U.S. patent application number 14/692214 was filed with the patent office on 2015-10-22 for analysis of compounds for pain and sensory disorders.
This patent application is currently assigned to Q-STATE BIOSCIENCES, INC.. The applicant listed for this patent is Q-STATE BIOSCIENCES, INC.. Invention is credited to Adam Cohen, Kevin C. Eggan, Evangelos Kiskinis, Joel Kralj.
Application Number | 20150301028 14/692214 |
Document ID | / |
Family ID | 53053109 |
Filed Date | 2015-10-22 |
United States Patent
Application |
20150301028 |
Kind Code |
A1 |
Eggan; Kevin C. ; et
al. |
October 22, 2015 |
ANALYSIS OF COMPOUNDS FOR PAIN AND SENSORY DISORDERS
Abstract
The invention generally relates to optical methods for
characterizing the effects of compounds on pain and other sensory
phenomena. The effect of compounds on pain and other sensory
phenomena may be characterized using dorsal root ganglion (DRG)
neurons or sensory neurons expressing optogenetic proteins that
allow neural activity to be stimulated and detected optically. The
invention provides cell-based optical assays for studying the
molecular and cellular bases of pain and sensory phenomena and as
platforms to screen and validate drugs, e.g., for pre-clinical
trials.
Inventors: |
Eggan; Kevin C.; (Boston,
MA) ; Cohen; Adam; (Cambridge, MA) ; Kralj;
Joel; (Somerville, MA) ; Kiskinis; Evangelos;
(Cambridge, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Q-STATE BIOSCIENCES, INC. |
Cambridge |
MA |
US |
|
|
Assignee: |
Q-STATE BIOSCIENCES, INC.
Cambridge
MA
|
Family ID: |
53053109 |
Appl. No.: |
14/692214 |
Filed: |
April 21, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61982589 |
Apr 22, 2014 |
|
|
|
Current U.S.
Class: |
435/29 |
Current CPC
Class: |
C12N 5/0619 20130101;
G01N 33/5091 20130101; G01N 33/5023 20130101; G01N 2333/705
20130101; G01N 33/502 20130101; G01N 2800/2842 20130101; C12N
2510/00 20130101; G01N 21/6486 20130101; G01N 2800/2835 20130101;
G01N 33/5058 20130101; C12N 2502/081 20130101; G01N 33/48728
20130101; G01N 33/6872 20130101; G01N 2800/302 20130101 |
International
Class: |
G01N 33/50 20060101
G01N033/50; G01N 33/68 20060101 G01N033/68 |
Claims
1. A method for screening a compound for pain treatment, the method
comprising: presenting a compound to a sample comprising a dorsal
root ganglion (DRG) neuron, wherein the DRG neuron expresses an
optical reporter of membrane electrical potential and a light-gated
ion channel; receiving, via a microscopy system, an optical signal
generated by the optical reporter in response to optical
stimulation of the sample following presentation of said compound;
and identifying the compound as a candidate for pain treatment
based on said optical signal.
2. The method of claim 1, wherein the DRG neuron comprises a target
ion channel with a suspected aberrant characteristic.
3. The method of claim 2, wherein the target ion channel is the
TRPV1 channel and the suspected aberrant characteristic comprises
over expression of TRPV1.
4. The method of claim 1, wherein the microscopy system further
comprises a charge-coupled device camera configured to capture the
optical signal from the DRG neuron.
5. The method of claim 1, wherein the microscopy system comprises a
digital micromirror device that provides the optical
stimulation.
6. The method of claim 1, wherein the DRG neuron also expresses a
protein that reports a change in an intracellular calcium
level.
7. The method of claim 6, wherein the DRG neuron is stimulated by a
second neuron that expresses the light-gated ion channel.
8. The method of claim 7, wherein the second neuron also expresses
the optical reporter of change in membrane potential.
9. The method of claim 6, wherein: the light-gated ion channel
comprises an algal channelrhodopsin; and the protein that reports
changes in intracellular calcium levels comprises a GCaMP
variant.
10. The method of claim 6, further comprising detecting a change in
AP waveform and a change in the intracellular calcium level upon
exposure of the neuron to the compound.
11. The method of claim 1, wherein the DRG neuron is an
hiPSC-derived DRG neuron.
12. The method of claim 1, further comprising spatially patterning
a plurality of DRG neurons in a cell culture on a substrate.
13. The method of claim 1, wherein the obtaining the optical signal
is performed using an optical microscopy system.
14. The method of claim 13, wherein the optical microscopy system
comprises at least one digital micromirror device.
15. The method of claim 1, wherein analyzing the optical signal
comprises detecting an effect of the compound on AP waveform.
16. The method of claim 1, further comprising exposing a cell
culture to an agent known to stimulate a nociceptor as well as the
compound and determining an effect of the compound with the agent
on the neuron.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application claims the benefit of, and priority to,
U.S. Provisional Application Ser. No. 61/982,589, filed Apr. 22,
2014, the contents of which are incorporated by reference.
FIELD OF THE INVENTION
[0002] The invention generally relates to optical methods for
characterizing the effects of compounds on pain and other sensory
phenomena.
BACKGROUND
[0003] Drugs for pain define a market with over $40 B in annual
sales. Important categories of pain drugs include non-steroidal
anti-inflammatory drugs (NSAIDs), opioids, and non-narcotics such
as acetaminophen. However, despite the great variety of quantity of
pain compounds that are sold today, there is a strong unmet need
for new pain medications. There is an important medical need for
more effective treatments for chronic neuropathic pain and there is
also a need for pain medications free of adverse cardiovascular or
gastrointestinal side effects. Additionally, there is an important
social need for potent pain medications with minimized risk of
abuse.
SUMMARY
[0004] The effect of compounds on pain and other sensory phenomena
may be characterized using dorsal root ganglion (DRG) neurons or
sensory neurons expressing optogenetic proteins that allow neural
activity to be stimulated and detected optically. The invention
provides cell-based optical assays for studying the molecular and
cellular bases of pain and sensory phenomena and as platforms to
screen and validate drugs, e.g., for pre-clinical trials. DRG
neurons may be obtained through differentiation from stem cells and
provide an in vitro system for studying the excitability of
nociceptors. Optogenetic constructs such as microbial rhodopsins
that initiate neuronal activity in response to illumination or emit
light in response to neuronal electrical activity allow such assays
to be optical, facilitating high throughput and rapid testing of a
wide range of compounds. Methods and constructs of the invention
can be used to study morphological and action potential properties
and firing patterns of DRG neurons and sensory neurons from humans
or other organisms such as mice. A large number of cells may be
assayed in parallel for their electrogenic properties and response
to compounds that produce pain, itch, or other sensations. Using
optogenetic voltage and ion (e.g., calcium) reporters of the
invention, the ionic conductances at play in neural phenomena can
be probed. The invention further provides stem cell techniques for
differentiating pluripotent stem cells (PSCs) into neurons of
specified sub-types such as DRG neurons or other sensory neurons,
with uses in screening and characterizing compounds' effects on
pain and sensation.
[0005] Methods of the invention include obtaining a cell culture
that includes at least one neuron. The neuron may be differentiated
from a pluripotent stem cell according to methods of the invention.
The neural cell is transformed with a genetically encoded optical
reporter, such as a transmembrane protein that fluoresces in
response to the generation of an action potential. The cell, by the
optical reporter, exhibits an optical signature in response to
neural stimulation and that signature may be observed and compared
to a control signature, such as may be observed from a control cell
with known properties. Differences between the observed signature
and the control signature reveal properties of a compound to which
the cell is exposed. Images captured by microscopy are analyzed
digitally to identify optical signatures such as spike trains and
associate the signatures with specific cells. Using genome-editing,
control cells may be created that are isogenic but-for specific
genetic variants that are suspected to be important to a disease,
condition, or sensory phenomenon. By these means, methods of the
invention can be used to see the consequences of that mutation
within the genetic context of the genome. The effects of not just a
single identified variant, but of that variant in the context of
all other alleles in the genome can be studied.
[0006] In certain aspects, the invention provides a method of
screening for pain compounds. The method includes providing a cell
culture comprising at least one neuron, causing the neuron to
express an optical reporter of change in membrane potential, and
exposing the cell culture to a compound. An optical signal from the
optical reporter in response to an optical stimulation of the cell
culture is obtained and analyzed to determine an effect of the
compound on the neuron.
[0007] The neuron is a DRG neuron. The method may be used with
neurons in which a target ion channel has suspected aberrant
activity. In some embodiments, the neuron also expresses a
light-gated ion channel. The neuron may express a light-gated ion
channel, a protein that reports a change in an intracellular
calcium level, or both. The light-gated ion channel may be an algal
channelrhodopsin and the protein that reports changes in
intracellular calcium levels may include a GCaMP variant.
[0008] In certain embodiments, the neuron is stimulated by a second
neuron that expresses a light-gated ion channel. The second neuron
may also express the optical reporter of change in membrane
potential. Preferably, the neuron is an hiPSC-derived DRG
neuron.
[0009] Analyzing the optical signal may include detecting an effect
of the compound on the AP waveform. The method may include
detecting a change in the AP waveform and a change in the
intracellular calcium level upon exposure of the neuron to the
compound. Methods may include spatially patterning a plurality of
neurons in the cell culture on a substrate. The optical signal may
be obtained using an optical microscopy system, which may include a
digital micromirror device.
[0010] In some embodiments, the cell is caused to express an
optical actuator that initiates an action potential in response to
optical stimulation. Stimulation of the cell may include
illuminating the optical actuator.
[0011] Causing the cell to express the optical reporter may be done
by transforming the cell with a vector bearing a genetically
encoded fluorescent voltage reporter. The vector may also include a
genetically encoded optical voltage actuator, such as a light-gated
ion channel.
