developed for
the controlled expression of genes in plant, microbe, and animal
cells, including mammalian cells, including the pL promoter
(induced by heat inactivation of the CI857 repressor), the pBAD
promoter (induced by the addition of arabinose to the cell growth
medium), and the rhamnose inducible promoter (induced by the
addition of rhamnose to the cell growth medium). Other systems
include the tetracycline-controlled transcriptional activation
system (Tet-On/Tet-Off, Clontech, Inc. (Palo Alto, Calif.); Bujard
and Gossen, PNAS, 89(12):5547-5551 (1992)), the Lac Switch
Inducible system (Wyborski et al., Environ Mol Mutagen,
28(4):447-58 (1996); DuCoeur et al., Strategies 5(3):70-72 (1992);
U.S. Patent No. 4,833,080), the ecdysone-inducible gene expression
system (No et al., PNAS, 93(8):3346-3351 (1996)), the cumate
gene-switch system (Mullick et al., BMC Biotechnology, 6:43
(2006)), and the tamoxifen-inducible gene expression (Zhang et al.,
Nucleic Acids Research, 24:543-548 (1996)) as well as others. In
the present methods used in the modules and instruments described
herein, it is preferred that at least one of the nucleic
acid-guided nuclease editing components (e.g., the nuclease and/or
the gRNA) is under the control of a promoter that is activated by a
rise in temperature, as such a promoter allows for the promoter to
be activated by an increase in temperature, and de-activated by a
decrease in temperature, thereby "turning off" the editing process.
Thus, in the scenario of a promoter that is de-activated by a
decrease in temperature, editing in the cell can be turned off
without having to change media; to remove, e.g., an inducible
biochemical in the medium that is used to induce editing.
Automated Multi-Module Cell Processing Instruments Comprising
FTEPs
[0111] The present disclosure relates to flow-through
electroporation devices or modules that can be used alone, or as
one module in automated multi-module cell processing instruments.
In some embodiments, the FTEP may be included as part of a reagent
cartridge, wherein the reagent cartridge may further include sample
receptacles, reagent receptacles, and/or waste receptacles, etc.;
additionally, in certain embodiments, the reagent cartridge will
comprise a script readable by a processor for dispensing the
reagents and controlling the electroporation device contained
within the reagent cartridge. An automated multi-module cell
processing instrument with an FTEP can be used to process many
different types of cells in a controlled, contained, and
reproducible manner, including bacterial cells, mammalian cells,
non-mammalian eukaryotic cells, yeast cells, fungi, archaea, and
the like.
Automated Cell Editing Instruments
[0112] FIG. 4A depicts an exemplary automated multi-module cell
processing instrument 400 to, e.g., perform one of the exemplary
workflows comprising a split protein reporter system as described
herein. The instrument 400, for example, may be and preferably is
designed as a stand-alone desktop instrument for use within a
laboratory environment. The instrument 400 may incorporate a
mixture of reusable and disposable components for performing the
various integrated processes in conducting automated genome
cleavage and/or editing in cells without human intervention.
Illustrated is a gantry 402, providing an automated mechanical
motion system (actuator) (not shown) that supplies XYZ axis motion
control to, e.g., an automated (i.e., robotic) liquid handling
system 458 including, e.g., an air displacement pipettor 432 which
allows for cell processing among multiple modules without human
intervention. In some automated multi-module cell processing
instruments, the air displacement pipettor 432 is moved by gantry
402 and the various modules and reagent cartridges remain
stationary; however, in other embodiments, the liquid handling
system 458 may stay stationary while the various modules and
reagent cartridges are moved. Also included in the automated
multi-module cell processing instrument 400 are reagent cartridges
410 comprising reservoirs 412 and transformation module 430 (e.g.,
a flow-through electroporation device as described in detail in
relation to FIGS. 1A-1P), as well as wash reservoirs 406, cell
input reservoir 451 and cell output reservoir 453. The wash
reservoirs 406 may be configured to accommodate large tubes, for
example, wash solutions, or solutions that are used often
throughout an iterative process. Although two of the reagent
cartridges 410 comprise a wash reservoir 406 in FIG. 4A, the wash
reservoirs instead could be included in a wash cartridge where the
reagent and wash cartridges are separate cartridges. In such a
case, the reagent cartridge 410 and wash cartridge 404 may be
identical except for the consumables (reagents or other components
contained within the various inserts) inserted therein. (See, e.g.,
FIGS. 2A and 2B.)
[0113] In some implementations, the reagent cartridges 410 are
disposable kits comprising reagents and cells for use in the
automated multi-module cell processing/editing instrument 400. For
example, a user may open and position each of the reagent
cartridges 410 comprising various desired inserts and reagents
within the chassis of the automated multi-module cell editing
instrument 400 prior to activating cell processing. Further, each
of the reagent cartridges 410 may be inserted into receptacles in
the chassis having different temperature zones appropriate for the
reagents contained therein.
[0114] Also illustrated in FIG. 4A is the robotic liquid handling
system 458 including the gantry 402 and air displacement pipettor
432. In some examples, the robotic handling system 458 may include
an automated liquid handling system such as those manufactured by
Tecan Group Ltd. of Mannedorf, Switzerland, Hamilton Company of
Reno, Nev. (see, e.g., WO2018015544A1), or Beckman Coulter, Inc. of
Fort Collins, Colo. (see, e.g., US20160018427A1). Pipette tips may
be provided in a pipette transfer tip supply (not shown) for use
with the air displacement pipettor 432.
[0115] Inserts or components of the reagent cartridges 410, in some
implementations, are marked with machine-readable indicia (not
shown), such as bar codes, for recognition by the robotic handling
system 458. For example, the robotic liquid handling system 458 may
scan one or more inserts within each of the reagent cartridges 410
to confirm contents. In other implementations, machine-readable
indicia may be marked upon each reagent cartridge 410, and a
processing system (not shown, but see element 437 of FIG. 4B) of
the automated multi-module cell editing instrument 400 may identify
a stored materials map based upon the machine-readable indicia. In
the embodiment illustrated in FIG. 4A, a cell growth module
comprises a cell growth vial 418 (described in greater detail below
in relation to FIGS. 5A-5D). Additionally seen is the TFF module
422 (described above in detail in relation to FIGS. 6A-6E) and
selection module 420. Also illustrated as part of the automated
multi-module cell processing instrument 400 of FIG. 4A is a
singulation module 440 (e.g., a solid wall isolation, incubation
and normalization device (SWIIN device) is shown here) described
herein in relation to FIGS. 7A-7E, served by, e.g., robotic liquid
handing system 458 and air displacement pipettor 432. Additionally
seen is a selection module 420. Also note the placement of three
heatsinks 455.
[0116] FIG. 4B is a simplified representation of the contents of
the exemplary multi-module cell processing instrument 400 depicted
in FIG. 4A. Cartridge-based source materials (such as in reagent
cartridges 410), for example, may be positioned in designated areas
on a deck of the instrument 400 for access by an air displacement
pipettor 432. The deck of the multi-module cell processing
instrument 400 may include a protection sink such that contaminants
spilling, dripping, or overflowing from any of the modules of the
instrument 400 are contained within a lip of the protection sink.
Also seen are reagent cartridges 410, which are shown disposed with
thermal assemblies 411 which can create temperature zones
appropriate for different regions. Note that one of the reagent
cartridges also comprises a flow-through electroporation device 430
(FTEP), served by FTEP interface (e.g., manifold arm) and actuator
431. Also seen is TFF module 422 with adjacent thermal assembly
425, where the TFF module is served by TFF interface (e.g.,
manifold arm) and actuator 433. Thermal assemblies 425, 435, and
445 encompass thermal electric devices such as Peltier devices, as
well as heatsinks, fans and coolers. The rotating growth vial 418
is within a growth module 434, where the growth module is served by
two thermal assemblies 435. A selection module is seen at 420. Also
seen is the SWIIN module 440, comprising a SWIIN cartridge 441,
where the SWIIN module also comprises a thermal assembly 445,
illumination 443 (in this embodiment, backlighting), evaporation
and condensation control 449, and where the SWIIN module is served
by SWIIN interface (e.g., manifold arm) and actuator 447. Also seen
in this view is touch screen display 401, display actuator 403,
illumination 405 (one on either side of multi-module cell
processing instrument 400), and cameras 439 (one illumination
device on either side of multi-module cell processing instrument
400). Finally, element 437 comprises electronics, such as circuit
control boards, high-voltage amplifiers, power supplies, and power
entry; as well as pneumatics, such as pumps, valves and
sensors.
[0117] FIG. 4C illustrates a front perspective view of multi-module
cell processing instrument 400 for use in as a desktop version of
the automated multi-module cell editing instrument 400. For
example, a chassis 490 may have a width of about 24-48 inches, a
height of about 24-48 inches and a depth of about 24-48 inches.
Chassis 490 may be and preferably is designed to hold all modules
and disposable supplies used in automated cell processing and to
perform all processes required without human intervention; that is,
chassis 490 is configured to provide an integrated, stand-alone
automated multi-module cell processing instrument. As illustrated
in FIG. 4C, chassis 490 includes touch screen display 401, cooling
grate 464, which allows for air flow via an internal fan (not
shown). The touch screen display provides information to a user
regarding the processing status of the automated multi-module cell
editing instrument 400 and accepts inputs from the user for
conducting the cell processing. In this embodiment, the chassis 490
is lifted by adjustable feet 470a, 470b, 470c and 470d (feet
470a-470c are shown in this FIG. 4C). Adjustable feet 470a-470d,
for example, allow for additional air flow beneath the chassis
490.
[0118] Inside the chassis 490, in some implementations, will be
most or all of the components described in relation to FIGS. 4A and
4B, including the robotic liquid handling system disposed along a
gantry, reagent cartridges 410 including a flow-through
electroporation device, a rotating growth vial 418 in a cell growth
module 434, a tangential flow filtration module 422, a SWIIN module
440 as well as interfaces and actuators for the various modules. In
addition, chassis 490 houses control circuitry, liquid handling
tubes, air pump controls, valves, sensors, thermal assemblies
(e.g., heating and cooling units) and other control mechanisms. For
examples of multi-module cell editing instruments, see U.S. Pat.
No. 10,253,316, issued 9 Apr. 2019; U.S. Pat. No. 10,329,559,
issued 25 Jun. 2019; U.S. Pat. No. 10,323,242, issued 18 Jun. 2019;
U.S. Pat. No. 10,421,959, issued 24 Sep. 2019; U.S. Pat. No.
10,465,185, issued 5 Nov. 2019; and U.S. Pat. No. 10,519,437,
issued 31 Dec. 2019; and U.S. Ser. No. 16/666,964, filed 29 Oct.
2019; and U.S. Ser. No. 16/680,643, filed 12 Nov. 2019 all of which
are herein incorporated by reference in their entirety.
Rotating Cell Growth Module
[0119] FIG. 5A shows one embodiment of a rotating growth vial 500
for use with the cell growth device described herein. The rotating
growth vial is an optically-transparent container having an open
end 504 for receiving liquid media and cells, a central vial region
506 that defines the primary container for growing cells, a
tapered-to-constricted region 518 defining at least one light path
510, a closed end 516, and a drive engagement mechanism 512. The
rotating growth vial has a central longitudinal axis 520 around
which the vial rotates, and the light path 510 is generally
perpendicular to the longitudinal axis of the vial. The first light
path 510 is positioned in the lower constricted portion of the
tapered-to-constricted region 518. Optionally, some embodiments of
the rotating growth vial 500 have a second light path 508 in the
tapered region of the tapered-to-constricted region 518. Both light
paths in this embodiment are positioned in a region of the rotating
growth vial that is constantly filled with the cell culture (cells
+growth media) and is not affected by the rotational speed of the
growth vial. The first light path 510 is shorter than the second
light path 508 allowing for sensitive measurement of OD values when
the OD values of the cell culture in the vial are at a high level
(e.g., later in the cell growth process), whereas the second light
path 508 allows for sensitive measurement of OD values when the OD
values of the cell culture in the vial are at a lower level (e.g.,
earlier in the cell growth process). Also shown is lip 502, which
allows the rotating growth vial to be seated in a growth module
(not shown) and further allows for easy handling by the user.
[0120] In some configurations of the rotating growth vial, the
rotating growth vial has two or more "paddles" or interior features
disposed within the rotating growth vial, extending from the inner
wall of the rotating growth vial toward the center of the central
vial region 506. In some aspects, the width of the paddles or
features varies with the size or volume of the rotating growth
vial, and may range from 1/20 to just over 1/3 the diameter of the
rotating growth vial, or from 1/15 to 1/4 the diameter of the
rotating growth vial, or from 1/10 to 1/5 the diameter of the
rotating growth vial. In some aspects, the length of the paddles
varies with the size or volume of the rotating growth vial, and may
range from 4/5 to 1/4 the length of the main body of the rotating
growth vial 500, or from 3/4 to 1/3 the length of the central body
region 506 of the rotating growth vial, or from 1/2 to 1/3 the
length of the central body region 506 of the rotating growth vial
500. In other aspects, there may be concentric rows of raised
features disposed on the inner surface of the main body of the
rotating growth vial arranged horizontally or vertically; and in
other aspects, there may be a spiral configuration of raised
features disposed on the inner surface of the main body of the
rotating growth vial. In alternative aspects, the concentric rows
of raised features or spiral configuration may be disposed upon a
post or center structure of the rotating growth vial. Though
described above as having two paddles, the rotating growth vial 500
may comprise 3, 4, 5, 6 or more paddles, and up to 20 paddles. The
number of paddles will depend upon, e.g., the size or volume of the
rotating growth vial 500. The paddles may be arranged symmetrically
as single paddles extending from the inner wall of the vial into
the interior of the vial, or the paddles may be symmetrically
arranged in groups of 2, 3, 4 or more paddles in a group (for
example, a pair of paddles opposite another pair of paddles)
extending from the inner wall of the vial into the interior of the
vial. In another embodiment, the paddles may extend from the middle
of the rotating growth vial out toward the wall of the rotating
growth vial, from, e.g., a post or other support structure in the
interior of the rotating growth vial.
[0121] The drive engagement mechanism 512 engages with a motor (not
shown) to rotate the vial. In some embodiments, the motor drives
the drive engagement mechanism 512 such that the rotating growth
vial is rotated in one direction only, and in other embodiments,
the rotating growth vial is rotated in a first direction for a
first amount of time or periodicity, rotated in a second direction
(i.e., the opposite direction) for a second amount of time or
periodicity, and this process may be repeated so that the rotating
growth vial (and the cell culture contents) are subjected to an
oscillating motion. Further, the choice of whether the culture is
subject to oscillation and the periodicity therefor may be selected
by the user. The first amount of time and the second amount of time
may be the same or may be different. The amount of time may be 1,
2, 3, 4, 5, or more seconds, or may be 1, 2, 3, 4 or more minutes.
In another embodiment, in an early stage of cell growth, the
rotating growth vial may be oscillated at a first periodicity
(e.g., every 60 seconds), and then at a later stage of cell growth,
the rotating growth vial may be oscillated at a second periodicity
(e.g., every one second) different from the first periodicity.
[0122] The rotating growth vial 500 may be reusable or, preferably,
the rotating growth vial is consumable. In some embodiments, the
rotating growth vial is consumable and is presented to the user
pre-filled with growth medium, where the vial is hermetically
sealed at the open end 504 with a foil or film seal. A
medium-filled rotating growth vial packaged in such a manner may be
part of a kit for use with a stand-alone cell growth device or with
a cell growth module that is part of an automated multi-module cell
processing instrument. To introduce cells into the vial, a user
need only pipette up a desired volume of cells and use the pipette
tip to punch through the foil or film seal of the vial. Open end
504 may optionally include an extended lip 502 to overlap and
engage with the cell growth device (not shown). In automated
systems, the rotating growth vial 500 may be tagged with a barcode
or other identifying means that can be read by a scanner or camera
that is part of the automated instrument (not shown).