[0012] Observing the signal can include observing a cluster of
different cells with a microscope and using a computer to isolate
the signal generated by the optical reporter from a plurality of
signals from the different cells. Methods of the invention may
include using the computer to isolate the signal by performing an
independent component analysis or other source-separation
algorithm. The computer may be used to identify a spike train
associated with the cell using standard spike-finding algorithms
that apply steps of filtering the data and then applying a
threshold. The computer may also be used to map propagation of
electrical spikes within a single cell by means of an analytical
algorithm such as a sub-Nyquist action potential timing algorithm.
Methods may include observing and analyzing a difference between
the observed signal and the expected signal. The difference may
manifest as a decreased or increased probability of a voltage spike
in response to the stimulation of the cell relative to a control, a
change in the propagation of the signal within a cell, a change in
the transformation of the signal upon synaptic transmission, or a
change in the waveform of the action potential.
[0013] Methods may include converting a somatic cell to an
electrically active cell, incorporating into the electrically
active cell an optical activator and an optical reporter of
electrical activity, and exposing the cells to at least one
compound. The converting step may proceed by direct lineage
conversion or conversion through an iPS intermediary.
[0014] The effect of the compound may be identified by comparing an
electrical signature to a control signature obtained from a control
cell. The method may include editing the genome of a neuron to
produce control cells such that the control cells and the neuron
are isogenic but for a mutation in the neuron.
[0015] In some embodiments, the signature is obtained by observing
a cluster of cells with a microscope and using a computer to
isolate a signal generated by the optical reporter from among a
plurality of signals from the cluster of cells. An image can be
obtained of a plurality of clusters of cells using the microscope
(i.e., all in a single image using a microscope of the invention).
The computer isolates the signal by performing an independent
component analysis and identifying a spike train produced by one
single cell.
[0016] In certain aspects, the invention provides a method for
measuring cellular membrane potential by maintaining in vitro a
neuron that expresses a genetically encoded optical reporter of
change in membrane potential, receiving an optical signal from the
reporter, creating an AP waveform using the optical signal, and
analyzing the AP waveform. The neuron may also express an optically
actuated ion channel, a protein that reports a change in an
intracellular calcium level, or both. The method may include
exposing the neuron to a compound and detecting a change in the AP
waveform and a change in the intracellular calcium level upon
exposure of the neuron to the compound. The optical reporter of
change in membrane potential may include a microbial rhodopsin, and
specifically may include a QuasAr reporter derived from
Archaerhodopsin 3. The optically actuated ion channel may include a
channelrhodopsin, and may specifically include the CheRiff protein
derived from Scherffelia dubia. The protein that reports changes in
intracellular calcium levels may include a GCaMP variant or an
RCaMP variant.
[0017] A key challenge in combining multiple optical modalities
(e.g. optical stimulation, voltage imaging, Ca.sup.2+ imaging) is
to avoid optical crosstalk between the modalities. The pulses of
light used to deliver optical stimulation should not induce
fluorescence of the reporters; the light used to image the
reporters should not actuate to light-gated ion channel; and the
fluorescence of each reporter should be readily distinguished from
the fluorescence of the others. In some aspects of the invention,
this separation of modalities is achieved by selecting an actuator
and reporters with little spectral overlap. In one embodiment, the
actuator is activated by violet light, the Ca.sup.2+ reporter is
excited by yellow light and emits orange light, and the voltage
reporter is excited by red light and emits near infrared light.
[0018] In other aspects of the invention the separation of
modalities is achieved by spatially segregating one or more
components into different cells or different regions of the dish.
In one embodiment, the actuator is activated by blue light, and
cells expressing the actuator are localized to one sub-region of
the dish. Other cells express a blue light-excited Ca.sup.2+
indicator and a red light-excited voltage indicator. These reporter
cells are grown in an adjacent region of the dish, in contact with
the actuator-expressing cells. Flashes of blue light targeted to
the actuator-expressing cells initiate APs. These APs trigger APs
in the reporter-expressing cells via in-plane conduction.
[0019] The invention may further comprise genetic constructs for
ensuring mutually exclusive gene expression of the light-gated ion
channel and the fluorescent reporter protein or proteins. Mutually
exclusive gene expression ensures that ionic currents through the
light-gated ion channel do not lead to perturbations in the ion
concentration in cells whose voltage and Ca.sup.2+ levels are being
measured.
[0020] In some embodiments, the neuron is stimulated by a second
neuron that expresses a light-gated ion channel. The second neuron
may also express the optical reporter of change in membrane
potential. The neuron and the second neuron may either or both be
hiPSC-derived neuron.
[0021] The method may include exposing the neuron to a compound,
and detecting an effect of the compound on the AP waveform. The
neuron may be exposed to the compound at different concentrations.
In certain embodiments, the neuron also expresses a protein that
reports a change in an intracellular calcium level, and the method
includes determining a change in the intracellular calcium level
associated with the exposure of the neuron to the compound. Methods
of the invention can include measuring any effect on voltage or
neuronal activity. Further, Ca.sup.2+ amplitude and presence of
Ca.sup.2+ sparks could be measured.
[0022] Aspects of the invention provide a cell with a eukaryotic
genome that expresses a voltage-indicating microbial rhodopsin and
a light-gated ion channel such as an algal channel rhodopsin as
described herein. The cell may be a neuron, cardiomyocyte, or other
electrically-active cell. The microbial rhodopsin may provide an
optical reporter of membrane electrical potential such as QuasAr1
or QuasAr2. Preferably the cell also expresses a protein that
reports a change in an intracellular calcium level such as a
genetically-encoded calcium indicator (GECI). Exemplary GECIs
include GCaMP variants. The GCaMP sensors generally included a GFP,
a calcium-binding calmodulin protein (CaM), and a CaM-binding
peptide. The protein that reports a change in an intracellular
calcium level may be, for example, jRCaMP1a, jRGECO1a, or RCaMP2.
In some embodiments, the light-gated ion channel comprises a
blue-shifted actuator with an excitation maximum at a wavelength
<450 nm and the protein that reports the change in the
intracellular calcium level comprises a red-shifted calcium
indicator with an excitation maximum between 520 nm and 570 nm
inclusive. The light-gated ion channel can include a blue-shifted
actuator such as TsChR or PsChR.
[0023] In preferred embodiments, the microbial rhodopsin, the
light-gated ion channel, or both are expressed from a gene that is
integrated into the metazoan genome. The microbial rhodopsin may be
a QuasAr protein with the light-gated ion channel a
channelrhodopsin, and the cell may also include a
genetically-encoded calcium indicator such as GCaMP6f, jRCaMP1a,
jRGECO1a, or RCaMP2. In some embodiments, the light-gated ion
channel includes a violet-excited optogenetic actuator and cell
further includes a red-shifted genetically-encoded calcium
indicator (e.g., the violet-excited optogenetic actuator is a
channelrhodopsin and the red-shifted genetically-encoded calcium
indicator is jRCaMP1a, jRGECO1a, or RCaMP2.
[0024] In some aspects, the invention provides a cell culture. The
cell culture includes a first plurality of animal cells that
express an optogenetic actuator and a second plurality of animal
cells electrically contiguous with the first plurality of animal
cells. The second plurality of animal cells expresses a
genetically-encoded optical reporter of activity. The optogenetic
actuator may include a channelrhodopsin, the genetically-encoded
optical reporter of activity may include a microbial optical
reporter of membrane electrical potential, or both. At least some
of the first or second plurality of animal cells may express a
genetically encoded Ca++ indicator. The genetically encoded Ca++
indicator may be, for example, a GCaMP variant such as GCaMP6f,
jRCaMP1a, jRGECO1a, or RCaMP2.
[0025] In some embodiments, the first plurality of animal cells are
spatially segregated from yet in electrical contact with the second
plurality of animal cells. The genetically-encoded optical reporter
activity may be a microbial optical reporter of membrane electrical
potential and at least some of the second plurality of animal cells
may express a genetically encoded Ca++ indicator.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] FIG. 1 diagrams a method for diagnosing a condition.
[0027] FIG. 2 illustrates exemplary pathways for converting cells
into specific neural subtypes.
[0028] FIG. 3 gives an overview of zinc-finger nuclease mediated
editing.
[0029] FIG. 4 presents a structural model of an optical reporter of
neural activity.
[0030] FIG. 5 diagrams components of an optical imaging
apparatus.
[0031] FIG. 6 illustrates the use of pulse sequences to record
action potentials.
[0032] FIG. 7 is an image of cells from which an individual is to
be isolated.
[0033] FIG. 8 illustrates the isolation of individual cells in a
field of view.
[0034] FIG. 9 shows the spike trains associated with individual
cells.
[0035] FIG. 10 shows individual cells in a cluster color-coded
after isolation.
[0036] FIG. 11 shows optical excitation being used to induce action
potentials.
[0037] FIG. 12 shows eigenvectors from a principal component
analysis (PCA).
[0038] FIG. 13 shows a relation between cumulative variance and
eigenvector number.
[0039] FIG. 14 gives a comparison of action potential
waveforms.
[0040] FIG. 15 shows an action potential timing map.
[0041] FIG. 16 shows the accuracy of timing extracted by methods of
the invention.
[0042] FIG. 17 gives an image of fluorescence distribution of an
optical actuator.
[0043] FIG. 18 presents frames from a SNAPT movie.
[0044] FIG. 19 compares spike probability of wild-type and mutant
cells.
[0045] FIG. 20 presents a system useful for performing methods of
the invention.
[0046] FIG. 21 gives a comparison of AP waveforms.
[0047] FIG. 22 shows plots of the average waveforms from the traces
in FIG. 21.
[0048] FIG. 23 presents phototoxicity and photobleaching
measurement of QuasAr2. Cells were imaged under continuous red
laser illumination (.about.50 W/cm.sup.2) for 500 s. Expanded views
of the fluorescence recording are shown in the lower panels.
[0049] FIG. 24 graphs the average AP waveform shapes for the
beginning (blue) and end (green) of the trace in FIG. 23.
[0050] FIG. 25 presents schematic structures of optogenetic
proteins used for stimulus and detection of voltage and
intracellular Ca2+.
[0051] FIG. 26 illustrates cellular plating configurations.
[0052] FIG. 27 shows cells expressing CheRiff plated in an annular
region.
DETAILED DESCRIPTION
[0053] The invention generally relates to optical methods for
characterizing the effects of compounds on pain and other sensory
phenomena. People detect pain, itch, and other sensations via
signaling from peripheral sensory neurons which include
nociceptors, mechanoreceptors, and proprioceptors. The body
includes a cluster of nerve cell bodies in the posterior root of a
spinal nerve known as a dorsal root ganglion. The axons of these
dorsal root ganglion (DRG) neurons are known as afferents. In the
peripheral nervous system, afferents refer to the axons that relay
sensory information into the central nervous system (i.e. the brain
and the spinal cord). Unlike other neuron types, an action
potential in a DRG neuron may initiate in the distal process in the
periphery, bypass the cell body, and continue to propagate along
the proximal process until reaching the synaptic terminal in the
posterior horn of spinal cord. DRG neurons play a role in
nociception--the sensing of harm. Proton-sensing G protein-coupled
receptors are expressed by DRG sensory neurons and might play a
role in acid-induced nociception. Additionally, the nerve endings
of DRG neurons have a variety of sensory receptors that are
activated by mechanical, thermal, chemical, and noxious stimuli. In
these sensory neurons, a group of ion channels thought to be
responsible for somatosensory transduction have been identified.
Compression of the dorsal root ganglion by a mechanical stimulus
lowers the voltage threshold needed to evoke a response and causes
action potentials to be fired. Thus DRG neurons are a type of
sensory neuron with an important role in pain sensation and other
sensory phenomena. The invention provides methods of
differentiating pluripotent stem cells (PSCs) into neurons of a
specified type, such as DRG neurons, as well as methods of
reprogramming somatic cells into neurons of a specified type. The
differentiated or transformed sensory neurons are electrically
active and exhibit distinct sensory neuron morphologies. Methods of
the invention may be used to stimulate and monitor membrane
voltage, changes in intracellular calcium, or both, all via
optogenetic constructs using light for stimulus and monitoring. The
optogenetic assays can be used to identify neurons that selectively
responded to diverse ligands known to activate itch- and
pain-sensing neurons as well as compounds that produce such
effects, or minimize such effects of other compounds, on sensory
neurons. The invention provides methods for producing genetically
diverse human sensory neurons suitable for drug screening and
mechanistic studies.
[0054] The invention provides methods for the optical diagnosis of
diseases affecting electrically active cells. Methods may be used
to diagnose diseases affecting neurons or cardiomyocytes, for
example. In some embodiments, methods of the invention are used to
diagnoses a condition known to be associated with a genetic
variant, or mutation.
[0055] FIG. 1 diagrams a method 101 for studying a phenomenon
according to embodiments of the invention. This may involve
obtaining 107 a cell. Genome editing techniques (e.g., use of
transcription activator-like effector nucleases (TALENs), the
CRISPR/Cas system, zinc finger domains) may be used to create a
control cell that is isogenic but-for a variant of interest. The
cell and the control are converted into an electrically excitable
cell such as a neuron, astrocyte, or cardiomyocyte. The cell may be
converted to a specific neural subtype (e.g., motor neuron). The
cells are caused to express 113 an optical reporter of neural
activity. For example, the cell may be transformed with a vector
comprising an optogenetic reporter and the cell may also be caused
to express an optogenetic actuator (aka activator) by
transformation. Optionally, a control cell may be obtained, e.g.,
by taking another sample, by genome editing, or by other suitable
techniques. Using microscopy and analytical methods described
herein, the cells are observed and specifically, the cells'
response to stimulation 119 (e.g., optical, synaptic, chemical, or
electrical actuation) may be observed. A cell's characteristic
signature such as a neural response as revealed by a spike train
may be observed 123. The observed signature is compared to a
control signature and a difference (or match) between the observed
signature and the control signature corresponds to a positive
diagnosis of the condition.
[0056] 1. Obtaining Cell(s) from a Person Suspected of Having a
Condition
[0057] Cells are obtained from a person suspected of having the
condition. Any suitable condition such as a genetic disorder,
mental or psychiatric condition, neurodegenerative disease or
neurodevelopmental disorder, or cardiac condition may be diagnosed.
Additionally, methods of the invention and the analytical pipelines
described herein may be applied to any condition for which an
electrophysiological phenotype has been developed. Exemplary
genetic disorders suitable for analysis by a pipeline defined by
methods of the invention include Cockayne syndrome, Down Syndrome,
Dravet syndrome, familial dysautonomia, Fragile X Syndrome,
Friedreich's ataxia, Gaucher disease, hereditary spastic
paraplegias, Machado-Joseph disease (also called spinocerebellar
ataxia type 3), Phelan-McDermid syndrome (PMDS), polyglutamine
(polyQ)-encoding CAG repeats, giant axonal neuropathy,
Charcot-Marie-Tooth disease, a variety of ataxias including
spinocerebellar ataxias, spinal muscular atrophy, and Timothy
syndrome. Exemplary neurodegenerative diseases include Alzheimer's
disease, frontotemporal lobar degeneration, Huntington's disease,
multiple sclerosis, Parkinson's disease, spinal and bulbar muscular
atrophy, and amyotrophic lateral sclerosis. Exemplary mental and
psychiatric conditions include schizophrenia. Exemplary
neurodevelopmental disorders include Rett syndrome. While discussed
here in terms of neuronal disorders, it will be appreciated that
the methods described herein may be extended to the diagnosis of
cardiac disorders and cells may be converted to cardiomyocytes.
Exemplary cardiac conditions include long-QT syndromes,
hypertrophic cardiomyopathies, and dilated cardiomyopathies.
Moreover, electrophysiological phenotypes for a variety of
conditions have been developed and reported in the literature.
[0058] Cockayne syndrome is a genetic disorder caused by mutations
in the ERCC6 and ERCC8 genes and characterized by growth failure,
impaired development of the nervous system, photosensitivity, and
premature aging. Cockayne syndrome is discussed in Andrade et al.,
2012, Evidence for premature aging due to oxidative stress in iPSCs
from Cockayne syndrome, Hum Mol Genet 21:3825-3834, the contents of
which are incorporated by reference.
[0059] Down syndrome is a genetic disorder caused by the presence
of all or part of a third copy of chromosome 21 and associated with
delayed growth, characteristic facial features, and intellectual
disability. Down Syndrome is discussed in Shi et al., 2012, A human
stem cell model of early Alzheimer's disease pathology in Down
syndrome, Sci Transl Med 4 (124):124ra129, the contents of which
are incorporated by reference.
[0060] Dravet syndrome, also known as Severe Myoclonic Epilepsy of
Infancy (SMEI), is a form of intractable epilepsy that begins in
infancy and is often associated with mutations in the SCN1A gene or
certain other genes such as SCN9A, SCN2B, PCDH19 or GABRG2. Dravet
syndrome is discussed in Higurashi et al., 2013, A human Dravet
syndrome model from patient induced pluripotent stem cells, Mol
Brain 6:19, the contents of which are incorporated by
reference.
[0061] Familial dysautonomia is a genetic disorder of the autonomic
nervous system caused by mutations in the IKBKAP gene and that
affects the development and survival of sensory, sympathetic and
some parasympathetic neurons in the autonomic and sensory nervous
system resulting in variable symptoms including: insensitivity to
pain, inability to produce tears, poor growth, and labile blood
pressure. Familial dysautonomia is discussed in Lee et al., 2009,
Modelling pathogenesis and treatment of familial dysautonomia using
patient-specific iPSCs, Nature 461:402-406, the contents of which
are incorporated by reference.
[0062] Fragile X syndrome is a genetic condition caused by
mutations in the FMR1 gene and that causes a range of developmental
problems including learning disabilities and cognitive impairment.
Fragile X Syndrome is discussed in Liu et al., 2012, Signaling
defects in iPSC-derived fragile X premutation neurons, Hum Mol
Genet 21:3795-3805, the contents of which are incorporated by
reference.
[0063] Friedreich ataxia is an autosomal recessive ataxia resulting
from a mutation of a gene locus on chromosome 9. The ataxia of
Friedreich's ataxia results from the degeneration of nerve tissue
in the spinal cord, in particular sensory neurons essential
(through connections with the cerebellum) for directing muscle
movement of the arms and legs. The spinal cord becomes thinner and
nerve cells lose some of their myelin sheath. Friedreich's ataxia
is discussed in Ku et al., 2010, Friedreich's ataxia induced
pluripotent stem cells model intergenerational GAA.TTC triplet
repeat instability, Cell Stem Cell 7 (5):631-7; Du et al., 2012,
Role of mismatch repair enzymes in GAA.TTC triplet-repeat expansion
in Friedreich ataxia induced pluripotent stem cells, J Biol Chem
287 (35):29861-29872; and Hick et al., 2013, Neurons and
cardiomyocytes derived from induced pluripotent stem cells as a
model for mitochondrial defects in Friedreich's ataxia, Dis Model
Mech 6 (3):608-21, the contents of each of which are incorporated
by reference.
[0064] Gaucher's disease is a genetic disease caused by a recessive
mutation in a gene located on chromosome 1 and in which lipids
accumulate in the body. Gaucher disease is discussed in Mazzulli et
al., 2011, Gaucher disease glucocerebrosidase and .alpha.-synuclein
form a bidirectional pathogenic loop in synucleinopathies, Cell 146
(1):37-52, the contents of which are incorporated by reference.