[0123] The volume of the rotating growth vial 500 and the volume of
the cell culture (including growth medium) may vary greatly, but
the volume of the rotating growth vial 500 must be large enough for
the cell culture in the growth vial to get proper aeration while
the vial is rotating and to generate an adequate number of cells.
In practice, the volume of the rotating growth vial 500 may range
from 1-250 ml, 2-100 ml, from 5-80 ml, 10-50 ml, or from 12-35 ml.
Likewise, the volume of the cell culture (cells+growth media)
should be appropriate to allow proper aeration in the rotating
growth vial. Thus, the volume of the cell culture should be
approximately 5-85% of the volume of the growth vial or from 20-60%
of the volume of the growth vial. For example, for a 35 ml growth
vial, the volume of the cell culture would be from about 1.8 ml to
about 27 ml, or from 5 ml to about 21 ml.
[0124] The rotating growth vial 500 preferably is fabricated from a
bio-compatible optically transparent material--or at least the
portion of the vial comprising the light path(s) is transparent.
Additionally, material from which the rotating growth vial is
fabricated should be able to be cooled to about 4.degree. C. or
lower and heated to about 55.degree. C. or higher to accommodate
both temperature-based cell assays and long-term storage at low
temperatures. Further, the material that is used to fabricate the
vial must be able to withstand temperatures up to 55.degree. C.
without deformation while spinning. Suitable materials include
glass, cyclic olefin copolymer (COC), polyvinyl chloride,
polyethylene, polyamide, polypropylene, polycarbonate, poly(methyl
methacrylate (PMMA), polysulfone, polyurethane, and co-polymers of
these and other polymers. Preferred materials include
polypropylene, polycarbonate, or polystyrene. In some embodiments,
the rotating growth vial is inexpensively fabricated by, e.g.,
injection molding or extrusion.
[0125] FIGS. 5B-5D show an embodiment of a cell growth module 550
comprising a rotating growth vial 500. FIG. 5B is a perspective
view of one embodiment of a cell growth module 550. FIG. 5C depicts
a cut-away view of the cell growth module 550 from FIG. 5B. In both
figures, the rotating growth vial 500 is seen positioned inside a
main housing 526 with the extended lip 502 of the rotating growth
vial 500 extending above the main housing 526. Additionally, end
housings 522, a lower housing 532, and flanges 524 are indicated in
both figures. Flanges 524 are used to attach the cell growth
device/module to heating/cooling means or to another structure (not
shown). FIG. 5C depicts additional detail. In FIG. 5C, upper
bearing 542 and lower bearing 530 are shown positioned in main
housing 526. Upper bearing 542 and lower bearing 530 support the
vertical load of rotating growth vial 500. Lower housing 532
contains the drive motor 536. The cell growth device 550 of FIG. 5C
comprises two light paths: a primary light path 534, and a
secondary light path 530. Light path 534 corresponds to light path
510 positioned in the constricted portion of the
tapered-to-constricted portion of the rotating growth vial, and
light path 530 corresponds to light path 508 in the tapered portion
of the tapered-to-constricted portion of the rotating growth vial.
Light paths 510 and 508 are not shown in FIG. 5C but may be seen
in, e.g., FIG. 5A. In addition to light paths 534 and 530, there is
an emission board 528 to illuminate the light path(s), and detector
board 546 to detect the light after the light travels through the
cell culture liquid in the rotating growth vial 500.
[0126] The drive motor 536 used to rotate the rotating growth vial
500 in some embodiments is a brushless DC type drive motor with
built-in drive controls that can be set to hold a constant
revolution per minute (RPM) between 0 and about 3000 RPM.
Alternatively, other motor types such as a stepper, servo, brushed
DC, and the like can be used. Optionally, the drive motor 506 may
also have direction control to allow reversing of the rotational
direction, and a tachometer to sense and report actual RPM. The
motor is controlled by a processor (not shown) according to, e.g.,
standard protocols programmed into the processor and/or user input,
and the motor may be configured to vary RPM to cause axial
precession of the cell culture thereby enhancing mixing, e.g., to
prevent cell aggregation, increase aeration, and optimize cellular
respiration.
[0127] Main housing 526, end housings 522 and lower housing 532 of
the cell growth device/module 550 may be fabricated from any
suitable, robust material including aluminum, stainless steel, and
other thermally conductive materials, including plastics. These
structures or portions thereof can be created through various
techniques, e.g., metal fabrication, injection molding, creation of
structural layers that are fused, etc. Whereas the rotating growth
vial 500 is envisioned in some embodiments to be reusable but
preferably is consumable, the other components of the cell growth
device 550 are preferably reusable and can function as a
stand-alone benchtop device or, as here, as a module in a
multi-module cell processing instrument.
[0128] The processor (not shown) of the cell growth system may be
programmed with information to be used as a "blank" or control for
the growing cell culture. A "blank" or control is a vessel
containing cell growth medium only, which yields 100% transmittance
and 0 OD, while the cell sample will deflect light rays and will
have a lower percent transmittance and higher OD. As the cells grow
in the media and become denser, transmittance will decrease and OD
will increase. The processor of the cell growth system may be
programmed to use wavelength values for blanks commensurate with
the growth media typically used in cell culture (whether, e.g.,
mammalian cells, bacterial cells, animal cells, yeast cells, etc.).
Alternatively, a second spectrophotometer and vessel may be
included in the cell growth system, where the second
spectrophotometer is used to read a blank at designated
intervals.
[0129] FIG. 5D illustrates a cell growth device/module 550 as part
of an assembly comprising the cell growth device 550 of FIG. 5B
coupled to light source 590, detector 592, and thermoelectric
components 594. The rotating growth vial 500 is inserted into the
cell growth device 550. Components of the light source 590 and
detector 592 (e.g., such as a photodiode with gain control to cover
5-log) are coupled to the main housing of the cell growth device
550. The lower housing 532 that houses the motor that rotates the
rotating growth vial is illustrated, as is one of the flanges 524
that secures the cell growth device to the assembly. Also
illustrated is a Peltier device or thermoelectric component 594. In
this embodiment, thermal control is accomplished by attachment and
electrical integration of the cell growth device 500 to the
thermoelectric component 594 via the flange 504 on the base of the
lower housing 532. Thermoelectric coolers/devices 594 are capable
of "pumping" heat to either side of a junction, either cooling a
surface or heating a surface depending on the direction of current
flow. In one embodiment, a thermistor is used to measure the
temperature of the main housing and then, through a standard
electronic proportional-integral-derivative (PID) controller loop,
the rotating growth vial 500 is controlled to approximately
+/-0.5.degree. C.
[0130] In certain embodiments, a rear-mounted power entry module
contains the safety fuses and the on-off switch, which when
switched on powers the internal AC and DC power supplies (not
shown) activating the processor. Measurements of optical densities
(OD) at programmed time intervals are accomplished using a 600 nm
Light Emitting Diode (LED) (not shown) that has been columnated
through an optic into the lower constricted portion of the rotating
growth vial which contains the cells of interest. The light
continues through a collection optic to the detection system which
consists of a (digital) gain-controlled silicone photodiode.
Generally, optical density is normally shown as the absolute value
of the logarithm with base 10 of the power transmission factors of
an optical attenuator: OD=-log10 (Power out/Power in). Since OD is
the measure of optical attenuation--that is, the sum of absorption,
scattering, and reflection--the cell growth device OD measurement
records the overall power transmission, so as the cells grow and
become denser in population, the OD (the loss of signal) increases.
The OD system is pre-calibrated against OD standards with these
values stored in an on-board memory accessible by the measurement
program.
[0131] In use, cells are inoculated (cells can be pipetted, e.g.,
from an automated liquid handling system or by a user) into
pre-filled growth media of a rotating growth vial 500 by piercing
though the foil or film seal. The programmed software of the cell
growth device 550 sets the control temperature for growth,
typically 30.degree. C., then slowly starts the rotation of the
rotating growth vial. The cell/growth media mixture slowly moves
vertically up the wall due to centrifugal force allowing the
rotating growth vial to expose a large surface area of the mixture
to a normal oxygen environment. The growth monitoring system takes
either continuous readings of the OD or OD measurements at pre-set
or pre-programmed time intervals. These measurements are stored in
internal memory and if requested the software plots the
measurements versus time to display a growth curve. If enhanced
mixing is required, e.g., to optimize growth conditions, the speed
of the vial rotation can be varied to cause an axial precession of
the liquid, and/or a complete directional change can be performed
at programmed intervals. The growth monitoring can be programmed to
automatically terminate the growth stage at a pre-determined OD,
and then quickly cool the mixture to a lower temperature to inhibit
further growth.
[0132] One application for the cell growth device 550 is to
constantly measure the optical density of a growing cell culture.
One advantage of the described cell growth device is that optical
density can be measured continuously (kinetic monitoring) or at
specific time intervals; e.g., every 5, 10, 15, 20, 30 45, or 60
seconds, or every 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 minutes. While
the cell growth device has been described in the context of
measuring the optical density (OD) of a growing cell culture, it
should, however, be understood by a skilled artisan given the
teachings of the present specification that other cell growth
parameters can be measured in addition to or instead of cell
culture OD. For example, spectroscopy using visible, UV, or near
infrared (NIR) light allows monitoring the concentration of
nutrients and/or wastes in the cell culture. Additionally,
spectroscopic measurements may be used to quantify multiple
chemical species simultaneously. Nonsymmetric chemical species may
be quantified by identification of characteristic absorbance
features in the NIR. Conversely, symmetric chemical species can be
readily quantified using Raman spectroscopy. Many critical
metabolites, such as glucose, glutamine, ammonia, and lactate have
distinct spectral features in the IR, such that they may be easily
quantified. The amount and frequencies of light absorbed by the
sample can be correlated to the type and concentration of chemical
species present in the sample. Each of these measurement types
provides specific advantages. FT-NIR provides the greatest light
penetration depth and can be used for thicker samples. FT-mid-IR
(MIR) provides information that is more easily discernible as being
specific for certain analytes as these wavelengths are closer to
the fundamental IR absorptions. FT-Raman is advantageous when
interference due to water is to be minimized. Other spectral
properties can be measured via, e.g., dielectric impedence
spectroscopy, visible fluorescence, fluorescence polarization, or
luminescence. Additionally, the cell growth device may include
additional sensors for measuring, e.g., dissolved oxygen, carbon
dioxide, pH, conductivity, and the like.
Cell Concentration Module
[0133] As described above in relation to the rotating growth vial
and cell growth module, in order to obtain an adequate number of
cells for transformation or transfection, cells typically are grown
to a specific optical density in medium appropriate for the growth
of the cells of interest; however, for effective transformation or
transfection, it is desirable to decrease the volume of the cells
as well as render the cells competent via buffer or medium
exchange. Thus, one sub-component or module that is desired in cell
processing systems for the processes listed above is a module or
component that can grow, perform buffer exchange, and/or
concentrate cells and render them competent so that they may be
transformed or transfected with the nucleic acids needed for
engineering or editing the cell's genome.
[0134] FIG. 6A shows a retentate member 622 (top), permeate member
620 (middle) and a tangential flow assembly 610 (bottom) comprising
the retentate member 622, membrane 624 (not seen in FIG. 6A), and
permeate member 620 (also not seen). In FIG. 6A, retentate member
622 comprises a tangential flow channel 602, which has a serpentine
configuration that initiates at one lower corner of retentate
member 622--specifically at retentate port 628--traverses across
and up then down and across retentate member 622, ending in the
other lower corner of retentate member 622 at a second retentate
port 628. Also seen on retentate member 622 are energy directors
691, which circumscribe the region where a membrane or filter (not
seen in this FIG. 6A) is seated, as well as interdigitate between
areas of channel 602. Energy directors 691 in this embodiment mate
with and serve to facilitate ultrasonic welding or bonding of
retentate member 622 with permeate/filtrate member 620 via the
energy director component 691 on permeate/filtrate member 620 (at
right). Additionally, countersinks 623 can be seen, two on the
bottom one at the top middle of retentate member 622. Countersinks
623 are used to couple and tangential flow assembly 610 to a
reservoir assembly (not seen in this FIG. 6A but see FIG. 6B).
[0135] Permeate/filtrate member 620 is seen in the middle of FIG.
6A and comprises, in addition to energy director 691, through-holes
for retentate ports 628 at each bottom corner (which mate with the
through-holes for retentate ports 628 at the bottom corners of
retentate member 622), as well as a tangential flow channel 602 and
two permeate/filtrate ports 626 positioned at the top and center of
permeate member 620. The tangential flow channel 602 structure in
this embodiment has a serpentine configuration and an undulating
geometry, although other geometries may be used. Permeate member
620 also comprises countersinks 623, coincident with the
countersinks 623 on retentate member 620.
[0136] At bottom of FIG. 6A is a tangential flow assembly 610
comprising the retentate member 622 positioned on top of an
assembled with permeate member 620. In this view, retentate member
622 is "on top" of the view, a membrane (not seen in this view of
the assembly) would be adjacent and under retentate member 622 and
permeate member 620 (also not seen in this view of the assembly) is
adjacent to and beneath the membrane. Again countersinks 623 are
seen, where the countersinks in the retentate member 622 and the
permeate member 620 are coincident and configured to mate with
threads or mating elements for the countersinks disposed on a
reservoir assembly (not seen in FIG. 6A but see FIG. 6B).
[0137] A membrane or filter is disposed between the retentate and
permeate members, where fluids can flow through the membrane but
cells cannot and are thus retained in the flow channel disposed in
the retentate member. Filters or membranes appropriate for use in
the TFF device/module are those that are solvent resistant, are
contamination free during filtration, and are able to retain the
types and sizes of cells of interest. For example, in order to
retain small cell types such as bacterial cells, pore sizes can be
as low as 0.2 .mu.m, however for other cell types, the pore sizes
can be as high as 20 .mu.m. Indeed, the pore sizes useful in the
TFF device/module include filters with sizes from 0.20 .mu.m, 0.21
.mu.m, 0.22 .mu.m, 0.23 .mu.m, 0.24 .mu.m, 0.25 .mu.m, 0.26 .mu.m,
0.27 .mu.m, 0.28 .mu.m, 0.29 .mu.m, 0.30 .mu.m, 0.31 .mu.m, 0.32
.mu.m, 0.33 .mu.m, 0.34 .mu.m, 0.35 .mu.m, 0.36 .mu.m, 0.37 .mu.m,
0.38 .mu.m, 0.39 .mu.m, 0.40 .mu.m, 0.41 .mu.m, 0.42 .mu.m, 0.43
.mu.m, 0.44 .mu.m, 0.45 .mu.m, 0.46 .mu.m, 0.47 .mu.m, 0.48 .mu.m,
0.49 .mu.m, 0.50 .mu.m and larger. The filters may be fabricated
from any suitable non-reactive material including cellulose mixed
ester (cellulose nitrate and acetate) (CME), polycarbonate (PC),
polyvinylidene fluoride (PVDF), polyethersulfone (PES),
polytetrafluoroethylene (PTFE), nylon, glass fiber, or metal
substrates as in the case of laser or electrochemical etching.