[0065] Hereditary Spastic Paraplegia (HSP)--also called Familial
Spastic Paraplegias, French Settlement Disease, or
Strumpell-Lorrain disease--refers to a group of inherited diseases
characterized by axonal degeneration and dysfunction resulting in
stiffness and contraction (spasticity) in the lower limbs.
Hereditary spastic paraplegias is discussed in Denton et al., 2014,
Loss of spastin function results in disease-specific axonal defects
in human pluripotent stem cell-based models of hereditary spastic
paraplegia, Stem Cells 32 (2):414-23, the contents of which are
incorporated by reference.
[0066] Spinocerebellar ataxia type 3 (SCA3), also known as
Machado-Joseph disease, is a neurodegenerative disease, an
autosomal dominantly inherited ataxia characterized by the slow
degeneration of the hindbrain. Machado-Joseph disease (also called
spinocerebellar ataxia type 3) is discussed in Koch et al., 2011,
Excitation-induced ataxin-3 aggregation in neurons from patients
with Machado-Joseph disease, Nature 480 (7378):543-546, the
contents of which are incorporated by reference.
[0067] Phelan-McDermid Syndrome (PMDS) is a progressive
neurodevelopmental disorder resulting from mutations in or
deletions of the neural protein, Shank3 and characterized by
developmental delay, impaired speech, and autism. Phelan-McDermid
syndrome (PMDS) is discussed in Shcheglovitov et al., 2013, SHANK3
and IGF1 restore synaptic deficits in neurons from 22q13 deletion
syndrome patients, Nature 503 (7475):267-71, the contents of which
are incorporated by reference.
[0068] Trinucleotide repeat disorders are characterized by
polyglutamine (polyQ)-encoding CAG repeats. Trinucleotide repeat
disorders refer to a set of genetic disorders caused by
trinucleotide repeat expansion, which disorders include
dentatorubropallidoluysian atrophy, Huntington's disease,
spinobulbar muscular atrophy, Spinocerebellar ataxia Type 1,
Spinocerebellar ataxia Type 2, Spinocerebellar ataxia Type 3 or
Machado-Joseph disease, Spinocerebellar ataxia Type 6,
Spinocerebellar ataxia Type 7, and Spinocerebellar ataxia Type 17,
as well as a variety of other ataxias. Trinucleotide repeat
disorders are discussed in HD iPSC Consortium, 2012, Induced
pluripotent stem cells from patients with Huntington's disease show
CAG-repeat-expansion-associated phenotypes. Cell Stem Cell 11
(2):264-278, the contents of which are incorporated by
reference.
[0069] Giant axonal neuropathy is a neurological disorder that
causes disorganization of neurofilaments, which form a structural
framework to define the shape and size of neurons. Giant axonal
neuropathy results from mutations in the GAN gene, which codes for
the protein gigaxonin. See Mahammad et al., 2013, Giant axonal
neuropathy-associated gigaxonin mutations impair intermediate
filament protein degredation, J Clin Invest 123 (5):1964-75.
[0070] Charcot Marie Tooth disease, also known as hereditary motor
and sensory neuropathy (HMSN) and peroneal muscular atrophy (PMA),
refers to several inherited disorders of the peripheral nervous
system characterized by progressive loss of muscle and sensation.
See, e.g., Harel and Lupski, 2014, Charcot Marie Tooth disease and
pathways to molecular based therapies, Clin Genet DOI:
10.1111/cge.12393.
[0071] Spinal muscular atrophy (SMA) is genetic disease caused by
mutations in the SMN1 gene, which encodes the survival of motor
neuron protein (SMN), the diminished abundance of which neurons
results in death of neuronal cells in the spinal cord and
system-wide atrophy. Spinal muscular atrophy is discussed in Ebert
et al., 2009, Induced pluripotent stem cells from a spinal muscular
atrophy patient, Nature 457 (7227):277-80; Sareen et al., 2012,
Inhibition of apoptosis blocks human motor neuron cell death in a
stem cell model of spinal muscular atrophy. PLoS One 7 (6):e39113;
and Corti et al., 2012, Genetic correction of human induced
pluripotent stem cells from patients with spinal muscular atrophy,
Sci Transl Med 4 (165):165ra162, the contents of each of which are
incorporated by reference.
[0072] Timothy syndrome is a genetic disorder arising from a
mutation in the Ca(v)1.2 Calcium Channel gene called CACNA1C and
characterized by a spectrum of problems that include an abnormally
prolonged cardiac "repolarization" time (long QT interval) and
other neurological and developmental defects, including heart
QT-prolongation, heart arrhythmias, structural heart defects,
syndactyly and autism spectrum disorders. Timothy syndrome is
discussed in Krey et al., 2013, Timothy syndrome is associated with
activity-dependent dendritic retraction in rodent and human
neurons, Nat Neurosci 16 (2):201-9, the contents of which are
incorporated by reference.
[0073] Mental and psychiatric disorders such as schizophrenia and
autism may involve cellular and molecular defects amenable to study
via stem cell models and may be caused by or associated with
certain genetic components that can be isolated using methods
herein. Schizophrenia is discussed in Brennand et al., 2011,
Modelling schizophrenia using human induced pluripotent stem cells,
Nature 473 (7346):221-225; and Chiang et al., 2011,
Integration-free induced pluripotent stem cells derived from
schizophrenia patients with a DISC1 mutation, Molecular Psych
16:358-360, the contents of each of which are incorporated by
reference.
[0074] Alzheimer's disease is a neurodegenerative disease of
uncertain cause (although mutations in certain genes have been
linked to the disorder) and is one of the most common forms of
dementia. Alzheimer's disease is discussed in Israel et al., 2012,
Probing sporadic and familial Alzheimer's disease using induced
pluripotent stem cells, Nature 482 (7384):216-20; Muratore et al.,
2014, The familial Alzheimer's disease APPV717I mutation alters APP
processing and tau expression in iPSC-derived neurons, Human
Molecular Genetics, in press; Kondo et al., 2013, Modeling
Alzheimer's disease with iPSCs reveals stress phenotypes associated
with intracellular Abeta and differential drug responsiveness, Cell
Stem Cell 12 (4):487-496; and Shi et al., 2012, A human stem cell
model of early Alzheimer's disease pathology in Down syndrome, Sci
Transl Med 4 (124):124ra129, the contents of each of which are
incorporated by reference.
[0075] Frontotemporal lobar degeneration (FTLD) is the name for a
group of clinically, pathologically and genetically heterogeneous
disorders including frontotemporal dementia (which subdivides to
include behavioral-variant frontotemporal dementia (bvFTLD);
semantic dementia (SD); and progressive nonfluent aphasia (PNFA))
associated with atrophy in the frontal lobe and temporal lobe of
the brain. Frontotemporal lobar degeneration is discussed in
Almeida et al, 2013, Modeling key pathological features of
frontotemporal dementia with C9ORF72 repeat expansion in
iPSC-derived human neurons, Acta Neuropathol 126 (3):385-399;
Almeida et al., 2012, Induced pluripotent stem cell models of
progranulin-deficient frontotemporal dementia uncover specific
reversible neuronal defects, Cell Rep 2 (4):789-798; and in Fong et
al., 2013, Genetic correction of tauopathy phenotypes in neurons
derived from human induced pluripotent stem cells, Stem Cell
Reports 1 (3):1-9, the contents of each of which are incorporated
by reference.
[0076] Huntington's disease is an inherited disease that causes the
progressive degeneration of nerve cells in the brain and is caused
by an autosomal dominant mutation in either of an individual's two
copies of a gene called Huntingtin (HTT) located on the short arm
of chromosome 4. Huntington's disease is discussed in HD iPSC
Consortium, 2012, Induced pluripotent stem cells from patients with
Huntington's disease show CAG-repeat-expansion-associated
phenotypes. Cell Stem Cell 11 (2):264-278; An et al., 2012, Genetic
correction of Huntington's disease phenotypes in induced
pluripotent stem cells, Cell Stem Cell 11 (2):253-263; and Camnasio
et al., 2012, The first reported generation of several induced
pluripotent stem cell lines from homozygous and heterozygous
Huntington's disease patients demonstrates mutation related
enhanced lysosomal activity, Neurobiol Dis 46 (1):41-51, the
contents of each of which are incorporated by reference.
[0077] Multiple sclerosis is a neurodegenerative disease in which
the insulating covers of nerve cells in the brain and spinal cord
are damaged. Multiple sclerosis is discussed in Song et al., 2012,
Neural differentiation of patient specific iPS cells as a novel
approach to study the pathophysiology of multiple sclerosis, Stem
Cell Res 8 (2):259-73, the contents of which are incorporated by
reference.
[0078] Parkinson's disease is a neurodegenerative disorder of the
central nervous system that involves the death of
dopamine-generating cells in the substantia nigra in the midbrain.
Parkinson's disease is discussed in Cooper et al., 2012,
Pharmacological rescue of mitochondrial deficits in iPSC-derived
neural cells from patients with familial Parkinson's disease, Sci
Transl Med 4 (141):141ra90; Chung et al., 2013, Identification and
rescue of .alpha.-synuclein toxicity in Parkinson patient-derived
neurons, Science 342 (6161):983-7; Seibler et al., 2011,
Mitochondrial Parkin recruitment is impaired in neurons derived
from mutant PINK1 induced pluripotent stem cells, J Neurosci 31
(16):5970-6; Sanchez-Danes et al., 2012, Disease-specific
phenotypes in dopamine neurons from human iPS-based models of
genetic and sporadic Parkinson's disease, EMBO Mol Med 4
(5):380-395; Sanders et al., 2013, LRRK2 mutations cause
mitochondrial DNA damage in iPSC-derived neural cells from
Parkinson's disease patients: reversal by gene correction.
Neurobiol Dis 62:381-6; and Reinhardt et al., 2013, Genetic
correction of a LRRK2 mutation in human iPSCs links parkinsonian
neurodegeneration to ERK-dependent changes in gene expression, Cell
Stem Cell 12 (3):354-367; LRRK2 mutant iPSC-derived DA neurons
demonstrate increased susceptibility to oxidative stress, the
contents of each of which are incorporated by reference.
[0079] Spinal and bulbar muscular atrophy (SBMA), also known as
spinobulbar muscular atrophy, bulbo-spinal atrophy, X-linked
bulbospinal neuropathy (XBSN), X-linked spinal muscular atrophy
type 1 (SMAX1), and Kennedy's disease (KD)--is a neurodegenerative
disease associated with mutation of the androgen receptor (AR) gene
and that results in muscle cramps and progressive weakness due to
degeneration of motor neurons in the brain stem and spinal cord.
Spinal and bulbar muscular atrophy is discussed in Nihei et al.,
2013, Enhanced aggregation of androgen receptor in induced
pluripotent stem cell-derived neurons from spinal and bulbar
muscular atrophy, J Biol Chem 288 (12):8043-52, the contents of
which are incorporated by reference.
[0080] Rett syndrome is a neurodevelopmental disorder generally
caused by a mutation in the methyl CpG binding protein 2, or MECP2,
gene and which is characterized by normal early growth and
development followed by a slowing of development, loss of
purposeful use of the hands, distinctive hand movements, slowed
brain and head growth, problems with walking, seizures, and
intellectual disability. Rett syndrome is discussed in Marchetto et
al., 2010, A model for neural development and treatment of Rett
syndrome using human induced pluripotent stem cells, Cell, 143
(4):527-39 and in Ananiev et al., 2011, Isogenic pairs of wild type
and mutant induced pluripotent stem cell (iPSC) lines from Rett
syndrome patients as in vitro disease model, PLoS One 6(9):e25255,
the contents of each of which are incorporated by reference.
[0081] In one illustrative example, the condition is amyotrophic
lateral sclerosis. Amyotrophic lateral sclerosis (ALS), often
referred to as "Lou Gehrig's Disease," is a neurodegenerative
disease associated with the progressive degeneration and death of
the motor neurons and a resultant loss of muscle control or
paralysis. Amyotrophic lateral sclerosis is discussed in Kiskinis
et al., 2014, Pathways disrupted in human ALS motor neurons
identified through genetic correction of mutant SOD1, Cell Stem
Cell (epub); Wainger et al., 2014, Intrinsic membrane
hyperexcitability of amyotrophic lateral sclerosis patient-derived
motor neurons, Cell Reports 7 (1):1-11; Donnelly et al., 2013, RNA
toxicity from the ALS/FTD C9orf72 expansion is mitigated by
antisense intervention, Neuron 80 (2):415-28; Alami, 2014,
Microtubule-dependent transport of TDP-43 mRNA granules in neurons
is impaired by ALS-causing mutations, Neuron 81 (3):536-543;
Donnelly et al., 2013, RNA toxicity from the ALS/FTD C9ORF72
expansion is mitigated by antisense intervention, Neuron 80
(2):415-428; Bilican et al, 2012, Mutant induced pluripotent stem
cell lines recapitulate aspects of TDP-43 proteinopathies and
reveal cell-specific vulnerability, PNAS 109 (15):5803-5808; Egawa
et al., 2012, Drug screening for ALS using patient-specific induced
pluripotent stem cells, Sci Transl Med 4 (145):145ra104; and in
Yang et al., 2013, A small molecule screen in stem-cell-derived
motor neurons identifies a kinase inhibitor as a candidate
therapeutic for ALS, Cell Stem Cell 12 (6):713-726, the contents of
each of which are incorporated by reference.
[0082] In one illustrative example, fibroblasts may be taken from a
patient known or suspected to have a mutation such as a mutation in
SOD1. Any suitable cell may be obtained and any suitable method of
obtaining a sample may be used. In some embodiments, a dermal
biopsy is performed to obtain dermal fibroblasts. The patient's
skin may be cleaned and given an injection of local anesthetic.
Once the skin is completely anesthetized, a sterile 3 mm punch is
used. The clinician may apply pressure and use a "drilling" motion
until the punch has pierced the epidermis. The punch will core a 3
mm cylinder of skin. The clinician may use forceps to lift the
dermis of the cored skin and a scalpel to cut the core free. The
biopsy sample may be transferred to a sterile BME fibroblast medium
after optional washing with PBS and evaporation of the PBS. The
biopsy site on the patient is dressed (e.g., with an adhesive
bandage). Suitable methods and devices for obtaining the cells are
discussed in U.S. Pat. No. 8,603,809; U.S. Pat. No. 8,403,160; U.S.
Pat. No. 5,591,444; U.S. Pub. 2012/0264623; and U.S. Pub.
2012/0214236, the contents of each of which are incorporated by
reference. Any tissue culture technique that is suitable for the
obtaining and propagating biopsy specimens may be used such as
those discussed in Freshney, Ed., 1986, Animal Cell Culture: A
Practical Approach, IRL Press, Oxford England; and Freshney, Ed.,
1987, Culture of Animal Cells: A Manual of Basic Techniques, Alan
R. Liss & Co., New York, both incorporated by reference.
[0083] 2. Converting Cell(s) into Neurons, Cardiomyocytes, or
Specific Neural Sub-types
[0084] Obtained cells may be converted into any electrically
excitable cells such as neurons, specific neuronal subtypes,
astrocytes or other glia, cardiomyocytes, or immune cells.
Additionally, cells may be converted and grown into co-cultures of
multiple cell types (e.g. neurons+glia, neurons+cardiomyocytes,
neurons+immune cells).
[0085] FIG. 2 illustrates exemplary pathways for converting cells
into specific neural subtypes. A cell may be converted to a
specific neural subtype (e.g., motor neuron). Suitable methods and
pathways for the conversion of cells include pathway 209,
conversion from somatic cells to induced pluripotent stem cells
(iPSCs) and conversion of iPSCs to specific cell types, or pathways
211 direct conversion of cells in specific cell types.
[0086] 2a. Conversion of Cells to iPSs and Conversion of iPSs to
Specific Cell Types
[0087] Following pathways 209, somatic cells may be reprogrammed
into induced pluripotent stem cells (iPSCs) using known methods
such as the use of defined transcription factors. The iPSCs are
characterized by their ability to proliferate indefinitely in
culture while preserving their developmental potential to
differentiate into derivatives of all three embryonic germ layers.
In certain embodiments, fibroblasts are converted to iPSC by
methods such as those discussed in Takahashi and Yamanaka, 2006,
Induction of pluripotent stem cells from mouse embryonic and adult
fibroblast cultures by defined factors Cell 126:663-676.; and
Takahashi, et al., 2007, Induction of pluripotent stem cells from
adult human fibroblasts by defined factors, Cell 131:861-872.
[0088] Induction of pluripotent stem cells from adult fibroblasts
can be done by methods that include introducing four factors,
Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions.
Human dermal fibroblasts (HDF) are obtained. A retroviruses
containing human Oct3/4, Sox2, Klf4, and c-Myc is introduced into
the HDF. Six days after transduction, the cells are harvested by
trypsinization and plated onto mitomycin C-treated SNL feeder
cells. See, e.g., McMahon and Bradley, 1990, Cell 62:1073-1085.
About one day later, the medium (DMEM containing 10% FBS) is
replaced with a primate ES cell culture medium supplemented with 4
ng/mL basic fibroblast growth factor (bFGF). See Takahashi, et al.,
2007, Cell 131:861. Later, hES cell-like colonies are picked and
mechanically disaggregated into small clumps without enzymatic
digestion. Each cell should exhibit morphology similar to that of
human ES cells, characterized by large nuclei and scant cytoplasm.
The cells after transduction of HDF are human iPS cells. DNA
fingerprinting, sequencing, or other such assays may be performed
to verify that the iPS cell lines are genetically matched to the
donor.
[0089] These iPS cells can then be differentiated into specific
neuronal subtypes. Pluripotent cells such as iPS cells are by
definition capable of differentiating into cell types
characteristic of different embryonic germ layers. A property of
both embryonic stem cells human iPS cells is their ability, when
plated in suspension culture, to form embryoid bodies (EBs). EBs
formed from iPS cells are treated with two small molecules: an
agonist of the sonic hedgehog (SHH) signaling pathway and retinoic
acid (RA). For more detail, see the methods described in Dimos et
al., 2008, Induced pluripotent stem cells generated from patients
with ALS can be differentiated into motor neurons, Science 321
(5893):1218-21; Amoroso et al., 2013, Accelerated high-yield
generation of limb-innervating motor neurons from human stem cells,
J Neurosci 33 (2):574-86; and Boulting et al., 2011, A functionally
characterized test set of human induced pluripotent stem cells, Nat
Biotech 29 (3):279-286.
[0090] When the differentiated EBs are allowed to adhere to a
laminin-coated surface, neuron-like outgrowths are observed and a
result is differentiation into specific neuronal subtypes.
Additional relevant discussion may be found in Davis-Dusenbery et
al., 2014, How to make spinal motor neurons, Development 141
(3):491-501; Sandoe and Eggan, 2013, Opportunities and challenges
of pluripotent stem cell neurodegenerative disease models, Nat
Neuroscience 16 (7):780-9; and Han et al., 2011, Constructing and
deconstructing stem cell models of neurological disease, Neuron 70
(4):626-44.