[0138] The length of the channel structure 602 may vary depending
on the volume of the cell culture to be grown and the optical
density of the cell culture to be concentrated. The length of the
channel structure typically is from 60 mm to 300 mm, or from 70 mm
to 200 mm, or from 80 mm to 100 mm. The cross-section configuration
of the flow channel 402 may be round, elliptical, oval, square,
rectangular, trapezoidal, or irregular. If square, rectangular, or
another shape with generally straight sides, the cross section may
be from about 10 .mu.m to 1000 .mu.m wide, or from 200 .mu.m to 800
.mu.m wide, or from 300 .mu.m to 700 .mu.m wide, or from 400 .mu.m
to 600 .mu.m wide; and from about 10 .mu.m to 1000 .mu.m high, or
from 200 .mu.m to 800 .mu.m high, or from 300 .mu.m to 700 .mu.m
high, or from 400 .mu.m to 600 .mu.m high. If the cross section of
the flow channel 102 is generally round, oval or elliptical, the
radius of the channel may be from about 50 .mu.m to 1000 .mu.m in
hydraulic radius, or from 5 .mu.m to 800 .mu.m in hydraulic radius,
or from 200 .mu.m to 700 .mu.m in hydraulic radius, or from 300
.mu.m to 600 .mu.m wide in hydraulic radius, or from about 200 to
500 .mu.m in hydraulic radius. Moreover, the volume of the channel
in the retentate 422 and permeate 620 members may be different
depending on the depth of the channel in each member.
[0139] FIG. 6B shows front perspective (upper figure) and rear
perspective (lower figure) views of a reservoir assembly 650
configured to be used with the tangential flow assembly 610 seen in
FIG. 6A. Seen in the front perspective view (e.g., "front" being
the side of reservoir assembly 650 that is coupled to the
tangential flow assembly 610 seen in FIG. 6A) are retentate
reservoirs 652 on either side of permeate reservoir 654. Also seen
are permeate ports 626, retentate ports 628, and three threads or
mating elements 625 for countersinks 623 (countersinks 623 not seen
in this FIG. 6B). Threads or mating elements 625 for countersinks
623 are configured to mate or couple the tangential flow assembly
610 (seen in FIG. 6A) to reservoir assembly 650. Alternatively or
in addition, fasteners, sonic welding or heat stakes may be used to
mate or couple the tangential flow assembly 610 to reservoir
assembly 650. In addition is seen gasket 645 covering the top of
reservoir assembly 650. Gasket 645 is described in detail in
relation to FIG. 6E. At left in FIG. 6B is a rear perspective view
of reservoir assembly 650, where "rear" is the side of reservoir
assembly 650 that is not coupled to the tangential flow assembly.
Seen are retentate reservoirs 652, permeate reservoir 654, and
gasket 645.
[0140] The TFF device may be fabricated from any robust material in
which channels (and channel branches) may be milled including
stainless steel, silicon, glass, aluminum, or plastics including
cyclic-olefin copolymer (COC), cyclo-olefin polymer (COP),
polystyrene, polyvinyl chloride, polyethylene, polyamide,
polyethylene, polypropylene, acrylonitrile butadiene,
polycarbonate, polyetheretheketone (PEEK), poly(methyl
methylacrylate) (PMMA), polysulfone, and polyurethane, and
co-polymers of these and other polymers. If the TFF device/module
is disposable, preferably it is made of plastic. In some
embodiments, the material used to fabricate the TFF device/module
is thermally-conductive so that the cell culture may be heated or
cooled to a desired temperature. In certain embodiments, the TFF
device is formed by precision mechanical machining, laser
machining, electro discharge machining (for metal devices); wet or
dry etching (for silicon devices); dry or wet etching, powder or
sandblasting, photostructuring (for glass devices); or
thermoforming, injection molding, hot embossing, or laser machining
(for plastic devices) using the materials mentioned above that are
amenable to this mass production techniques.
[0141] FIG. 6C depicts a top-down view of the reservoir assemblies
650 shown in FIG. 6B. FIG. 6D depicts a cover 644 for reservoir
assembly 650 shown in FIG. 6B and 6E depicts a gasket 645 that in
operation is disposed on cover 644 of reservoir assemblies 650
shown in FIG. 6B. FIG. 6C is a top-down view of reservoir assembly
650, showing the tops of the two retentate reservoirs 652, one on
either side of permeate reservoir 654. Also seen are grooves 632
that will mate with a pneumatic port (not shown), and fluid
channels 634 that reside at the bottom of retentate reservoirs 652,
which fluidically couple the retentate reservoirs 652 with the
retentate ports 628 (not shown), via the through-holes for the
retentate ports in permeate member 620 and membrane 624 (also not
shown). FIG. 6D depicts a cover 644 that is configured to be
disposed upon the top of reservoir assembly 650. Cover 644 has
round cut-outs at the top of retentate reservoirs 652 and
permeate/filtrate reservoir 654. Again at the bottom of retentate
reservoirs 652 fluid channels 634 can be seen, where fluid channels
634 fluidically couple retentate reservoirs 652 with the retentate
ports 628 (not shown). Also shown are three pneumatic ports 630 for
each retentate reservoir 652 and permeate/filtrate reservoir 654.
FIG. 6E depicts a gasket 645 that is configures to be disposed upon
the cover 644 of reservoir assembly 650. Seen are three fluid
transfer ports 642 for each retentate reservoir 652 and for
permeate/filtrate reservoir 654. Again, three pneumatic ports 630,
for each retentate reservoir 652 and for permeate/filtrate
reservoir 654, are shown.
[0142] The overall work flow for cell growth comprises loading a
cell culture to be grown into a first retentate reservoir,
optionally bubbling air or an appropriate gas through the cell
culture, passing or flowing the cell culture through the first
retentate port then tangentially through the TFF channel structure
while collecting medium or buffer through one or both of the
permeate ports 606, collecting the cell culture through a second
retentate port 604 into a second retentate reservoir, optionally
adding additional or different medium to the cell culture and
optionally bubbling air or gas through the cell culture, then
repeating the process, all while measuring, e.g., the optical
density of the cell culture in the retentate reservoirs
continuously or at desired intervals. Measurements of optical
densities (OD) at programmed time intervals are accomplished using
a 600 nm Light Emitting Diode (LED) that has been columnated
through an optic into the retentate reservoir(s) containing the
growing cells. The light continues through a collection optic to
the detection system which consists of a (digital) gain-controlled
silicone photodiode. Generally, optical density is shown as the
absolute value of the logarithm with base 10 of the power
transmission factors of an optical attenuator: OD=-log10 (Power
out/Power in). Since OD is the measure of optical attenuation--that
is, the sum of absorption, scattering, and reflection--the TFF
device OD measurement records the overall power transmission, so as
the cells grow and become denser in population, the OD (the loss of
signal) increases. The OD system is pre-calibrated against OD
standards with these values stored in an on-board memory accessible
by the measurement program.
[0143] In the channel structure, the membrane bifurcating the flow
channels retains the cells on one side of the membrane (the
retentate side 622) and allows unwanted medium or buffer to flow
across the membrane into a filtrate or permeate side (e.g.,
permeate member 620) of the device. Bubbling air or other
appropriate gas through the cell culture both aerates and mixes the
culture to enhance cell growth. During the process, medium that is
removed during the flow through the channel structure is removed
through the permeate/filtrate ports 606. Alternatively, cells can
be grown in one reservoir with bubbling or agitation without
passing the cells through the TFF channel from one reservoir to the
other.
[0144] The overall workflow for cell concentration using the TFF
device/module involves flowing a cell culture or cell sample
tangentially through the channel structure. As with the cell growth
process, the membrane bifurcating the flow channels retains the
cells on one side of the membrane and allows unwanted medium or
buffer to flow across the membrane into a permeate/filtrate side
(e.g., permeate member 620) of the device. In this process, a fixed
volume of cells in medium or buffer is driven through the device
until the cell sample is collected into one of the retentate ports
604, and the medium/buffer that has passed through the membrane is
collected through one or both of the permeate/filtrate ports 606.
All types of prokaryotic and eukaryotic cells--both adherent and
non-adherent cells--can be grown in the TFF device. Adherent cells
may be grown on beads or other cell scaffolds suspended in medium
that flow through the TFF device.
[0145] The medium or buffer used to suspend the cells in the cell
concentration device/module may be any suitable medium or buffer
for the type of cells being transformed or transfected, such as LB,
SOC, TPD, YPG, YPAD, MEM, DMEM, IMDM, RPMI, Hanks', PBS and
Ringer's solution, where the media may be provided in a reagent
cartridge as part of a kit. For culture of adherent cells, cells
may be disposed on beads, microcarriers, or other type of scaffold
suspended in medium. Most normal mammalian tissue-derived
cells--except those derived from the hematopoietic system--are
anchorage dependent and need a surface or cell culture support for
normal proliferation. In the rotating growth vial described herein,
microcarrier technology is leveraged. Microcarriers of particular
use typically have a diameter of 100-300 .mu.m and have a density
slightly greater than that of the culture medium (thus facilitating
an easy separation of cells and medium for, e.g., medium exchange)
yet the density must also be sufficiently low to allow complete
suspension of the carriers at a minimum stirring rate in order to
avoid hydrodynamic damage to the cells. Many different types of
microcarriers are available, and different microcarriers are
optimized for different types of cells. There are positively
charged carriers, such as Cytodex 1 (dextran-based, GE Healthcare),
DE-52 (cellulose-based, Sigma-Aldrich Labware), DE-53
(cellulose-based, Sigma-Aldrich Labware), and HLX 11-170
(polystyrene-based); collagen- or ECM-(extracellular matrix) coated
carriers, such as Cytodex 3 (dextran-based, GE Healthcare) or
HyQ-sphere Pro-F 102-4 (polystyrene-based, Thermo Scientific);
non-charged carriers, like HyQ-sphere P 102-4 (Thermo Scientific);
or macroporous carriers based on gelatin (Cultisphere, Percell
Biolytica) or cellulose (Cytopore, GE Healthcare).
[0146] In both the cell growth and concentration processes, passing
the cell sample through the TFF device and collecting the cells in
one of the retentate ports 604 while collecting the medium in one
of the permeate/filtrate ports 606 is considered "one pass" of the
cell sample. The transfer between retentate reservoirs "flips" the
culture. The retentate and permeatee ports collecting the cells and
medium, respectively, for a given pass reside on the same end of
TFF device/module with fluidic connections arranged so that there
are two distinct flow layers for the retentate and
permeate/filtrate sides, but if the retentate port 604 resides on
the retentate member of device/module (that is, the cells are
driven through the channel above the membrane and the filtrate
(medium) passes to the portion of the channel below the membrane),
the permeate/filtrate port 606 will reside on the permeate member
of device/module and vice versa (that is, if the cell sample is
driven through the channel below the membrane, the filtrate
(medium) passes to the portion of the channel above the membrane).
Due to the high pressures used to transfer the cell culture and
fluids through the flow channel of the TFF device, the effect of
gravity is negligible.
[0147] At the conclusion of a "pass" in either of the growth and
concentration processes, the cell sample is collected by passing
through the retentate port 604 and into the retentate reservoir
(not shown). To initiate another "pass", the cell sample is passed
again through the TFF device, this time in a flow direction that is
reversed from the first pass. The cell sample is collected by
passing through the retentate port 604 and into retentate reservoir
(not shown) on the opposite end of the device/module from the
retentate port 604 that was used to collect cells during the first
pass. Likewise, the medium/buffer that passes through the membrane
on the second pass is collected through the permeate port 606 on
the opposite end of the device/module from the permeate port 606
that was used to collect the filtrate during the first pass, or
through both ports. This alternating process of passing the
retentate (the concentrated cell sample) through the device/module
is repeated until the cells have been grown to a desired optical
density, and/or concentrated to a desired volume, and both permeate
ports (i.e., if there are more than one) can be open during the
passes to reduce operating time. In addition, buffer exchange may
be effected by adding a desired buffer (or fresh medium) to the
cell sample in the retentate reservoir, before initiating another
"pass", and repeating this process until the old medium or buffer
is diluted and filtered out and the cells reside in fresh medium or
buffer. Note that buffer exchange and cell growth may (and
typically do) take place simultaneously, and buffer exchange and
cell concentration may (and typically do) take place
simultaneously. For further information and alternative embodiments
on TFFs see, e.g., U.S. Ser. No. 16/516,701, filed 5 Sep. 2019.
[0148] As an alternative to the TFF module described above, a cell
concentration module comprising a hollow filter may be employed.
Examples of filters suitable for use in the present disclosure
include membrane filters, ceramic filters and metal filters. The
filter may be used in any shape; the filter may, for example, be
cylindrical or essentially flat. Preferably, the filter used is a
membrane filter, most preferably a hollow fiber filter. The term
"hollow fiber" is meant to include a tubular membrane. The internal
diameter of the tube is at least 0.1 mm, more preferably at least
0.5 mm, most preferably at least 0.75 mm and preferably the
internal diameter of the tube is at most 10 mm, more preferably at
most 6 mm, most preferably at most 1 mm. Filter modules comprising
hollow fibers are commercially available from various companies,
including G.E. Life Sciences (Marlborough, Mass.) and InnovaPrep
(Drexel, Mo.). Specific examples of hollow fiber filter systems
that can be used, modified or adapted for use in the present
methods and systems include, but are not limited to, U.S. Pat. Nos.
9,738,918; 9,593,359; 9,574,977; 9,534,989; 9,446,354;. 9,295,824;
8,956,880; 8,758,623; 8,726,744; 8,677,839; 8,677,840; 8,584,536;
8,584,535; and 8,110,112.
Nucleic Acid Assembly Module
[0149] Certain embodiments of the automated multi-module cell
editing instruments comprising FTEPs of the present disclosure
optionally include a nucleic acid assembly module. The nucleic acid
assembly module is configured to accept and assemble the nucleic
acids necessary to be porated into desired cells using the FTEP and
to facilitate the desired genome editing events. In general, the
term "vector" refers to a nucleic acid molecule capable of
transporting a desired nucleic acid to which it has been linked
into a cell. Vectors include, but are not limited to, nucleic acid
molecules that are single-stranded, double-stranded, or partially
double-stranded; nucleic acid molecules that include one or more
free ends, no free ends (e.g., circular); nucleic acid molecules
that include DNA, RNA, or both; and other varieties of
polynucleotides known in the art. One type of vector is a
"plasmid," which refers to a circular double stranded DNA loop into
which additional DNA segments can be inserted, such as by standard
molecular cloning techniques. Another type of vector is a viral
vector, where virally-derived DNA or RNA sequences are present in
the vector for packaging into a virus (e.g. retroviruses,
replication defective retroviruses, adenoviruses, replication
defective adenoviruses, and adeno-associated viruses). Viral
vectors also include polynucleotides carried by a virus for
transfection into a host cell. Certain vectors are capable of
autonomous replication in a host cell into which they are
introduced (e.g. bacterial vectors having a bacterial origin of
replication and episomal mammalian vectors). Other vectors (e.g.,
non-episomal mammalian vectors) are integrated into the genome of a
host cell upon introduction into the host cell, and thereby are
replicated along with the host genome. Moreover, certain vectors
are capable of directing the expression of genes to which they are
operatively-linked. Such vectors are referred to herein as
"expression vectors" or "editing vectors." Common expression
vectors of utility in recombinant DNA techniques are often in the
form of plasmids. Additional vectors include fosmids, phagemids,
BACs, YACs, and other synthetic chromosomes.
[0150] Recombinant expression vectors can include a nucleic acid in
a form suitable for transcription, and for some nucleic acid
sequences, translation and expression of the nucleic acid in a host
cell, which means that the recombinant expression vectors include
one or more regulatory elements--which may be selected on the basis
of the host cells to be used for expression--that are
operatively-linked to the nucleic acid sequence to be expressed.