[0091] 2b. Direct Conversion of Cells in Specific Cell Types
[0092] By pathway 211, human somatic cells are obtained and direct
lineage conversion of the somatic cells into motor neurons may be
performed. Conversion may include the use of lineage-specific
transcription factors to induce the conversion of specific cell
types from unrelated somatic cells. See, e.g., Davis-Dusenbery et
al., 2014, How to make spinal motor neurons, Development 141:491;
Graf, 2011, Historical origins of transdifferentiation and
reprogramming, Cell Stem Cell 9:504-516. It has been shown that a
set of neural lineage-specific transcription factors, or BAM
factors, causes the conversion of fibroblasts into induced neuronal
(iN) cells. Vierbuchen 2010 Nature 463:1035. MicroRNAs and
additional pro-neuronal factors, including NeuroD1, may cooperate
with or replace the BAM factors during conversion of human
fibroblasts into neurons. See, for example, Ambasudhan et al.,
2011, Direct reprogramming of adult human fibroblasts to functional
neurons under defined conditions, Cell Stem Cell 9:113-118; Pang et
al., 2011, Induction of human neuronal cells by defined
transcription factors, Nature 476:220-223; also see Yoo et al.,
2011, MicroRNA mediated conversion of human fibroblasts to neurons,
Nature 476:228-231.
[0093] 2c. Maintenance of Differentiated Cells
[0094] Differentiated cells such as motor neurons may be
dissociated and plated onto glass coverslips coated with
poly-d-lysine and laminin. Motor neurons may be fed with a suitable
medium such as a neurobasal medium supplemented with N2, B27, GDNF,
BDNF, and CTNF. Cells may be maintained in a suitable medium such
as an N2 medium (DMEM/F 12 [1:1] supplemented with laminin [1
.mu.g/mL; Invitrogen], FGF-2 [10 ng/ml; R&D Systems,
Minneapolis, Minn.], and N2 supplement [1%; Invitrogen]), further
supplemented with GDNF, BDNF, and CNTF, all at 10 ng/ml. Suitable
media are described in Son et al., 2011, Conversion of mouse and
human fibroblasts into functional spinal motor neurons, Cell Stem
Cell 9:205-218; Vierbuchen et al., 2010, Direct conversion of
fibroblasts to functional neurons by defined factors, Nature4
63:1035-1041; Kuo et al., 2003, Differentiation of monkey embryonic
stem cells into neural lineages, Biology of Reproduction
68:1727-1735; and Wernig et al., 2002, Tau EGFP embryonic stem
cells: an efficient tool for neuronal lineage selection and
transplantation. J Neuroscience Res 69:918-24, each incorporated by
reference.
[0095] 3. Control Cell Line or Signature
[0096] Methods of the invention include causing the cell to express
an optical reporter, observing a signature generated by the optical
reporter, and comparing the observed signature to a control
signature. The control signature may be obtained by obtaining a
control cell that is also of the specific neural subtype and is
genetically and phenotypically similar to the test cells. In
certain embodiments--where, for example, a patient has a known
mutation or allele at a certain locus--genetic editing is performed
to generate a control cell line that but for the known mutation is
isogenic with the test cell line. For example, where a patient is
known to have the SOD1A4V mutation, genetic editing techniques can
introduce a SOD1V4A mutation into the cell line to create a control
cell line with a wild-type genotype and phenotype. Genetic or
genome editing techniques may proceed via zinc-finger domain
methods, transcription activator-like effector nucleases (TALENs),
or clustered regularly interspaced short palindromic repeat
(CRISPR) nucleases.
[0097] Genome editing techniques (e.g., use of zinc finger domains)
may be used to create a control cell that is isogenic but-for a
variant of interest. In certain embodiments, genome editing
techniques are applied to the iPS cells. For example, a second
corrected line (SOD1V4A) may be generated using zinc finger domains
resulting in two otherwise isogenic lines. After that, diseased and
corrected iPS cells may be differentiated into motor neurons using
embryoid bodies according to the methods described above.
[0098] Genomic editing may be performed by any suitable method
known in the art. For example, the chromosomal sequence encoding
the target gene of interest may be edited using TALENs technology.
TALENS are artificial restriction enzymes generated by fusing a TAL
effector DNA binding domain to a DNA cleavage domain. In some
embodiments, genome editing is performed using CRISPR technology.
TALENs and CRISPR methods provide one-to-one relationship to the
target sites, i.e. one unit of the tandem repeat in the TALE domain
recognizes one nucleotide in the target site, and the crRNA or gRNA
of CRISPR/Cas system hybridizes to the complementary sequence in
the DNA target. Methods can include using a pair of TALENs or a
Cas9 protein with one gRNA to generate double-strand breaks in the
target. The breaks are then repaired via non-homologous end-joining
or homologous recombination (HR).
[0099] TALENs uses a nonspecific DNA-cleaving nuclease fused to a
DNA-binding domain that can be to target essentially any sequence.
For TALEN technology, target sites are identified and expression
vectors are made. See Liu et al, 2012, Efficient and specific
modifications of the Drosophila genome by means of an easy TALEN
strategy, J. Genet. Genomics 39:209-215. The linearized expression
vectors (e.g., by Not1) and used as template for mRNA synthesis. A
commercially available kit may be use such as the mMESSAGE mMACHINE
SP6 transcription kit from Life Technologies (Carlsbad, Calif.).
See Joung & Sander, 2013, TALENs: a wideliy applicable
technology for targeted genome editing, Nat Rev Mol Cell Bio
14:49-55.
[0100] CRISPR methodologies employ a nuclease, CRISPR-associated
(Cas9), that complexes with small RNAs as guides (gRNAs) to cleave
DNA in a sequence-specific manner upstream of the protospacer
adjacent motif (PAM) in any genomic location. CRISPR may use
separate guide RNAs known as the crRNA and tracrRNA. These two
separate RNAs have been combined into a single RNA to enable
site-specific mammalian genome cutting through the design of a
short guide RNA. Cas9 and guide RNA (gRNA) may be synthesized by
known methods. Cas9/guide-RNA (gRNA) uses a non-specific DNA
cleavage protein Cas9, and an RNA oligo to hybridize to target and
recruit the Cas9/gRNA complex. See Chang et al., 2013, Genome
editing with RNA-guided Cas9 nuclease in zebrafish embryos, Cell
Res 23:465-472; Hwang et al., 2013, Efficient genome editing in
zebrafish using a CRISPR-Cas system, Nat. Biotechnol 31:227-229;
Xiao et al., 2013, Chromosomal deletions and inversions mediated by
TALENS and CRISPR/Cas in zebrafish, Nucl Acids Res 1-11.
[0101] In certain embodiments, genome editing is performed using
zinc finger nuclease-mediated process as described, for example, in
U.S. Pub. 2011/0023144 to Weinstein.
[0102] FIG. 3 gives an overview of a method 301 for zing-finger
nuclease mediated editing. Briefly, the method includes introducing
into the iPS cell at least one RNA molecule encoding a targeted
zinc finger nuclease 305 and, optionally, at least one accessory
polynucleotide. The cell includes target sequence 311. The cell is
incubated to allow expression of the zinc finger nuclease 305,
wherein a double-stranded break 317 is introduced into the targeted
chromosomal sequence 311 by the zinc finger nuclease 305. In some
embodiments, a donor polynucleotide or exchange polynucleotide 321
is introduced. Target DNA 311 along with exchange polynucleotide
321 may be repaired by an error-prone non-homologous end-joining
DNA repair process or a homology-directed DNA repair process. This
may be used to produce a control line with a control genome 315
that is isogenic to original genome 311 but for a changed site. The
genomic editing may be used to establish a control line (e.g.,
where the patient is known to have a certain mutation, the zinc
finger process may revert the genomic DNA to wild type) or to
introduce a mutation (e.g., non-sense, missense, or frameshift) or
to affect transcription or expression.
[0103] Typically, a zinc finger nuclease comprises a DNA binding
domain (i.e., zinc finger) and a cleavage domain (i.e., nuclease)
and this gene may be introduced as mRNA (e.g., 5' capped,
polyadenylated, or both). Zinc finger binding domains may be
engineered to recognize and bind to any nucleic acid sequence of
choice. See, for example, Beerli & Barbas, 2002, Engineering
polydactyl zinc-finger transcription factors, Nat. Biotechnol,
20:135-141; Pabo et al., 2001, Design and selection of novel
Cys2His2 zinc finger proteins, Ann. Rev. Biochem 70:313-340; Isalan
et al., 2001, A rapid generally applicable method to engineer zinc
fingers illustrated by targeting the HIV-1 promoter, Nat.
Biotechnol 19:656-660; and Santiago et al., 2008, Targeted gene
knockout in mammalian cells by using engineered zinc-finger
nucleases, PNAS 105:5809-5814. An engineered zinc finger binding
domain may have a novel binding specificity compared to a
naturally-occurring zinc finger protein. Engineering methods
include, but are not limited to, rational design and various types
of selection. A zinc finger binding domain may be designed to
recognize a target DNA sequence via zinc finger recognition regions
(i.e., zinc fingers). See for example, U.S. Pat. Nos. 6,607,882;
6,534,261 and 6,453,242, incorporated by reference. Exemplary
methods of selecting a zinc finger recognition region may include
phage display and two-hybrid systems, and are disclosed in U.S.
Pat. No. 5,789,538; U.S. Pat. No. 5,925,523; U.S. Pat. No.
6,007,988; U.S. Pat. No. 6,013,453; U.S. Pat. No. 6,410,248; U.S.
Pat. No. 6,140,466; U.S. Pat. No. 6,200,759; and U.S. Pat. No.
6,242,568, each of which is incorporated by reference.