Within a recombinant expression vector, "operably linked" is
intended to mean that the nucleotide sequence of interest is linked
to the regulatory element(s) in a manner that allows for
transcription, and for some nucleic acid sequences, translation and
expression of the nucleotide sequence (e.g., in an in vitro
transcription/translation system or in a host cell when the vector
is introduced into the host cell). Appropriate recombination and
cloning methods are disclosed in US Pub. No. 2004/0171156, the
contents of which are herein incorporated by reference in their
entirety for all purposes.
[0151] In some embodiments, a regulatory element is operably linked
to one or more elements of a targetable nuclease system so as to
drive transcription, and for some nucleic acid sequences,
translation and expression of the one or more components of the
targetable nuclease system.
[0152] In addition, the polynucleotide sequence encoding the
nucleic acid-guided nuclease can be codon optimized for expression
in particular cells, such as prokaryotic or eukaryotic cells.
Eukaryotic cells can be yeast, fungi, algae, plant, animal, or
human cells. Eukaryotic cells may be those of or derived from a
particular organism, such as a mammal, including but not limited to
human, mouse, rat, rabbit, dog, or non-human mammal including
non-human primate. In addition or alternatively, a vector may
include a regulatory element operably linked to a polynucleotide
sequence, which, when transcribed, forms a guide RNA.
[0153] The nucleic acid assembly module can be configured to
perform a wide variety of different nucleic acid assembly
techniques in an automated fashion. Nucleic acid assembly
techniques that can be performed in the nucleic acid assembly
module of the disclosed automated multi-module cell editing
instruments include, but are not limited to, those assembly methods
that use restriction endonucleases, including PCR, BioBrick
assembly (U.S. Pat. No. 9,361,427), Type IIS cloning (e.g.,
GoldenGate assembly, European Patent Application Publication EP 2
395 087 A1), and Ligase Cycling Reaction (de Kok, ACS Synth Biol.,
3(2):97-106 (2014); Engler, et al., PLoS One, 3(11):e3647 (2008);
and U.S. Pat. No. 6,143,527). In other embodiments, the nucleic
acid assembly techniques performed by the disclosed automated
multi-module cell editing instruments are based on overlaps between
adjacent parts of the nucleic acids, such as Gibson Assembly.RTM.,
CPEC, SLIC, Ligase Cycling etc. Additional assembly methods include
gap repair in yeast (Bessa, Yeast, 29(10):419-23 (2012)), gateway
cloning (Ohtsuka, Curr Pharm Biotechnol, 10(2):244-51 (2009)); U.S.
Pat. Nos. 5,888,732; and 6,277,608), and topoisomerase-mediated
cloning (Udo, PLoS One, 10(9):e0139349 (2015); and U.S. Pat. No.
6,916,632). These and other nucleic acid assembly techniques are
described, e.g., in Sands and Brent, Curr Protoc Mol Biol.,
113:3.26.1-3.26.20 (2016).
[0154] The nucleic acid assembly module is temperature controlled
depending upon the type of nucleic acid assembly used in the
automated multi-module cell editing instrument. For example, when
PCR is utilized in the nucleic acid assembly module, the module
includes a thermocycling capability allowing the temperatures to
cycle between denaturation, annealing and extension steps. When
single temperature assembly methods (e.g., isothermal assembly
methods) are utilized in the nucleic acid assembly module, the
module provides the ability to reach and hold at the temperature
that optimizes the specific assembly process being performed. These
temperatures and the duration for maintaining these temperatures
can be determined by a preprogrammed set of parameters executed by
a script, or manually controlled by the user using the processing
system of the automated multi-module cell editing instrument.
[0155] In one embodiment, the nucleic acid assembly module is a
module to perform assembly using a single, isothermal reaction.
Certain isothermal assembly methods can combine simultaneously up
to 15 nucleic acid fragments based on sequence identity. The
assembly method provides, in some embodiments, nucleic acids to be
assembled which include an approximate 20-40 base overlap with
adjacent nucleic acid fragments. The fragments are mixed with a
cocktail of three enzymes--an exonuclease, a polymerase, and a
ligase-along with buffer components. Because the process is
isothermal and can be performed in a 1-step or 2-step method using
a single reaction vessel, isothermal assembly reactions are ideal
for use in an automated multi-module cell editing instrument. The
1-step method allows for the assembly of up to five different
fragments using a single step isothermal process. The fragments and
the master mix of enzymes are combined and incubated at 50.degree.
C. for up to one hour. For the creation of more complex constructs
with up to fifteen fragments or for incorporating fragments from
100 bp up to 10 kb, typically the 2-step is used, where the 2-step
reaction requires two separate additions of master mix; one for the
exonuclease and annealing step and a second for the polymerase and
ligation steps.
Cell Enrichment Module
[0156] One optional aspect of the present disclosure provides
automated modules and instruments for nucleic acid-guided nuclease
genome editing that implement enrichment techniques for cells whose
genomes have been properly edited. The enrichment module performs
methods that use cell singulation and normalization to reduce
growth competition between edited and unedited cells or utilizes
methods that take advantage of inducing editing at a specific time
during cell growth. Singulation overcomes growth bias from unedited
cells or cells containing edits conferring growth advantages or
disadvantages. The methods, modules and instruments may be applied
to all cell types including, archaeal, prokaryotic, and eukaryotic
(e.g., yeast, fungal, plant and animal) cells.
[0157] Singulating or substantially singulating, induction of
editing, and normalization of cell colonies leads. to 2-250.times.,
10-225.times., 25-200.times.. 40-175.times.. 50-150.times.,
60-100.times., or 5-100.times. gains in identifying edited cells
over prior art methods and generates arrayed or pooled edited cells
comprising genome libraries. Additionally, the methods, modules,
and instruments may be leveraged to create iterative editing
systems to generate combinatorial libraries, identify rare cell
edits, and enable high-throughput enrichment applications to
identify editing activity.
[0158] The compositions and methods described herein improve
nucleic acid-guided nuclease editing systems in which nucleic
acid-guided nucleases (e.g., RNA-guided nucleases) are used to edit
specific target regions in an organism's genome. FIG. 7A depicts a
solid wall device 7050 and a workflow for singulating cells in
microwells in the solid wall device, where in this workflow one or
both of the gRNA and nuclease are under the control of an inducible
promoter. At the top left of the figure (i), there is depicted
solid wall device 7050 with microwells 7052. A section 7054 of
solid wall device 7050 is shown at (ii), also depicting microwells
7052. At (iii), a side cross-section of solid wall device 7050 is
shown, and microwells 7052 have been loaded, where, in this
embodiment, Poisson loading has taken place; that is, each
microwell has one (e.g., microwells 7052, 7056) or no cells, and
the likelihood that any one microwell has more than one cell is
low. Note, however, that in alternative embodiments substantial
singulation--partitioning cells into small "groups" of less than 20
cells per partition, and more preferably less than 10 cells per
partition--may be performed depending on the plexity of the
library. At (iv), workflow 7040 is illustrated where substrate 7050
having microwells 7052 shows microwells 7056 with one cell per
microwell, microwells 7057 with no cells in the microwells, and one
microwell 7060 with two cells in the microwell. In step 7051, the
cells in the microwells are allowed to double approximately 2-50
times to form clonal colonies (v), then editing is induced 7053 by
heating the substrate (e.g., for temperature-induced editing) or
flowing chemicals under or over the substrate (e.g., sugars,
antibiotics for chemical-induced editing) or by moving the solid
wall device to a different medium, which is particularly facile if
the solid wall device is placed on a fluid permeable membrane which
forms the bottom of microwells 7052. After induction of editing
7053, many cells in the colonies of cells that have been edited die
as a result of the double-strand cuts caused by active editing, and
there is possibly a lag in growth for the edited cells that do
survive but must repair and recover following editing (microwells
7058), where cells that do not undergo editing thrive (microwells
7059) (vi). All cells are allowed to grow to continue to establish
colonies and normalize, where the colonies of edited cells in
microwells 7058 catch up in size and/or cell number with the cells
in microwells 7059 that do not undergo editing (vii) due to cell
senescence as the unedited cells reach stationary phase. Once the
cell colonies are normalized, either pooling of all cells in the
microwells can take place, in which case the cells are enriched for
edited cells by eliminating the bias from non-editing cells and
fitness effects from editing; alternatively, colony growth in the
microwells is monitored after editing, and slow growing colonies
(e.g., the cells in microwells 7058) are identified and selected
(e.g., "cherry picked") resulting in even greater enrichment of
edited cells.
[0159] In growing the cells, the medium used will depend, of
course, on the type of cells being edited--e.g., bacterial, yeast
or mammalian. For example, medium for bacterial growth includes LB,
SOC, M9 Minimal medium, and Magic medium; medium for yeast cell
growth includes TPD, YPG, YPAD, and synthetic minimal medium; and
medium for mammalian cell growth includes MEM, DMEM, IMDM, RPMI,
and Hanks.
[0160] A module useful for performing the method depicted in FIGS.
7A is a solid wall isolation, incubation, and normalization (SWIIN)
module. FIG. 7B depicts an embodiment of a SWIIN module 750 from an
exploded top perspective view. In SWIIN module 750 the retentate
member is formed on the bottom of a top of a SWIIN module component
and the permeate member is formed on the top of the bottom of a
SWIIN module component.
[0161] The SWIIN module 750 in FIG. 7B comprises from the top down,
a reservoir gasket or cover 758, a retentate member 704 (where a
retentate flow channel cannot be seen in this FIG. 7B), a
perforated member 701 swaged with a filter (filter not seen in FIG.
7B), a permeate member 708 comprising integrated reservoirs
(permeate reservoirs 752 and retentate reservoirs 754), and two
reservoir seals 762, which seal the bottom of permeate reservoirs
752 and retentate reservoirs 754. A permeate channel 760a can be
seen disposed on the top of permeate member 708, defined by a
raised portion 776 of serpentine channel 760a, and ultrasonic tabs
764 can be seen disposed on the top of permeate member 708 as well.
The perforations that form the wells on perforated member 701 are
not seen in this FIG. 7B; however, through-holes 766 to accommodate
the ultrasonic tabs 764 are seen. In addition, supports 770 are
disposed at either end of SWIIN module 750 to support SWIIN module
750 and to elevate permeate member 708 and retentate member 704
above reservoirs 752 and 754 to minimize bubbles or air entering
the fluid path from the permeate reservoir to serpentine channel
760a or the fluid path from the retentate reservoir to serpentine
channel 760b (neither fluid path is seen in this FIG. 7B).
[0162] In this FIG. 7B, it can be seen that the serpentine channel
760a that is disposed on the top of permeate member 708 traverses
permeate member 708 for most of the length of permeate member 708
except for the portion of permeate member 708 that comprises
permeate reservoirs 752 and retentate reservoirs 754 and for most
of the width of permeate member 708. As used herein with respect to
the distribution channels in the retentate member or permeate
member, "most of the length" means about 95% of the length of the
retentate member or permeate member, or about 90%, 85%, 80%, 75%,
or 70% of the length of the retentate member or permeate member. As
used herein with respect to the distribution channels in the
retentate member or permeate member, "most of the width" means
about 95% of the width of the retentate member or permeate member,
or about 90%, 85%, 80%, 75%, or 70% of the width of the retentate
member or permeate member.
[0163] In this embodiment of a SWIIN module, the perforated member
includes through-holes to accommodate ultrasonic tabs disposed on
the permeate member. Thus, in this embodiment the perforated member
is fabricated from 316 stainless steel, and the perforations form
the walls of microwells while a filter or membrane is used to form
the bottom of the microwells. Typically, the perforations
(microwells) are approximately 150 .mu.m-200 .mu.m in diameter, and
the perforated member is approximately 125 .mu.m deep, resulting in
microwells having a volume of approximately 2.5 nl, with a total of
approximately 200,000 microwells. The distance between the
microwells is approximately 279 .mu.m center-to-center. Though here
the microwells have a volume of approximately 2.5 nl, the volume of
the microwells may be from 1 to 25 nl, or preferably from 2 to 10
nl, and even more preferably from 2 to 4 nl. As for the filter or
membrane, like the filter described previously, filters appropriate
for use are solvent resistant, contamination free during
filtration, and are able to retain the types and sizes of cells of
interest. For example, in order to retain small cell types such as
bacterial cells, pore sizes can be as low as 0.10 .mu.m, however
for other cell types (e.g., such as for mammalian cells), the pore
sizes can be as high as 10.0 .mu.m-20.0 .mu.m or more. Indeed, the
pore sizes useful in the cell concentration device/module include
filters with sizes from 0.10 .mu.m, 0.11 .mu.m, 0.12 .mu.m, 0.13
.mu.m, 0.14 .mu.m, 0.15 .mu.m, 0.16 .mu.m, 0.17 .mu.m, 0.18 .mu.m,
0.19 .mu.m, 0.20 .mu.m, 0.21 .mu.m, 0.22 .mu.m, 0.23 .mu.m, 0.24
.mu.m, 0.25 .mu.m, 0.26 .mu.m, 0.27 .mu.m, 0.28 .mu.m, 0.29 .mu.m,
0.30 .mu.m, 0.31 .mu.m, 0.32 .mu.m, 0.33 .mu.m, 0.34 .mu.m, 0.35
.mu.m, 0.36 .mu.m, 0.37 .mu.m, 0.38 .mu.m, 0.39 .mu.m, 0.40 .mu.m,
0.41 .mu.m, 0.42 .mu.m, 0.43 .mu.m, 0.44 .mu.m, 0.45 .mu.m, 0.46
.mu.m, 0.47 .mu.m, 0.48 .mu.m, 0.49 .mu.m, 0.50 .mu.m and larger.
The filters may be fabricated from any suitable material including
cellulose mixed ester (cellulose nitrate and acetate) (CME),
polycarbonate (PC), polyvinylidene fluoride (PVDF),
polyethersulfone (PES), polytetrafluoroethylene (PTFE), nylon, or
glass fiber.
[0164] The cross-section configuration of the mated serpentine
channel may be round, elliptical, oval, square, rectangular,
trapezoidal, or irregular. If square, rectangular, or another shape
with generally straight sides, the cross section may be from about
2 mm to 15 mm wide, or from 3 mm to 12 mm wide, or from 5 mm to 10
mm wide. If the cross section of the mated serpentine channel is
generally round, oval or elliptical, the radius of the channel may
be from about 3 mm to 20 mm in hydraulic radius, or from 5 mm to 15
mm in hydraulic radius, or from 8 mm to 12 mm in hydraulic
radius.
[0165] Serpentine channels 760a and 760b can have approximately the
same volume or the serpentine channels 760a and 760b may have
different volumes. For example, each "side" or portion 760a, 760b
of the serpentine channel may have a volume of, e.g., 2 mL, or
serpentine channel 760a of permeate member 708 may have a volume of
2 mL, and the serpentine channel 760b of retentate member 704 may
have a volume of, e.g., 3 mL. The volume of fluid in the serpentine
channel may range from about 2 mL to about 80 mL, or about 4 mL to
60 mL, or from 5 mL to 40 mL, or from 6 mL to 20 mL (note these
volumes apply to a SWIIN module comprising a, e.g., 50-500K
perforation member). The volume of the reservoirs may range from 5
mL to 50 mL, or from 7 mL to 40 mL, or from 8 mL to 30 mL or from
10 mL to 20 mL, and the volumes of all reservoirs may be the same
or the volumes of the reservoirs may differ (e.g., the volume of
the permeate reservoirs is greater than that of the retentate
reservoirs).