[0104] Zinc finger binding domains and methods for design and
construction of fusion proteins (and polynucleotides encoding same)
are known to those of skill in the art and are described in detail
in U.S. Pub. 2005/0064474 and U.S. Pub. 2006/0188987, each
incorporated by reference. Zinc finger recognition regions,
multi-fingered zinc finger proteins, or combinations thereof may be
linked together using suitable linker sequences, including for
example, linkers of five or more amino acids in length. See, U.S.
Pat. Nos. 6,479,626; 6,903,185; and 7,153,949, incorporated by
reference.
[0105] The zinc finger nuclease may use a nuclear localization
sequence (NLS). A NLS is an amino acid sequence which facilitates
targeting the zinc finger nuclease protein into the nucleus to
introduce a double stranded break at the target sequence in the
chromosome. Nuclear localization signals are known in the art. See,
for example, Makkerh, 1996, Comparative mutagenesis of nuclear
localization signals reveals the importance of neutral and acidic
amino acids, Current Biology 6:1025-1027.
[0106] A zinc finger nuclease also includes a cleavage domain. The
cleavage domain portion of the zinc finger nucleases may be
obtained from any suitable endonuclease or exonuclease such as
restriction endonucleases and homing endonucleases. See, for
example, Belfort & Roberts, 1997, Homing endonucleases: keeping
the house in order, Nucleic Acids Res 25 (17):3379-3388. A cleavage
domain may be derived from an enzyme that requires dimerization for
cleavage activity. Two zinc finger nucleases may be required for
cleavage, as each nuclease comprises a monomer of the active enzyme
dimer. Alternatively, a single zinc finger nuclease may comprise
both monomers to create an active enzyme dimer. Restriction
endonucleases present may be capable of sequence-specific binding
and cleavage of DNA at or near the site of binding. Certain
restriction enzymes (e.g., Type IIS) cleave DNA at sites removed
from the recognition site and have separable binding and cleavage
domains. For example, the Type IIS enzyme FokI, active as a dimer,
catalyzes double-stranded cleavage of DNA, at 9 nucleotides from
its recognition site on one strand and 13 nucleotides from its
recognition site on the other. The FokI enzyme used in a zinc
finger nuclease may be considered a cleavage monomer. Thus, for
targeted double-stranded cleavage using a FokI cleavage domain, two
zinc finger nucleases, each comprising a FokI cleavage monomer, may
be used to reconstitute an active enzyme dimer. See Wah, et al.,
1998, Structure of FokI has implications for DNA cleavage, PNAS
95:10564-10569; U.S. Pat. Nos. 5,356,802; 5,436,150 and 5,487,994,
each incorporated by reference. In certain embodiments, the
cleavage domain may comprise one or more engineered cleavage
monomers that minimize or prevent homo-dimerization, as described,
for example, in U.S. Patent Publication Nos. 2005/0064474,
2006/0188987, and 2008/0131962, each incorporated by reference.
[0107] Genomic editing by the zinc finger nuclease-mediated process
may include introducing at least one donor polynucleotide
comprising a sequence into the cell. A donor polynucleotide
preferably includes the sequence to be introduced flanked by an
upstream and downstream sequence that share sequence similarity
with either side of the site of integration in the chromosome. The
upstream and downstream sequences in the donor polynucleotide are
selected to promote recombination between the chromosomal sequence
of interest and the donor polynucleotide. Typically, the donor
polynucleotide will be DNA. The donor polynucleotide may be a DNA
plasmid, a bacterial artificial chromosome (BAC), a yeast
artificial chromosome (YAC), a viral vector, a linear piece of DNA,
a PCR fragment, a naked nucleic acid, and may employ a delivery
vehicle such as a liposome. The sequence of the donor
polynucleotide may include exons, introns, regulatory sequences, or
combinations thereof.
[0108] The double stranded break is repaired via homologous
recombination with the donor polynucleotide such that the desired
sequence is integrated into the chromosome.
[0109] In some embodiments, methods for genome editing include
introducing into the cell an exchange polynucleotide (typically
DNA) with a sequence that is substantially identical to the
chromosomal sequence at the site of cleavage and which further
comprises at least one specific nucleotide change. Where the cells
have been obtained from a subject suspected to have a
neurodegenerative disease, a method such as TALENs, CRISPRs, or
zinc fingers may be used to make a control cell line. For example,
if the cell line is SOD1A4V, methods may be used to produce a cell
line that is isogenic but SOD1V4A. While any such technology may be
used, the following illustrates genome editing via zinc finger
nucleases.
[0110] In general, with zinc-finger nucleases, the sequence of the
exchange polynucleotide will share enough sequence identity with
the chromosomal sequence such that the two sequences may be
exchanged by homologous recombination. The sequence in the exchange
polynucleotide comprises at least one specific nucleotide change
with respect to the sequence of the corresponding chromosomal
sequence. For example, one nucleotide in a specific codon may be
changed to another nucleotide such that the codon codes for a
different amino acid. In one embodiment, the sequence in the
exchange polynucleotide may comprise one specific nucleotide change
such that the encoded protein comprises one amino acid change.
[0111] In the zinc finger nuclease-mediated process for modifying a
chromosomal sequence, a double stranded break introduced into the
chromosomal sequence by the zinc finger nuclease is repaired, via
homologous recombination with the exchange polynucleotide, such
that the sequence in the exchange polynucleotide may be exchanged
with a portion of the chromosomal sequence. The presence of the
double stranded break facilitates homologous recombination and
repair of the break. The exchange polynucleotide may be physically
integrated or, alternatively, the exchange polynucleotide may be
used as a template for repair of the break, resulting in the
exchange of the sequence information in the exchange polynucleotide
with the sequence information in that portion of the chromosomal
sequence. Thus, a portion of the endogenous chromosomal sequence
may be converted to the sequence of the exchange
polynucleotide.
[0112] To mediate zinc finger nuclease genomic editing, at least
one nucleic acid molecule encoding a zinc finger nuclease and,
optionally, at least one exchange polynucleotide or at least one
donor polynucleotide are delivered to the cell of interest.
Suitable methods of introducing the nucleic acids to the cell
include microinjection, electroporation, calcium phosphate-mediated
transfection, cationic transfection, liposome transfection, heat
shock transfection, lipofection, and delivery via liposomes,
immunoliposomes, virosomes, or artificial virions.
[0113] The method of inducing genomic editing with a zinc finger
nuclease further comprises culturing the cell comprising the
introduced nucleic acid to allow expression of the zinc finger
nuclease. Cells comprising the introduced nucleic acids may be
cultured using standard procedures to allow expression of the zinc
finger nuclease. Typically, the cells are cultured at an
appropriate temperature and in appropriate media with the necessary
O2/CO2 ratio to allow the expression of the zinc finger nuclease.
Suitable non-limiting examples of media include M2, M16, KSOM,
BMOC, and HTF media. Standard cell culture techniques are
described, for example, in Santiago et al, 2008, Targeted gene
knockout in mammalian cells by using engineered zinc finger
nucleases, PNAS 105:5809-5814; Moehle et al., 2007, Targeted gene
addition into a specified location in the human genome using
designed zinc finger nucleases PNAS 104:3055-3060; Urnov et al.,
2005, Highly efficient endogenous human gene correction using
designed zinc-finger nucleases, Nature 435 (7042):646-51; and
Lombardo et al., 2007, Gene editing in human stem cells using zinc
finger nucleases and integrase-defective lentiviral vector
delivery, Nat Biotechnol 25 (11):1298-306. Those of skill in the
art appreciate that methods for culturing cells are known in the
art and can and will vary depending on conditions. Upon expression
of the zinc finger nuclease, the target sequence is edited. In
cases in which the cell includes an expressed zinc finger nuclease
as well as a donor (or exchange) polynucleotide, the zinc finger
nuclease recognizes, binds, and cleaves the target sequence in the
chromosome. The double-stranded break introduced by the zinc finger
nuclease is repaired, via homologous recombination with the donor
(or exchange) polynucleotide, such that the sequence in the donor
polynucleotide is integrated into the chromosomal sequence (or a
portion of the chromosomal sequence is converted to the sequence in
the exchange polynucleotide). As a consequence, a sequence may be
integrated into the chromosomal sequence (or a portion of the
chromosomal sequence may be modified).
[0114] Using genome editing for modifying a chromosomal sequence,
an isogenic (but for the mutation of interest) control line can be
generated. In certain embodiments, a control cells are obtained
from healthy individuals, i.e., without using genome editing on
cells taken from the subject. The control line can be used in the
analytical methods described herein to generate a control signature
for comparison to test data. In some embodiments, a control
signature is stored on-file after having been previously generated
and stored and the stored control signature is used (e.g., a
digital file such as a graph or series of measurements stored in a
non-transitory memory in a computer system). For example, a control
signature could be generated by assaying a large population of
subjects of known phenotype or genotype and storing an aggregate
result as a control signature for later downstream comparisons.
[0115] 4. Causing Cells to Express Optogenetic Systems
[0116] 4a. Causing a Cell to Express an Optogenetic Reporter
[0117] The patient's test cell line and the optional control line
may be caused to express an optical reporter of neural or
electrical activity. Examples of neural activity include action
potentials in a neuron or fusion of vesicles releasing
neurotransmitters. Exemplary electrical activity includes action
potentials in a neuron, cardiomyocyte, astrocyte or other
electrically active cell. Further examples of neural or electrical
activity include ion pumping or release or changing ionic gradients
across membranes. Causing a cell to express an optical reporter of
neural activity can be done with a fluorescent reporter of vesicle
fusion. Expressing an optical reporter of neural or electrical
activity can include transformation with an optogenetic reporter.
For example, the cell may be transformed with a vector comprising
an optogenetic reporter and the cell may also be caused to express
an optogenetic actuator by transformation. In certain embodiments,
the differentiated neurons are cultured (e.g., for about 4 days)
and then infected with lentivirus bearing a genetically encoded
optical reporter of neural activity and optionally an optical
voltage actuator.