[0166] The serpentine channel portions 760a and 760b of the
permeate member 708 and retentate member 704, respectively, are
approximately 200 mm long, 130 mm wide, and 4 mm thick, though in
other embodiments, the retentate and permeate members can be from
75 mm to 400 mm in length, or from 100 mm to 300 mm in length, or
from 150 mm to 250 mm in length; from 50 mm to 250 mm in width, or
from 75 mm to 200 mm in width, or from 100 mm to 150 mm in width;
and from 2 mm to 15 mm in thickness, or from 4 mm to 10 mm in
thickness, or from 5 mm to 8 mm in thickness. Embodiments the
retentate (and permeate) members may be fabricated from PMMA
(poly(methyl methacrylate) or other materials may be used,
including polycarbonate, cyclic olefin co-polymer (COC), glass,
polyvinyl chloride, polyethylene, polyamide, polypropylene,
polysulfone, polyurethane, and co-polymers of these and other
polymers. Preferably at least the retentate member is fabricated
from a transparent material so that the cells can be visualized
(see, e.g., FIG. 7E and the description thereof). For example, a
video camera may be used to monitor cell growth by, e.g., density
change measurements based on an image of an empty well, with phase
contrast, or if, e.g., a chromogenic marker, such as a chromogenic
protein, is used to add a distinguishable color to the cells.
Chromogenic markers such as blitzen blue, dreidel teal, virginia
violet, vixen purple, prancer purple, tinsel purple, maccabee
purple, donner magenta, cupid pink, seraphina pink, scrooge orange,
and leor orange (the Chromogenic Protein Paintbox, all available
from ATUM (Newark, Calif.)) obviate the need to use fluorescence,
although fluorescent cell markers, fluorescent proteins, and
chemiluminescent cell markers may also be used.
[0167] Because the retentate member preferably is transparent,
colony growth in the SWIIN module can be monitored by automated
devices such as those sold by JoVE (ScanLag.TM. system, Cambridge,
Mass.) (also see Levin-Reisman, et al., Nature Methods, 7:737-39
(2010)). Cell growth for, e.g., mammalian cells may be monitored
by, e.g., the growth monitor sold by IncuCyte (Ann Arbor, Mich.)
(see also, Choudhry, PLos One, 11(2):e0148469 (2016)). Further,
automated colony pickers may be employed, such as those sold by,
e.g., TECAN (Pickolo.TM. system, Mannedorf, Switzerland); Hudson
Inc. (RapidPick.TM., Springfield, N.J.); Molecular Devices (QPix
400 .TM. system, San Jose, Calif.); and Singer Instruments
(PIXL.TM. system, Somerset, UK).
[0168] Due to the heating and cooling of the SWIIN module,
condensation may accumulate on the retentate member which may
interfere with accurate visualization of the growing cell colonies.
Condensation of the SWIIN module 750 may be controlled by, e.g.,
moving heated air over the top of (e.g., retentate member) of the
SWIIN module 750, or by applying a transparent heated lid over at
least the serpentine channel portion 760b of the retentate member
704. See, e.g., FIG. 7E and the description thereof infra.
[0169] In SWIIN module 750 cells and medium--at a dilution
appropriate for Poisson or substantial Poisson distribution of the
cells in the microwells of the perforated member--are flowed into
serpentine channel 760b from ports in retentate member 704, and the
cells settle in the microwells while the medium passes through the
filter into serpentine channel 760a in permeate member 708. The
cells are retained in the microwells of perforated member 701 as
the cells cannot travel through filter 703. Appropriate medium may
be introduced into permeate member 708 through permeate ports 711.
The medium flows upward through filter 703 to nourish the cells in
the microwells (perforations) of perforated member 701.
Additionally, buffer exchange can be effected by cycling medium
through the retentate and permeate members. In operation, the cells
are deposited into the microwells, are grown for an initial, e.g.,
2-100 doublings, editing is induced by, e.g., raising the
temperature of the SWIIN to 42.degree. C. to induce a temperature
inducible promoter or by removing growth medium from the permeate
member and replacing the growth medium with a medium comprising a
chemical component that induces an inducible promoter.
[0170] Once editing has taken place, the temperature of the SWIIN
may be decreased, or the inducing medium may be removed and
replaced with fresh medium lacking the chemical component thereby
de-activating the inducible promoter. The cells then continue to
grow in the SWIIN module 750 until the growth of the cell colonies
in the microwells is normalized. For the normalization protocol,
once the colonies are normalized, the colonies are flushed from the
microwells by applying fluid or air pressure (or both) to the
permeate member serpentine channel 760a and thus to filter 703 and
pooled. Alternatively, if cherry picking is desired, the growth of
the cell colonies in the microwells is monitored, and slow-growing
colonies are directly selected; or, fast-growing colonies are
eliminated.
[0171] FIG. 7C is a top perspective view of a SWIIN module with the
retentate and perforated members in partial cross section. In this
FIG. 7C, it can be seen that serpentine channel 760a is disposed on
the top of permeate member 708 is defined by raised portions 776
and traverses permeate member 708 for most of the length and width
of permeate member 708 except for the portion of permeate member
708 that comprises the permeate and retentate reservoirs (note only
one retentate reservoir 752 can be seen). Moving from left to
right, reservoir gasket 758 is disposed upon the integrated
reservoir cover 778 (cover not seen in this FIG. 7C) of retentate
member 704. Gasket 758 comprises reservoir access apertures 732a,
732b, 732c, and 732d, as well as pneumatic ports 733a, 733b, 733c
and 733d. Also at the far left end is support 770. Disposed under
permeate reservoir 752 can be seen one of two reservoir seals 762.
In addition to the retentate member being in cross section, the
perforated member 701 and filter 703 (filter 703 is not seen in
this FIG. 7C) are in cross section. Note that there are a number of
ultrasonic tabs 764 disposed at the right end of SWIIN module 750
and on raised portion 776 which defines the channel turns of
serpentine channel 760a, including ultrasonic tabs 764 extending
through through-holes 766 of perforated member 701. There is also a
support 770 at the end distal reservoirs 752, 754 of permeate
member 708.
[0172] FIG. 7D is a side perspective view of an assembled SWIIIN
module 750, including, from right to left, reservoir gasket 758
disposed upon integrated reservoir cover 778 (not seen) of
retentate member 704. Gasket 758 may be fabricated from rubber,
silicone, nitrile rubber, polytetrafluoroethylene, a plastic
polymer such as polychlorotrifluoroethylene, or other flexible,
compressible material. Gasket 758 comprises reservoir access
apertures 732a, 732b, 732c, and 732d, as well as pneumatic ports
733a, 733b, 733c and 733d. Also at the far-left end is support 770
of permeate member 708. In addition, permeate reservoir 752 can be
seen, as well as one reservoir seal 762. At the far-right end is a
second support 770.
[0173] Imaging of cell colonies growing in the wells of the SWIIN
is desired in most implementations for, e.g., monitoring both cell
growth and device performance and imaging is necessary for
cherry-picking implementations. Real-time monitoring of cell growth
in the SWIIN requires backlighting, retentate plate (top plate)
condensation management and a system-level approach to temperature
control, air flow, and thermal management. In some implementations,
imaging employs a camera or CCD device with sufficient resolution
to be able to image individual wells. For example, in some
configurations a camera with a 9-pixel pitch is used (that is,
there are 9 pixels center-to-center for each well). Processing the
images may, in some implementations, utilize reading the images in
grayscale, rating each pixel from low to high, where wells with no
cells will be brightest (due to full or nearly-full light
transmission from the backlight) and wells with cells will be dim
(due to cells blocking light transmission from the backlight).
After processing the images, thresholding is performed to determine
which pixels will be called "bright" or "dim", spot finding is
performed to find bright pixels and arrange them into blocks, and
then the spots are arranged on a hexagonal grid of pixels that
correspond to the spots. Once arranged, the measure of intensity of
each well is extracted, by, e.g., looking at one or more pixels in
the middle of the spot, looking at several to many pixels at random
or pre-set positions, or averaging.times.number of pixels in the
spot. In addition, background intensity may be subtracted.
Thresholding is again used to call each well positive (e.g.,
containing cells) or negative (e.g., no cells in the well). The
imaging information may be used in several ways, including taking
images at time points for monitoring cell growth. Monitoring cell
growth can be used to, e.g., remove the "muffin tops" of
fast-growing cells followed by removal of all cells or removal of
cells in "rounds" as described above, or recover cells from
specific wells (e.g., slow-growing cell colonies); alternatively,
wells containing fast-growing cells can be identified and areas of
UV light covering the fast-growing cell colonies can be projected
(or rastered with shutters) onto the SWIIN to irradiate or inhibit
growth of those cells. Imaging may also be used to assure proper
fluid flow in the serpentine channel 760.
[0174] FIG. 7E depicts the embodiment of the SWIIN module in FIGS.
7B-7D further comprising a heat management system including a
heater and a heated cover. The heater cover facilitates the
condensation management that is required for imaging. Assembly 798
comprises a SWIIN module 750 seen lengthwise in cross section,
where one permeate reservoir 752 is seen. Disposed immediately upon
SWIIN module 750 is cover 794 and disposed immediately below SWIIN
module 750 is backlight 780, which allows for imaging. Beneath and
adjacent to the backlight and SWIIN module is insulation 782, which
is disposed over a heatsink 784. In this FIG. 7E, the fins of the
heatsink would be in-out of the page. In addition there is also
axial fan 786 and heat sink 788, as well as two thermoelectric
coolers 792, and a controller 790 to control the pneumatics,
thermoelectric coolers, fan, solenoid valves, etc. The arrows
denote cool air coming into the unit and hot air being removed from
the unit. It should be noted that control of heating allows for
growth of many different types of cells (prokaryotic and
eukaryotic) as well as strains of cells that are, e.g., temperature
sensitive, etc., and allows use of temperature-sensitive promoters.
Temperature control allows for protocols to be adjusted to account
for differences in transformation efficiency, cell growth and
viability. For more details regarding solid wall isolation
incubation and normalization devices see U.S. Ser. No. 16/399,988,
filed 30 Apr. 2019; U.S. Ser. No. 16/454,865, filed 26 Jun. 2019;
U.S. Ser. No. 16/540,606, filed 14 Aug. 2019; U.S. Ser. No.
16/597,826, filed 9 Oct. 2019; and U.S. Ser. No. 16/597,831, filed
9 Oct. 2019. For alternative isolation, incubation and
normalization modules, see U.S. Pat. No. 16/536,049, filed 8 Aug.
2019.
Use of the Cell Growth Device
[0175] FIG. 8 is a flow chart of an example method 800 for using an
automated multi-module cell editing instrument such as the systems
illustrated in FIGS. 4A-4C which include the FTEP devices described
in relation to FIGS. 1A-1P. A processing system, for example,
directs the processing stage of the method 800. For example, a
software script may identify settings for each processing stage and
instructions for movement of a robotic handling system to perform
the actions of the method 800. In some embodiments, a software
instruction script may be identified by a reagent cartridge
supplied to the automated multi-module cell editing instrument. For
example, the reagent cartridge may include machine-readable
indicia, such as a bar code or QR code, including identification of
a script stored in a memory of the automated multi-module cell
editing instrument. In another example, the reagent cartridge may
contain a downloadable script embedded in machine-readable indicia
such as a radio frequency (RF) tag. In other embodiments, the user
may identify a script, for example through downloading the script
via a wired or wireless connection to the processing system of the
automated multi-module cell editing instrument or through selecting
a stored script through a user interface of the automated
multi-module cell editing instrument. In a particular example, the
automated multi-module cell editing instrument may include a touch
screen interface for submitting user settings and activating cell
processing. Again, the automated multi-module cell processing
instrument is a stand-alone instrument, and between the script,
reagent reservoirs, and liquid handling system facilitates live
cell editing in an entirely automated manner without human
intervention.
[0176] In some implementations, the method 800 begins with
transferring cells to a cell growth module (802). The growth module
may be any growth module amendable to automation such as, for
example, the cell growth module 550 described in relation to FIGS.
5B-5D. In a particular example, the processing system may direct
the robotic handling system to transfer cells to the growth module.
In another example, the cells may be transferred from a reagent
cartridge to the growth module by the robotic handling system. In
some embodiments, the growth vial may contain growth media and be
supplied, e.g., as part of a kit. In other embodiments, the growth
vial may be filled with medium transferred, e.g., via the liquid
handling device, from a reagent container.
[0177] In some embodiments, prior to transferring the cells (e.g.,
from the reagent cartridge or from a vial added to the instrument),
machine-readable indicia may be scanned upon the vial or other
container situated in a position designated for cells to confirm
that the vial or container is marked as containing cells. Further,
the machine-readable indicia may indicate a type of cells provided
to the instrument. The type of cells, in some embodiments, may
cause the instrument to select a particular processing script
(e.g., series of instructions for the robotic handling system and
settings and activation of the various modules).
[0178] In some implementations, the cells are grown in the growth
module to a desired optical density (804). For example, the
processing system may manage a temperature setting of the growth
module for incubating the cells during the growth cycle. The
processing system may further receive sensor signals from the
growth module indicative of optical density and analyze the sensor
signals to monitor growth of the cells. In some embodiments, a user
may set growth parameters for managing growth of the cells. For
example, temperature, and the degree of agitation of the cells.
Further, in some embodiments, the user may be updated regarding the
growth process. The updates, in some examples, may include a
message presented on a user interface of the automated multi-module
cell editing instrument, a text message to a user's cell phone
number, an email message to an email account, or a message
transmitted to an app executing upon a portable electronic device
(e.g., cell phone, tablet, etc.). Responsive to the messages, in
some embodiments, the user may modify parameters, such as
temperature, to adjust cell growth. For example, the user may
submit updated parameters through a user interface of the automated
multi-module cell editing instrument or through a portable
computing device application in communication with the automated
multi-module cell editing instrument, such as a user interface
(see, e.g., touch screen display 401 of FIG. 4C).
[0179] Although described in relation to optical density, in other
implementations cell growth within the growth module may be
monitored using a different measure of cell density and
physiological state such as, in some examples, pH, dissolved
oxygen, released enzymes, acoustic properties, and electrical
properties.
[0180] In some implementations, upon reaching the desired optical
density (804), the cells are transferred from the growth module to
a filtration module or cell wash and concentration module (806).
The robotic handling system, for example, may transfer the cells
from the growth module to the cell concentration module. The cell
concentration module, for example, may be (and typically is)
designed to render the cells electrocompetent. See FIGS. 6A-6D in
relation to the TFF device, above. The cells are rendered
electrocompetent and eluted in the filtration module or cell wash
and concentration module (808). The cells may be eluted using a
wash solution. For example, the cells may be eluted using reagents
from a reagent supply.
[0181] Once the cells have been rendered electrocompetent and
suspended in an appropriate volume such as 50 .mu.L to 10 mL, or
100 .mu.L to 9 mL, or 150 .mu.L to 8 mL, or 250 .mu.L to 7 mL, or
500 .mu.L to 6 mL, or 750 .mu.L to 5 mL for transformation (808),
the cells are transferred to, e.g., an FTEP module (812). The
robotic handling system, for example, may transfer the cells from
the cell concentration device or module to the FTEP 812. The
filtration module may be physically coupled to the FTEP device, or
these modules may be separate.
[0182] In some implementations, nucleic acids are prepared outside
of the automated multi-module cell editing instrument. For example,
an assembled vector or other nucleic acid assembly may be included
as a reagent in, e.g., a reagent cartridge 810 by a user prior to
running the transformation process and other processes in the
method 800. If provided in a reagent cartridge, the nucleic acid
assembly (e.g., editing vector library) is transferred to the FTEP
device as well.
[0183] The cells are transformed in the FTEP module with the
editing vector provided in the reagent cartridge (814). A buffer or
medium may be transferred to the transformation module and added to
the cells so that the cells may be suspended in a buffer or medium
that is favorable for cell survival during electroporation. Prior
to transferring the buffer or medium, machine-readable indicia may
be scanned upon the vial or other container or reservoir situated
in the position designated for the buffer or medium to confirm the
contents of the vial, container, or reservoir. Further, the
machine-readable indicia may indicate a type of buffer or medium
provided to the instrument. The type of buffer or medium, in some
embodiments, may cause the instrument to select a particular
processing script (e.g., settings and activation of the
transformation module appropriate for the particular buffer or
medium). For bacterial cell electroporation, low conductance
mediums, such as water or glycerol solutions, may be used to reduce
the heat production by transient high current. For yeast cells, a
sorbitol solution may be used. For mammalian cell electroporation,
cells may be suspended in a highly conductive medium or buffer,
such as MEM, DMEM, IMDM, RPMI, Hanks', PBS, HBSS, HeBS and Ringer's
solution. In a particular example, the robotic handling system may
transfer a buffer solution to FTEP module from the reagent
cartridge. As described in relation to FIGS.1A-1P and 3A-3F, the
FTEP device may be a disposable FTEP device and/or the FTEP device
may be provided as part of the reagent cartridge. Alternatively,
the FTEP device may a separate module.
[0184] Once transformed, the cells are transferred to, e.g., a
second growth/recovery/editing module (816) such as the cell growth
module described in relation to FIGS. 5A-5D. The robotic handling
system, for example, may transfer the transformed cells to the
second growth module through a sipper or pipettor interface. In
another example, the robotic handling system may transfer a vial
containing the transformed cells from a chamber of the
transformation module to a chamber of the second growth module.
[0185] The second growth module, in some embodiments, acts as a
recovery module, allowing the cells to recover from the
transformation process. In other embodiments, the cells may be
provided to a separate recovery module prior to being transported
to the second growth module. During recovery, the second growth
module allows the transformed cells to uptake and, in certain
aspects, integrate the introduced nucleic acids into the genome of
the cell. The second growth module may be configured to incubate
the cells at any user-defined temperature optimal for cell growth,
preferably 25.degree., 30.degree., or 37.degree. C.
[0186] In some embodiments, the second growth module behaves as a
selection module, selecting the transformed cells based on an
antibiotic or other reagent. In one example, the RNA-guided
nuclease (RGN) protein system is used for selection to cleave the
genomes of cells that have not received the desired edit. In the
example of an antibiotic selection agent, the antibiotic may be
added to the second growth module to enact selection. Suitable
antibiotic resistance genes include, but are not limited to, genes
such as ampicillin-resistance gene, tetracycline-resistance gene,
kanamycin-resistance gene, neomycin-resistance gene,
canavanine-resistance gene, blasticidin-resistance gene,
hygromycin-resistance gene, puromycin-resistance gene, or
chloramphenicol-resistance gene. The robotic handling system, for
example, may transfer the antibiotic to the second growth module
through a sipper or pipettor interface. In some embodiments,
removing dead cell background is aided by using lytic enhancers
such as detergents, osmotic stress by hyponic wash, temperature,
enzymes, proteases, bacteriophage, reducing agents, or chaotropes.
The processing system, for example, may alter environmental
variables, such as temperature, to induce selection, while the
robotic handling system may deliver additional materials (e.g.,
detergents, enzymes, reducing agents, etc.) to aid in selection. In
other embodiments, cell removal and/or media exchange by filtration
is used to reduce dead cell background.
[0187] In further embodiments, in addition to or as an alternative
to applying selection, the second growth module serves as an
editing module, allowing for genome editing in the transformed
cells. Alternatively, in other embodiments, the cells post-recovery
and post-selection (if performed) are transferred to a separate
editing module. As an editing module, the second growth module
induces editing of the cells' genomes, e.g., through facilitating
expression of the introduced nucleic acids. Expression of the
nuclease and/or editing cassette nucleic acids may involve one or
more of chemical, light, viral, or temperature induction methods.
The second growth module, for example, may be configured to heat or
cool the cells during a temperature induction process. In a
particular illustration, the cells may be induced by heating at
42.degree. C.-50.degree. C. Further to the illustration, the cells
may then be cooled to 0-10.degree. C. after induction. In the
example of chemical or viral induction, an inducing agent may be
transferred to the second growth module to induce editing. If an
inducible nuclease and/or editing cassette was introduced to the
cells during editing, it can be induced through introduction of an
inducer molecule. The inducing agent or inducer molecule, in some
implementations, is transferred to the second growth module by the
robotic handling system, e.g., through a pipettor or sipper
interface.
[0188] In some implementations, if no additional cell editing is
desired (818), the cells may be transferred from the cell growth
module to a storage unit for later removal from the automated
multi-module cell editing instrument (820). The robotic handling
system, for example, may transfer the cells to a storage unit
through a sipper or pipettor interface. In another example, the
robotic handling system may transfer a vial containing the cells
from a chamber of the second growth module to a vial or tube within
the storage unit.
[0189] In some implementations, if additional cell editing is
desired (818), the cells may be transferred to a growth module
(802), grown to a desired OD (804), transferred to a cell
concentration module (806), then concentrated and rendered
electrocompetent (808). Further, in some embodiments, a new
assembled nucleic acid sample may be prepared by the nucleic acid
assembly module at this time, or, alternatively, a second fully
assembled nucleic acid may be directly introduced to the cells
from, e.g., the reagent cartridge. Prior to recursive editing, in
some embodiments, the automated multi-module cell editing
instrument may require additional materials be supplied by the
user, e.g., through the introduction of one or more separate
reagents vials or cartridge.
[0190] The steps may be the same or different during the second
round of editing. For example, in some embodiments, upon a
subsequent execution of step 804, a selective growth medium is
transferred to the growth module to enable selection of edited
cells from the first round of editing. The robotic handling system
may transfer the selective growth medium from a vial or container
in a reagent cartridge situated in a position designated for
selective growth medium. Prior to transferring the selective growth
medium, machine-readable indicia may be scanned upon the vial or
other container or reservoir situated in the position designated
for the selective growth medium to confirm the contents of the
vial, container, or reservoir. Further, the machine-readable
indicia may indicate a type of selective growth medium provided to
the instrument. The type of selective growth medium, in some
embodiments, may cause the instrument to select a particular
processing script (e.g., settings and activation of the growth
module appropriate for the particular selective growth medium).
Particular examples of recursive editing workflows are described in
relation to FIG. 10.
[0191] In some implementations, the method 800 can be timed to
introduce materials and/or complete the editing cycle or growth
cycle in coordination with a user's schedule. For example, the
automated multi-module cell editing instrument may provide the user
the ability to schedule completion of one or more cell processing
cycles (e.g., one or more recursive edits) such that the method 800
is enacted with a goal of completion at the user's preferred time.
The time scheduling, for example, may be set through a user
interface. For illustration only, a user may set completion of a
first cycle to 4:00 PM so that the user can supply additional
cartridges of materials to the automated multi-module cell editing
instrument to enable overnight processing of another round of cell
editing. Thus, a user may time the programs so that two or more
cycles may be programmed in a specific time period, e.g., a 24-hour
period.
[0192] In some implementations, throughout the method 800, the
automated multi-module cell editing instrument may alert the user
to its current status. For example, the user interface may present
a graphical indication of the present stage of processing. In a
particular example, a front face of the automated multi-module call
processing instrument may be overlaid with a user interface (e.g.,
touch screen) that presents an animated graphic depicting present
status of the cell processing. The user interface may further
present any user and/or default settings associated with the
current processing stage (e.g., temperature setting, time setting,
etc.). In certain implementations, the status may be communicated
to a user via a wireless communications controller.
[0193] Although illustrated as a particular series of operations,
in other embodiments, more or fewer steps may be included in the
method 800. For example, in some embodiments, prior to engaging in
each round of editing, the contents of reservoirs, reagent
cartridges, and/or vials may be screened to confirm appropriate
materials are available to proceed with processing. For example, in
some embodiments, one or more imaging sensors (e.g., barcode
scanners, cameras, etc.) may confirm contents at various locations
within the housing of the automated multi-module cell editing
instrument. In one example, multiple imaging sensors may be
disposed within the housing of the automated multi-module cell
editing instrument, each imaging sensor configured to detect one or
more materials (e.g., machine-readable indicia such as barcodes or
QR codes, shapes/sizes of materials, etc.). In another example, at
least one imaging sensor may be moved by the robotic handling
system to multiple locations to detect one or more materials. In
further embodiments, one or more weight sensors may detect presence
or absence of disposable or replaceable materials. In an
illustrative example, the transfer tip supply holder may include a
weight sensor to detect whether or not tips have been loaded into
the region. In another illustrative example, an optical sensor may
detect that a level of liquid waste has reached a threshold level,
requiring disposal prior to continuation of cell processing or
addition of liquid if the minimum level has not been reached to
proceed. Requests for additional materials, removal of waste
supplies, or other user interventions (e.g., manual cleaning of one
or more elements, etc.), in some implementations, are presented on
a graphical user interface of the automated multi-module cell
editing instrument. The automated multi-module cell editing
instrument, in some implementations, contacts the user with
requests for new materials or other manual interventions, for
example, through a software app, email, or text message.
[0194] FIG. 9 is a simplified block diagram of an embodiment of an
exemplary automated multi-module cell processing instrument 900
comprising a singulation/growth/editing/normalization module 940
for enrichment for edited cells. The cell processing instrument 900
may include a housing 944, a reservoir of cells to be transformed
or transfected 902, and a growth module (a cell growth device) 904.
The cells to be transformed are transferred from a reservoir 902 to
the growth module 904 to be cultured until the cells hit a target
OD. Once the cells hit the target OD, the growth module 904 may
cool or freeze the cells for later processing, or the cells may be
transferred to a cell concentration module 930 where the cells are
rendered electrocompetent and concentrated to a volume optimal for
cell transformation. Once concentrated, the cells are then
transferred to the flow-through electroporation module 905 (e.g.,
transformation/transfection module).
[0195] In addition to the reservoir 902 for storing the cells, the
automated multi-module cell processing instrument 900 may include a
reservoir for storing editing oligonucleotide cassettes 916 and a
reservoir for storing an expression vector backbone 918. Both the
editing oligonucleotide cassettes and the expression vector
backbone are transferred from the reagent cartridge to a nucleic
acid assembly module 920, where the editing oligonucleotide
cassettes are inserted into the expression vector backbone. The
assembled nucleic acids may be transferred into an optional
purification module 922 for desalting and/or other purification
and/or concentration procedures needed to prepare the assembled
nucleic acids for transformation. Alternatively, pre-assembled
nucleic acids, e.g., an editing vector, may be stored within
reservoir 916 or 918. Once the processes carried out by the
purification module 922 are complete, the assembled nucleic acids
are transferred to, e.g., an electroporation device 905, which
already contains the cell culture grown to a target OD and rendered
electrocompetent via cell concentration module 1130. In
electroporation device 905, the assembled nucleic acids are
introduced into the cells. Following electroporation, the cells are
transferred into a combined recovery/dilution/selection module
910.
[0196] Following recovery, and, optionally, selection, the cells
are transferred to a singulation, selection, growth, induction,
editing, and normalization module 940, where the cells are diluted
and compartmentalized such that there is an average of one cell per
compartment. Once singulated, the cells grown in, e.g., selective
medium, for a pre-determined number of doublings. Once these
initial colonies are established, editing is induced and the edited
cells are allowed to establish colonies, which are grown to
terminal size (e.g., the colonies are normalized). In some
embodiments, editing is induced by one or more of the editing
components being under the control of an inducible promoter. In
some embodiments, the inducible promoter is activated by a rise in
temperature and "deactivated" by lowering the temperature.
Alternatively, in embodiments where the singulation device is a
solid wall device comprising a filter forming the bottom of the
microwell, the solid wall device can be transferred to a plate
(e.g., agar plate or even to liquid medium) comprising a medium
with a component that activates induced editing, then transferred
to a medium that deactivates editing. Once the colonies are grown
to terminal size, the colonies are pooled. Again, singulation
overcomes growth bias from unedited cells and growth bias resulting
from fitness effects of different edits.
[0197] The recovery, dilution, selection, singulation, induction,
editing and growth modules may all be separate, may be arranged and
combined as shown in FIG. 9, or may be arranged or combined in
other configurations. In certain embodiments, all of recovery,
selection, singulation, growth, editing, and normalization are
performed in a solid wall device. Alternatively, recovery,
selection, and dilution, if necessary, are performed in liquid
medium in a separate vessel (module), then transferred to the solid
wall singulation/growth/induction/editing/normalization module.
[0198] Once the normalized cell colonies are pooled, the cells may
be stored, e.g., in a storage module 912, where the cells can be
kept at, e.g., 4.degree. C. until the cells are retrieved 914 for
further study. Alternatively, the cells may be used in another
round of editing. The multi-module cell processing instrument 900
is controlled by a processor 942 configured to operate the
instrument 900 based on user input, as directed by one or more
scripts, or as a combination of user input or a script. The
processor 942 may control the timing, duration, temperature, and
operations of the various modules of the instrument 900 and the
dispensing of reagents. For example, the processor 942 may cool the
cells post-transformation until editing is desired, upon which time
the temperature may be raised to a temperature conducive of genome
editing and cell growth. The processor may be programmed with
standard protocol parameters from which a user may select, a user
may specify one or more parameters manually, or one or more scripts
associated with the reagent cartridge may specify one or more
operations and/or reaction parameters. In addition, the processor
942 may notify the user (e.g., via an application to a smart phone
or other device) that the cells have reached the target OD as well
as update the user as to the progress of the cells in the various
modules in the multi-module cell processing instrument 900.
[0199] The automated multi-module cell processing instrument 900 is
a nuclease-directed genome editing system and can be used in single
editing systems (e.g., introducing one or more edits to a cellular
genome in a single editing process). The system of FIG. 10,
described below, is configured to perform sequential editing, e.g.,
using different nuclease-directed systems sequentially to provide
two or more genome edits in a cell; and/or recursive editing, e.g.
utilizing a single nuclease-directed system to introduce
sequentially two or more genome edits in a cell.
[0200] FIG. 10 illustrates another embodiment of a multi-module
cell processing instrument 1000. This embodiment depicts an
exemplary system that performs recursive gene editing on a cell
population. As with the embodiment shown in FIG. 9, the cell
processing instrument 1000 may include a housing 1044, a reservoir
for storing cells to be transformed or transfected 1002, and a cell
growth module (comprising, e.g., a rotating growth vial) 1004. The
cells to be transformed are transferred from a reservoir to the
cell growth module 1004 to be cultured until the cells hit a target
OD. Once the cells hit the target OD, the growth module may cool or
freeze the cells for later processing or transfer the cells to a
cell concentration module 1060 where the cells are subjected to
buffer exchange and rendered electrocompetent, and the volume of
the cells may be reduced substantially. Once the cells have been
concentrated to an appropriate volume, the cells are transferred to
electroporation device or module 1008. In addition to the reservoir
for storing cells, the multi-module cell processing instrument 1000
includes a reservoir for storing the vector pre-assembled with
editing oligonucleotide cassettes 1052. The pre-assembled nucleic
acid vectors are transferred to the electroporation device 1008,
which already contains the cell culture grown to a target OD. In
the electroporation device 1008, the nucleic acids are
electroporated into the cells. Following electroporation, the cells
are transferred into an optional recovery (and optionally,
dilution) module 1056, where the cells are allowed to recover
briefly post-transformation.
[0201] After recovery, the cells may be transferred to a storage
module 1012, where the cells can be stored at, e.g., 4.degree. C.
for later processing, or the cells may be diluted and transferred
to a selection/growth/induction/editing module/device 1058. The
cells are allowed to grow and editing is then induced by providing
conditions (e.g., temperature, addition of an inducing or
repressing chemical) to induce editing. Note that the
selection/growth/induction and editing modules may be the same
module or device, where all processes are performed in, e.g., a
solid wall singulation device, or selection and/or dilution may
take place in a separate vessel before the cells are transferred to
an induction/editing module. As an alternative to singulation in,
e.g., a solid wall device, the transformed cells may be grown
in--and editing can be induced in--bulk liquid (see, e.g., U.S.
Ser. No. 16/545,097, filed 20 Aug. 2019. Once the putatively-edited
cells are pooled, they may be subjected to another round of
editing, beginning with growth, cell concentration and treatment to
render electrocompetent, and transformation by yet another donor
nucleic acid in another editing cassette via the electroporation
device/module 1008.
[0202] In electroporation device 1008, the cells selected from the
first round of editing are transformed by a second set of editing
oligos (or other type of oligos) and the cycle is repeated until
the cells have been transformed and edited by a desired number of,
e.g., editing cassettes. The multi-module cell processing
instrument 1000 exemplified in FIG. 10 is controlled by a processor
1042 configured to operate the instrument based on user input or is
controlled by one or more scripts including at least one script
associated with the reagent cartridge. The processor 1042 may
control the timing, duration, and temperature of various processes,
the dispensing of reagents, and other operations of the various
modules of the instrument 1000. For example, a script or the
processor may control the dispensing of cells, reagents, vectors,
and editing oligonucleotides; which editing oligonucleotides are
used for cell editing and in what order; the time, temperature and
other conditions used in the recovery and expression module, the
wavelength at which OD is read in the cell growth module, the
target OD to which the cells are grown, and the target time at
which the cells will reach the target OD. In addition, the
processor may be programmed to notify a user (e.g., via an
application) as to the progress of the cells in the automated
multi-module cell processing instrument.
[0203] It should be apparent to one of ordinary skill in the art
given the present disclosure that the process described may be
recursive and multiplexed; that is, cells may go through the
workflow described in relation to FIG. 10, then the resulting
edited culture may go through another (or several or many) rounds
of additional editing (e.g., recursive editing) with different
editing vectors. For example, the cells from round 1 of editing may
be diluted and an aliquot of the edited cells edited by editing
vector A may be combined with editing vector B, an aliquot of the
edited cells edited by editing vector A may be combined with
editing vector C, an aliquot of the edited cells edited by editing
vector A may be combined with editing vector D, and so on for a
second round of editing. After round two, an aliquot of each of the
double-edited cells may be subjected to a third round of editing,
where, e.g., aliquots of each of the AB-, AC-, AD-edited cells are
combined with additional editing vectors, such as editing vectors
X, Y, and Z. That is that double-edited cells AB may be combined
with and edited by vectors X, Y, and Z to produce triple-edited
edited cells ABX, ABY, and ABZ; double-edited cells AC may be
combined with and edited by vectors X, Y, and Z to produce
triple-edited cells ACX, ACY, and ACZ; and double-edited cells AD
may be combined with and edited by vectors X, Y, and Z to produce
triple-edited cells ADX, ADY, and ADZ, and so on. In this process,
many permutations and combinations of edits can be executed,
leading to very diverse cell populations and cell libraries. In any
recursive process, it is advantageous to "cure" the previous engine
and editing vectors (or single engine+editing vector in a single
vector system). "Curing" is a process in which one or more vectors
used in the prior round of editing is eliminated from the
transformed cells. Curing can be accomplished by, e.g., cleaving
the vector(s) using a curing plasmid thereby rendering the editing
and/or engine vector (or single, combined vector) nonfunctional;
diluting the vector(s) in the cell population via cell growth (that
is, the more growth cycles the cells go through, the fewer daughter
cells will retain the editing or engine vector(s)), or by, e.g.,
utilizing a heat-sensitive origin of replication on the editing or
engine vector (or combined engine+editing vector). The conditions
for curing will depend on the mechanism used for curing; that is,
in this example, how the curing plasmid cleaves the editing and/or
engine plasmid.
[0204] FIG. 11 is a simplified block diagram of an embodiment of an
exemplary automated multi-module cell processing instrument 1100
comprising, e.g., a bulk liquid growth module for induced editing
and enrichment for edited cells. (See, e.g., U.S. Ser. No.
16/545,097, filed 20 Aug. 2019.) The cell processing instrument
1100 may include a housing 1144, a reservoir of cells to be
transformed or transfected 1102, and a growth module (a cell growth
device) 1104. The cells to be transformed are transferred from a
reservoir 1102 to the growth module 1104 to be cultured until the
cells hit a target OD. Once the cells hit the target OD, the growth
module may cool or freeze the cells for later processing, or the
cells may be transferred to a cell concentration module 1130 where
the cells are rendered electrocompetent and concentrated to a
volume optimal for cell transformation. Once concentrated, the
cells are then transferred to an electroporation module 1108 (e.g.,
transformation/transfection module).
[0205] In addition to the reservoir 1102 for storing the cells, the
instrument 1100 may include a reservoir for storing editing
cassettes 1116 and a reservoir for storing an expression vector
backbone 1118. Both the editing oligonucleotide cassettes and the
expression vector backbone are transferred from the reagent
cartridge to a nucleic acid assembly module 1120, where the editing
oligonucleotide cassettes are inserted into the expression vector
backbone. The assembled nucleic acids may be transferred into an
optional purification module 1122 for desalting and/or other
purification and/or concentration procedures needed to prepare the
assembled nucleic acids for transformation. Alternatively,
pre-assembled nucleic acids, e.g., an editing vector, may be stored
within reservoir 1116 or 1118. Once the processes carried out by
the purification module 1122 are complete, the assembled nucleic
acids are transferred to, e.g., an electroporation device or module
1108, which already contains the cell culture grown to a target OD
and rendered electrocompetent via cell concentration module 1130.
In electroporation device 1108, the assembled nucleic acids are
introduced into the cells. Following electroporation, the cells are
transferred into a combined recovery/selection module 1110.
[0206] Following recovery, and, optionally, selection, the cells
are transferred to a growth, induction, and editing module (bulk
liquid culture) 1140. The cells are allowed to grow until the cells
reach the stationary growth phase (or nearly so), then editing is
induced by induction of transcription of one or both of the
nuclease and gRNA. In some embodiments, editing is induced by
transcription of one or both of the nuclease and the gRNA being
under the control of an inducible promoter. In some embodiments,
the inducible promoter is a pL promoter where the promoter is
activated by a rise in temperature and "deactivated" by lowering
the temperature.
[0207] The recovery, selection, growth, induction, editing and
storage modules may all be separate, may be arranged and combined
as shown in FIG. 11, or may be arranged or combined in other
configurations. In certain embodiments, recovery and selection are
performed in one module, and growth, editing, and re-growth are
performed in a separate module. Alternatively, recovery, selection,
growth, editing, and re-growth are performed in a single
module.
[0208] Once the cells are edited and re-grown (e.g., recovered from
editing), the cells may be stored, e.g., in a storage module 1112,
where the cells can be kept at, e.g., 4.degree. C. until the cells
are retrieved for further study (e.g., cell retrieval 1114).
Alternatively, the cells may be used in another round of editing.
The multi-module cell processing instrument 1100 is controlled by a
processor 1142 configured to operate the instrument based on user
input, as directed by one or more scripts, or as a combination of
user input or a script. The processor 1142 may control the timing,
duration, temperature, and operations of the various modules of the
instrument 1100 and the dispensing of reagents. For example, the
processor 1142 may cool the cells post-transformation until editing
is desired, upon which time the temperature may be raised to a
temperature conducive of genome editing and cell growth. The
processor may be programmed with standard protocol parameters from
which a user may select, a user may specify one or more parameters
manually, or one or more scripts associated with the reagent
cartridge may specify one or more operations and/or reaction
parameters. In addition, the processor may notify the user (e.g.,
via an application to a smart phone or other device) that the cells
have reached the target OD, as well as update the user as to the
progress of the cells in the various modules in the multi-module
system.
EXAMPLES
[0209] The following examples are put forth so as to provide those
of ordinary skill in the art with a complete disclosure and
description of how to make and use the present invention, and are
not intended to limit the scope of what the inventors regard as
their invention, nor are they intended to represent or imply that
the experiments below are all of or the only experiments performed.
It will be appreciated by persons skilled in the art that numerous
variations and/or modifications may be made to the invention as
shown in the specific aspects without departing from the spirit or
scope of the invention as broadly described. The present aspects
are, therefore, to be considered in all respects as illustrative
and not restrictive.
Example I: Growth in the Cell Growth Module
[0210] One embodiment of the cell growth device as described herein
was tested against a conventional cell shaker shaking a 5 ml tube
and an orbital shaker shaking a 125 ml baffled flask to evaluate
cell growth in bacterial and yeast cells. Additionally, growth of a
bacterial cell culture and a yeast cell culture was monitored in
real time using an embodiment of the cell growth device described
herein.
[0211] In a first example, 20 ml EC23 cells (E. coli cells) in LB
were grown in a 35 ml rotating growth vial at 30.degree. C. using
the cell growth device as described herein. The rotating growth
vial was spun at 600 rpm and oscillated (i.e., the rotation
direction was changed) every 1 second. OD was measured in the cell
growth device. In parallel, 5 ml EC23 cells in LB were grown in an
orbital shaker in a 5 ml tube at 30.degree. C. and were shaken at
750 rpm; the OD.sub.600 was measured at intervals using a
NanoDrop.TM. spectrophotometer (Thermo Fisher Scientific). The
rotating growth vial/cell growth device performed better than the
cell shaker in growing the cells to OD.sub.600 2.6 in slightly over
4 hours (data not shown).
[0212] Two additional experiments were performed, this time
comparing the rotating growth vial/cell growth device with paddles
to a baffled flask and an orbital shaker. In one experiment, 20 ml
EC138 cells (E. coli cells) in LB were grown in a 35 ml rotating
growth vial with a 4-paddle configuration at 30.degree. C. The
rotating growth vial was spun at 600 rpm and oscillated (i.e., the
rotation direction was changed) every 1 second. In parallel, 20 ml
EC138 cells in LB were grown in a 125 ml baffled flask at
30.degree. C. using an orbital shaker. OD.sub.600 was measured at
intervals using a NanoDrop.TM. spectrophotometer (Thermo Fisher
Scientific). The results demonstrated that the rotating growth
vial/cell growth device performed as well as the orbital shaker in
growing the cells to OD.sub.600 1.0. In a second experiment, 20 ml
EC138 cells (E. coli cells) in LB were grown in a 35 ml rotating
growth vial with a 2-paddle configuration at 30.degree. C. using
the cell growth device as described herein. The rotating growth
vial was spun at 600 rpm and oscillated (i.e., the rotation
direction was changed) every 1 second. In parallel, 20 ml EC138
cells in LB were grown in a 125 ml baffled flask at 30.degree. C.
using an orbital shaker. OD.sub.600 was measured at intervals using
a NanoDrop.TM. spectrophotometer (Thermo Fisher Scientific). The
results demonstrated that the rotating growth vial/cell growth
device performed as well--or better--as the orbital shaker in
growing the cells to OD.sub.600 1.2.
[0213] In yet another experiment, the rotating growth vial/cell
growth device was used to measure OD.sub.600 in real time. The
results of real time measurement of growth of an EC138 cell culture
at 30.degree. C. using oscillating rotation and employing a
2-paddle rotating growth vial were that OD.sub.600 2.6 was reached
in 4.4 hours.
[0214] In another experiment, the rotating growth vial/cell growth
device was used to measure OD.sub.600 in real time of yeast s288c
cells in YPAD. The cells were grown at 30.degree. C. using
oscillating rotation and employing a 2-paddle rotating growth vial.
For the yeast cells, OD.sub.600 6.0 was reached in 14 hours.
Example II: Cell Concentration
[0215] The TFF module as described above in relation to FIGS. 6B-6F
has been used successfully to process and perform buffer exchange
on both E. coli and yeast cultures. In concentrating an E. coli
culture, the following steps were performed:
[0216] First, a 20 ml culture of E. coli in LB grown to OD 0.5-0.62
was passed through the TFF device in one direction, then passed
through the TFF device in the opposite direction. At this point,
the cells were concentrated to a volume of approximately 5 ml.
Next, 50 ml of 10% glycerol was added to the concentrated cells,
and the cells were passed through the TFF device in one direction,
in the opposite direction, and back in the first direction for a
total of three passes. Again the cells were concentrated to a
volume of approximately 5 ml. Again, 50 ml of 10% glycerol was
added to the 5 ml of cells and the cells were passed through the
TFF device for three passes. This process was repeated; that is,
again 50 ml 10% glycerol was added to cells concentrated to 5 ml,
and the cells were passed three times through the TFF device. At
the end of the third pass of the three 50 ml 10% glycerol washes,
the cells were again concentrated to approximately 5 ml of 10%
glycerol. The cells were then passed in alternating directions
through the TFF device three more times, wherein the cells were
concentrated into a volume of approximately 400 .mu.l.
[0217] Filtrate conductivity and filter processing time was
measured for E. coli. Filter performance was quantified by
measuring the time and number of filter passes required to obtain a
target solution electrical conductivity. Cell retention was
determined by comparing the optical density (OD600) of the cell
culture both before and after filtration. Filter health was
monitored by measuring the transmembrane flow rate during each
filter pass. Target conductivity (.about.16 .mu.S/cm) was achieved
in approximately 30 minutes utilizing three 50 ml 10% glycerol
washes and three passes of the cells through the device for each
wash. The volume of the cells was reduced from 20 ml to 400 .mu.l,
and recovery of approximately 90% of the cells has been
achieved.
[0218] The same process was repeated with yeast cell cultures. A
yeast culture was initially concentrated to approximately 5 ml
using two passes through the TFF device in opposite directions. The
cells were washed with 50 ml of 1M sorbitol three times, with three
passes through the TFF device after each wash. After the third pass
of the cells following the last wash with 1M sorbitol, the cells
were passed through the TFF device two times, wherein the yeast
cell culture was concentrated to approximately 525 .mu.l. The
filter buffer exchange performance for yeast cells was determined
by measuring filtrate conductivity and filter processing time.
Target conductivity (.about.10 .mu.S/cm) was achieved in
approximately 23 minutes utilizing three 50 ml 1M sorbitol washes
and three passes through the TFF device for each wash. The volume
of the cells was reduced from 20 ml to 525 .mu.l. Recovery of
approximately 90% of the cells has been achieved.
EXAMPLE III: Production and Transformation of Electrocompetent E.
coli and S. cerevisiae
[0219] For testing transformation in the FTEP device,
electrocompetent E. coli cells were created. To create a starter
culture, 6 ml volumes of LB chlor-25 (LB with 25 .mu.g/ml
chloramphenicol) were transferred to 14 ml culture tubes. A 25
.mu.l aliquot of E. coli was used to inoculate the LB chlor-25
tubes. Following inoculation, the tubes were placed at a 45.degree.
angle in the shaking incubator set to 250 RPM and 30.degree. C. for
overnight growth, between 12-16 hrs. The OD600 value should be
between 2.0 and 4.0. A 1:100 inoculum volume of the 250 ml LB
chlor-25 tubes were transferred to four sterile 500 ml baffled
shake flasks, i.e., 2.5 ml per 250 ml volume shake flask. The
flasks were placed in a shaking incubator set to 250 RPM and
30.degree. C. The growth was monitored by measuring OD600 every 1
to 2 hr. When the OD600 of the culture was between 0.5-0.6 (approx.
3-4 hrs), the flasks were removed from the incubator. The cells
were centrifuged at 4300 RPM, 10 min, 4.degree. C. The supernatant
was removed, and 100 ml of ice-cold 10% glycerol was transferred to
each sample. The cells were gently resuspended, and the wash
procedure performed three times, each time with the cells
resuspended in 10% glycerol. After the fourth centrifugation, the
cell resuspension was transferred to a 50 ml conical Falcon tube
and additional ice-cold 10% glycerol added to bring the volume up
to 30 ml. The cells were again centrifuged at 4300 RPM, 10 min,
4.degree. C., the supernatant removed, and the cell pellet
resuspended in 10ml ice-cold glycerol. The cells are aliquoted in
1:100 dilutions of cell suspension and ice-cold glycerol.
[0220] For further testing transformation of the FTEP device, S.
cerevisiae cells were created using the methods as generally set
forth in Bergkessel and Guthrie, Methods Enzymol., 529:311-20
(2013). Briefly, YPD or YPAD media was inoculated for overnight
growth from colonies on a YP+glycerol agar plate to produce 150 mL
of cells. The following morning, the overnight culture was diluted
to an OD600 of approximately 0.3. Cells were incubated at
30.degree. C. in a shaking incubator until they reached an OD600 of
1.5+/-0.1.
[0221] A conditioning buffer was prepared using 100 mM lithium
acetate and 10 mM dithiothreitol. A total of 100 mL of buffer were
prepared for every 100 mL of cells grown. Cells were harvested in
250 mL bottles by centrifugation at 4300 rpm for 6 minutes, and the
supernatant removed. The cells were suspended in conditioning
buffer, then the suspension transferred into an appropriate flask
and shaken at 200 RPM and 30 .degree. C. for 30 minutes. The
suspension was transferred to 250 mL bottles and spun at 4300 rpm
for 6 minutes. The supernatant was removed and the pellets
resuspended in cold 1 M sorbitol. These steps were repeated three
times for a total of three wash-spin-decant steps. The pellet was
suspended in sorbitol so that 20 mL of OD 1.5 culture were
resuspended in 500 .mu.L. For each 500 .mu.L, volume of resuspended
cells, a 100 .mu.L, volume containing DNA and Tween80 was added to
the cell suspension.
[0222] A comparative electroporation experiment was performed to
determine the efficiency of transformation of electrocompetent S.
cerevisiae and E. coli using the obstruction array FTEP device
described, benchmarked against a NEPA electroporation device and a
single constriction FTEP. See FIG. 12A for a comparison of the
single constriction FTEP device and the obstruction array FTEP
device. In the obstruction array FTEP device tested, ramps in the
central region (one before and one after the array moving from the
inlet proximal region of the flow channel toward the outlet
proximal region of the flow channel) decreases the channel height
from 100 .mu.m near the electrode channels to 50 .mu.m at the
obstruction. The flow rate was controlled with a pressure control
system, and the performance of the obstruction array FTEP device
was tested at various voltages and pressures. The suspension of
cells with DNA was loaded into the FTEP inlet reservoir. The
transformed cells flowed directly from the inlet and inlet channel,
through the flow channel, through the outlet channel, and into the
outlet. The cells were transferred into a tube containing
additional recovery medium and placed in an incubator shaker at
30.degree. C. shaking at 250 rpm for 3 hours. The cells were plated
to determine the colony forming units (CFUs) that survived
electroporation and the CFUs that survived electroporation and took
up a plasmid. Plates were incubated at 30.degree. C.; E. coli
colonies were counted after approximately 24 hrs.
[0223] FIG. 12B shows data revealing that the obstruction array
FTEP device demonstrated equivalent uptake of DNA by S. cerevisiae
as compared to the single constriction FTEP device and a NEPA
(cuvette) device. The single left-most bar indicates the cell input
for each datapoint. For each datapoint, the left bar indicates the
number of cells that survived electroporation, and the right bar
indicates the number of cells that were transformed with the DNA.
Replicates were performed for each datapoint and the bars are the
means of the duplicates. FIG. 12C shows data revealing that a
different obstruction array FTEP device with a minimum flow path
width of 100 .mu.m and minimum height of 50 .mu.m demonstrated
uptake of DNA by S. cerevisiae within a factor of 1.3 as compared
to the single constriction FTEP device. The single left-most bar
indicates the cell input for each datapoint. For each datapoint,
the left bar indicates the number of cells that survived
electroporation, and the right bar indicates the number of cells
that were transformed with the DNA. Replicates were performed for
each datapoint and the bars are the means of the duplicates. FIG.
12D shows data revealing that an obstruction array FTEP device with
a minimum flow path width of 40 .mu.m and a minimum height of 50
.mu.m demonstrated uptake of DNA by E. coli within a factor of 5 as
compared to the single constriction FTEP device and a NEPA
(cuvette) device. The single left-most bar indicates the cell input
for each datapoint. For each datapoint, the left bar indicates the
number of cells that survived electroporation (bars with angled
lines from bottom left to top right), and the right bar indicates
the number of cells that were transformed with the editing plasmid
(i.e., uptake) (bars with angled lines from top left to bottom
right). Replicates were performed for each datapoint and the bars
are the means of the duplicates.
Example IV: Optimization of FTEP Configuration
[0224] For optimizing transformation in the parallel-obstruction
FTEP device embodiment shown in FIGS. 1L-1N, electrocompetent S288c
cells were created. FIG. 13 shows at left a plot of simulated
electric field strength vs. residence time for the "hour
glass"-shaped FTEP embodiment pictured above the plot (conducted at
2.75 kV, 3 psi). The plot shows the energy electric field strength
(kV/cm) experienced by cells at d=0 (at the center of the FTEP
device), d=12.5 .mu.m (from the center), d=20 .mu.m (from the
center), and d=22.5 .mu.m (from the center). The dotted line at
approximately 9 kV/cm shows the electric field strength experienced
by cells porated in a Nepa Gene cuvette. Note that in the "hour
glass" FTEP configuration, the cells experience a spike in electric
field strength significantly above that experienced in a cuvette.
FIG. 13 at right shows a plot of simulated electric field strength
vs. residence time for the "abrupt step" FTEP embodiment shown
above the plot (conducted at 2.0 kV, 0.9 psi). Note that with this
embodiment of an FTEP, it is possible to control the magnitude of a
constant electric field strength experienced by the cells. Again,
the plot shows the electric field strength E (kV/cm) experienced by
cells at d=0 (at the center of the FTEP device), d=12.5 .mu.m (from
the center), d=20 .mu.m (from the center), and d=22.5 .mu.m (from
the center). The dotted line at approximately 9 kV/cm shows the
electric field strength experienced by cells porated in a NepaGene
cuvette.
[0225] FIG. 14 shows the results of a sweep of various electric
field strengths and residence times with S288c, achieved by varying
the applied voltage and pressure, for the parallel-obstruction FTEP
embodiment shown in FIGS. 1L-1N. The right plot of FIG. 13
demonstrates that the "abrupt step" configuration of FTEP allows
for control over the magnitude of a constant electric field
strength experienced by cells in the FTEP device; however, though
the "abrupt step" configuration allows for control of field
strength, the configuration of a single "abrupt step" can lead to
clogging of the flow channel, which in turn leads to catastrophic
failure of the FTEP device. To decrease the likelihood of clogging
while still maintaining a channel configuration that allows tuning
of field strength and residence time, the parallel-obstruction FTEP
embodiment shown in FIGS. 1L-1N was tested. In this embodiment, the
obstructions are elongated ovals (1.0 mm in length) which form 8
parallel "lanes" in the center region of the flow channel. Note
that for the 1.0 mm-long center obstruction configuration the
optimal applied voltage was 3 kV with an applied pressure of 6.8
psi, leading to an uptake value of 8.51E+04 CFUs.
[0226] FIG. 15 shows at top the results of a sweep of various
electric field strengths and residence times with S288c, achieved
by varying the applied voltage and pressure, for the
parallel-obstruction FTEP embodiment shown in FIGS. 1L-1N. In this
embodiment, the obstructions are elongated ovals that are 0.5 mm in
length, which form 8 parallel "lanes" in the center region of the
flow channel. Note that the optimal applied voltage was 1.5 kV with
an applied pressure of 2.6 psi, leading to an uptake value of
2.55E+04 CFUs. At top shows a comparison between the
parallel-obstruction FTEP embodiment shown in FIGS. 1L-1N with 1.0
mm-long obstructions vs. 0.5 mm-long obstructions. Note that the
magnitude of a constant electric field strength and residence time
within the electric field can be controlled in this embodiment FTEP
by adjusting the applied voltage and pressure.
Example V: Fully-Automated Singleplex RGN-Directed Editing Run
[0227] Singleplex automated genomic editing using MAD7 nuclease was
successfully performed with an automated multi-module instrument of
the disclosure. See U.S. Pat. No. 9,982,279; and U.S. Ser. No.
16/024,831 filed 30 Jun. 2018; U.S. Ser. No. 16/024,816 filed 30
Jun. 2018; U.S. Ser. No. 16/147,353 filed 28 Sep. 2018; U.S. Ser.
No. 16/147,865 filed 30 Sep. 2018; and U.S. Ser. No. 16/147,871
filed 30 Jun. 2018.
[0228] An ampR plasmid backbone and a lacZ_F172* editing cassette
were assembled via Gibson Assembly.RTM. into an "editing vector" in
an isothermal nucleic acid assembly module included in the
automated instrument. lacZ_F172 functionally knocks out the lacZ
gene. "lacZ_F172*" indicates that the edit happens at the 172nd
residue in the lacZ amino acid sequence. Following assembly, the
product was de-salted in the isothermal nucleic acid assembly
module using AMPure beads, washed with 80% ethanol, and eluted in
buffer. The assembled editing vector and recombineering-ready,
electrocompetent E. coli cells were transferred into a
transformation module for electroporation. The cells and nucleic
acids were combined and allowed to mix for 1 minute, and
electroporation was performed for 30 seconds. The parameters for
the poring pulse were: voltage, 2400 V; length, 5 ms; interval, 50
ms; number of pulses, 1; polarity, +. The parameters for the
transfer pulses were: Voltage, 150 V; length, 50 ms; interval, 50
ms; number of pulses, 20; polarity, +/-. Following electroporation,
the cells were transferred to a recovery module (another growth
module) and allowed to recover in SOC medium containing
chloramphenicol. Carbenicillin was added to the medium after 1
hour, and the cells were allowed to recover for another 2 hours.
After recovery, the cells were held at 4.degree. C. until recovered
by the user.
[0229] After the automated process and recovery, an aliquot of
cells was plated on MacConkey agar base supplemented with lactose
(as the sugar substrate), chloramphenicol and carbenicillin and
grown until colonies appeared. White colonies represented
functionally edited cells, purple colonies represented un-edited
cells. All liquid transfers were performed by the automated liquid
handling device of the automated multi-module cell processing
instrument.
[0230] The result of the automated processing was that
approximately 1.0E.sup.-03 total cells were transformed (comparable
to conventional benchtop results), and the editing efficiency was
83.5%. The lacZ_172 edit in the white colonies was confirmed by
sequencing of the edited region of the genome of the cells.
Further, steps of the automated cell processing were observed
remotely by webcam and text messages were sent to update the status
of the automated processing procedure.
Example VI: Fully-Automated Recursive Editing Run
[0231] Recursive editing was successfully achieved using the
automated multi-module cell processing instrument. An ampR plasmid
backbone and a lacZ_V10* editing cassette were assembled via Gibson
Assembly.RTM. into an "editing vector" in an isothermal nucleic
acid assembly module included in the automated system. Similar to
the lacZ_F172 edit, the lacZ_V10 edit functionally knocks out the
lacZ gene. " lacZ_V10" indicates that the edit happens at amino
acid position 10 in the lacZ amino acid sequence. Following
assembly, the product was de-salted in the isothermal nucleic acid
assembly module using AMPure beads, washed with 80% ethanol, and
eluted in buffer. The first assembled editing vector and the
recombineering-ready electrocompetent E. coli cells were
transferred into a transformation module for electroporation. The
cells and nucleic acids were combined and allowed to mix for 1
minute, and electroporation was performed for 30 seconds. The
parameters for the poring pulse were: voltage, 2400 V; length, 5
ms; interval, 50 ms; number of pulses, 1; polarity, +. The
parameters for the transfer pulses were: Voltage, 150 V; length, 50
ms; interval, 50 ms; number of pulses, 20; polarity, +/-. Following
electroporation, the cells were transferred to a recovery module
(another growth module) allowed to recover in SOC medium containing
chloramphenicol. Carbenicillin was added to the medium after 1
hour, and the cells were grown for another 2 hours. The cells were
then transferred to a centrifuge module and a media exchange was
then performed. Cells were resuspended in TB containing
chloramphenicol and carbenicillin where the cells were grown to
OD600 of 2.7, then concentrated and rendered electrocompetent.
[0232] During cell growth, a second editing vector was prepared in
the isothermal nucleic acid assembly module. The second editing
vector comprised a kanamycin resistance gene, and the editing
cassette comprised a galK Y145* edit. If successful, the galK Y145*
edit confers on the cells the ability to uptake and metabolize
galactose. The edit generated by the galK Y154* cassette introduces
a stop codon at the 154th amino acid reside, changing the tyrosine
amino acid to a stop codon. This edit makes the galK gene product
non-functional and inhibits the cells from being able to metabolize
galactose. Following assembly, the second editing vector product
was de-salted in the isothermal nucleic acid assembly module using
AMPure beads, washed with 80% ethanol, and eluted in buffer. The
assembled second editing vector and the electrocompetent E. coli
cells (that were transformed with and selected for the first
editing vector) were transferred into a transformation module for
electroporation, using the same parameters as detailed above.
Following electroporation, the cells were transferred to a recovery
module (another growth module), allowed to recover in SOC medium
containing carbenicillin. After recovery, the cells were held at
4.degree. C. until retrieved, after which an aliquot of cells were
plated on LB agar supplemented with chloramphenicol, and kanamycin.
To quantify both lacZ and galK edits, replica patch plates were
generated on two media types: 1) MacConkey agar base supplemented
with lactose (as the sugar substrate), chloramphenicol, and
kanamycin, and 2) MacConkey agar base supplemented with galactose
(as the sugar substrate), chloramphenicol, and kanamycin. All
liquid transfers were performed by the automated liquid handling
device of the automated multi-module cell processing
instrument.
[0233] In this recursive editing experiment, 41% of the colonies
screened had both the lacZ and galK edits, the results of which
were comparable to the double editing efficiencies obtained using a
"benchtop" or manual approach.
[0234] While this invention is satisfied by embodiments in many
different forms, as described in detail in connection with
preferred embodiments of the invention, it is understood that the
present disclosure is to be considered as exemplary of the
principles of the invention and is not intended to limit the
invention to the specific embodiments illustrated and described
herein. Numerous variations may be made by persons skilled in the
art without departure from the spirit of the invention. The scope
of the invention will be measured by the appended claims and their
equivalents. The abstract and the title are not to be construed as
limiting the scope of the present invention, as their purpose is to
enable the appropriate authorities, as well as the general public,
to quickly determine the general nature of the invention. In the
claims that follow, unless the term "means" is used, none of the
features or elements recited therein should be construed as
means-plus-function limitations pursuant to 35 U.S.C. .sctn. 112,
916.
* * * * *