[0118] Any suitable optical reporter of neural activity may be
used. Exemplary reporters include fluorescent reporters of
transmembrane voltage differences, pHluorin-based reporters of
synaptic vesicle fusion, and genetically encoded calcium
indicators. In a preferred embodiment, a genetically encoded
voltage indicator is used. Genetically encoded voltage indicators
that may be used or modified for use with methods of the invention
include FlaSh (Siegel, 1997, A genetically encoded optical probe of
membrane voltage. Neuron 19:735-741); SPARC (Ataka, 2002, A
genetically targetable fluorescent probe of channel gating with
rapid kinetics, Biophys J 82:509-516); and VSFP1 (Sakai et al.,
2001, Design and characterization of a DNA encoded,
voltage-sensitive fluorescent protein, Euro J Neuroscience
13:2314-2318). A genetically encoded voltage indicator based on the
paddle domain of a voltage-gated phosphatase is CiVSP (Murata et
al., 2005, Phosphoinositide phosphatase activity coupled to an
intrinsic voltage sensor, Nature 435:1239-1243). Another indicator
is the hybrid hVOS indicator (Chanda et al., 2005, A hybrid
approach to measuring electrical activity in genetically specified
neurons, Nat Neuroscience 8:1619-1626), which transduces the
voltage dependent migration of dipicrylamine (DPA) through the
membrane leaflet to "dark FRET" (fluorescence resonance energy
transfer) with a membrane-targeted GFP.
[0119] Optical reporters that may be suitable for use with the
invention include those from the family of proteins of known
microbial rhodopsins. A reporter based on a microbial rhodopsin may
provide high sensitivity and speed. Suitable indicators include
those that use the endogenous fluorescence of the microbial
rhodopsin protein Archaerhodopsin 3 (Arch) from Halorubum
sodomense. Arch resolves action potentials with high
signal-to-noise (SNR) and low phototoxicity. A mutant form of Arch,
D95N, has been shown not to exhibit a hyperpolarizing current
associated with some indicators. Other mutant forms of Arch, termed
QuasAr1 and QuasAr2, have been shown to exhibit improved
brightness, sensitivity to voltage, speed of response, and
trafficking to the neuronal plasma membrane. Arch and the
above-mentioned variants target eukaryotic membranes and can image
single action potentials and subthreshold depolarization in
cultured mammalian neurons. See Kralj et al, 2012, Optical
recording of action potentials in mammalian neurons using a
microbial rhodopsin, Nat Methods 9:90-95. Thus Arch and variants of
Arch such as Arch (D95N) may provide good optical reporters of
neural activity according to embodiments of the invention.
[0120] In some embodiments, an improved variant of Arch such as
QuasAr1 or QuasAr2 is used. QuasAr1 comprises Arch with the
mutations: P6OS, T80S, D95H, D106H, and F161V. QuasAr2 comprises
Arch with the mutations: P60S, T80S, D95Q, D106H, and F161V.
Positions Asp95 and Asp106 of Arch (which are structurally aligned
with positions Asp85 and Asp96 of bacteriorhodopsin, and have been
reported to play key roles in proton translocation during the photo
cycle) are targets for modification because they flank the Schiff
base in the proton-transport chain and are likely important in
determining voltage sensitivity and speed. The other mutations
improve the brightness of the protein. Starting with an Arch gene,
it may be beneficial to add endoplasmic reticulum (ER) export
motifs and a trafficking sequence (TS) according to methods known
in the art.
[0121] FIG. 4 presents a structural model of Quasar1 based on
homologous protein Arch-2 (PDB: 2EI4, described in Enami et al,
2006, Crystal structures of archaerhodopsin-1 and-2: Common
structural motif in Archaeal light-driven proton pumps, J Mol Bio.
358:675-685). Mutations T80S and F161V are located in the periphery
of the protein, while P60S is close to the Schiff base of the
retinal chromophore. Given their location, T80S and F161V
substitutions are unlikely to have a direct impact on the
photo-physical properties of the protein, and are more likely to
have a role in improving the folding efficiency. In contrast, the
close proximity of the P60S substitution to the Schiff base
suggests that this mutation has a more direct influence on the
photo-physical properties. The QuasAr indicators may exhibit
improved voltage sensitivity, response kinetics, membrane
trafficking and diminished dependence of brightness on illumination
intensity relative to Arch. The fluorescence quantum yields of
solubilized QuasAr1 and 2 may be 19- and 10-fold enhanced,
respectively, relative to the non-pumping voltage indicator Arch
(D95N). QuasAr1 may be 15-fold brighter than wild-type Arch, and
QuasAr2 may be 3.3-fold brighter. Neither mutant shows the optical
nonlinearity seen in the wild-type protein. Fluorescence of Arch,
QuasAr1, and QuasAr2 increase nearly linearly with membrane voltage
between -100 mV and +50 mV. Fluorescence recordings may be acquired
on an epifluorescence microscope, described in Kralj et al., 2012,
Optical recording of action potentials in mammalian neurons using a
microbial rhodopsin, Nat. Methods 9:90-95.
[0122] QuasAr1 and QuasAr2 each refer to a specific variant of
Arch. As discussed, archaerhodopsin 3 (Arch) functions as a fast
and sensitive voltage indicator. Improved versions of Arch include
the QuasArs (`quality superior to Arch`), described in Hochbaum et
al., 2014. QuasAr1 differs from wild-type Arch by the mutations
P60S, T80S, D95H, D106H and F161V. QuasAr2 differed from QuasAr1 by
the mutation H95Q. QuasAr1 and QuasAr2 report action potentials
(APs).
[0123] FIG. 21 gives a comparison of AP waveforms as measured by
the genetically encoded voltage indicator QuasAr2 and the
voltage-sensitive dye, FluoVolt. Cells were sparsely transfected
with the QuasAr2 construct and then treated with FluoVolt dye.
QuasAr2 was excited by red laser light at a wavelength of 635 nm
with fluorescence detection centered at 720 nm. FluoVolt was
excited by 488 nm laser light with fluorescence detection centered
at 525 nm. The top panel shows the simultaneously recorded AP
waveforms from a cell expressing QuasAr2 (red line) and labeled
with FluoVolt (green line). The similarity of these traces
establishes that QuasAr2 fluorescence accurately represents the
underlying AP waveform. The lower trace compares the FluoVolt AP
waveform in the presence (FluoVolt+, QuasAr2+, green) and absence
(FluoVolt+, QuasAr2-, cyan) of QuasAr2 expression. The similarity
of these two traces establishes that expression of QuasAr2 does not
perturb the AP waveform.
[0124] FIG. 22 shows plots of the average waveforms from the traces
in FIG. 21.
[0125] FIG. 23 presents phototoxicity and photobleaching
measurement of QuasAr2. Cells were imaged under continuous red
laser illumination (.about.50 W/cm.sup.2) for 500 s. Expanded views
of the fluorescence recording are shown in the lower panels.
[0126] FIG. 24 graphs the average AP waveform shapes for the
beginning (blue) and end (green) of the trace in FIG. 23.
[0127] Arch and the above-mentioned variants target eukaryotic
membranes and can image single action potentials and subthreshold
depolarization in cultured mammalian neurons. See Kralj et al,
2012, Optical recording of action potentials in mammalian neurons
using a microbial rhodopsin, Nat Methods 9:90-95 and Hochbaum et
al., All-optical electrophysiology in mammalian neurons using
engineered microbial rhodopsins, Nature Methods, 11,825-833 (2014),
both incorporated by reference. Thus Arch and variants of Arch may
provide good optical reporters of electrical activity according to
embodiments of the invention.
[0128] The invention provides optical reporters based on
Archaerhodopsins that function in mammalian cells, including human
stem cell-derived neurons. These proteins indicate electrical
dynamics with sub-millisecond temporal resolution and sub-micron
spatial resolution and may be used in non-contact, high-throughput,
and high-content studies of electrical dynamics in cells and
tissues using optical measurement of membrane potential. These
reporters are broadly useful, particularly in eukaryotic, such as
mammalian, including human cells.
[0129] The invention includes reporters based on Archaerhodopsin 3
(Arch 3) and its homologues. Arch 3 is Archaerhodopsin from H.
sodomense and it is known as a genetically-encoded reagent for
high-performance yellow/green-light neural silencing. Gene sequence
at GenBank: GU045593.1 (synthetic construct Arch 3 gene, complete
cds. Submitted Sep. 28, 2009). These proteins localize to the
plasma membrane in eukaryotic cells and show voltage-dependent
fluorescence.
[0130] Fluorescence recordings may be acquired on an
epifluorescence microscope, described in Hochbaum et al.,
All-optical electrophysiology in mammalian neurons using engineered
microbial rhodopsins, Nature Methods, 11, 825-833 (2014),
incorporated by reference.
[0131] Optical reporters of the invention show high sensitivity. In
mammalian cells, Archaerhodopsin-based reporters show about 3-fold
increase in fluorescence between -150 mV and +150 mV. The response
is linear over most of this range. Membrane voltage can be measured
with a precision of <1 mV in a 1 s interval. Reporters of the
invention show high speed. QuasAr1 shows 90% of its step response
in 0.05 ms. The upstroke of a cardiac AP lasts approximately 1 ms,
so the speeds of Arch-derived indicators meet the benchmark for
imaging electrical activity. Reporters of the invention show high
photo-stability and are comparable to GFP in the number of
fluorescence photons produced prior to photobleaching. The
reporters may also show far red spectrum. The Arch-derived
voltage-indicating protein reporters, sometimes referred to as
genetically encoded voltage indicators (GEVIs), may be excited with
a laser at wavelengths between 590-640 nm, and the emission is in
the near infrared, peaked at 710 nm. The emission is farther to the
red than any other existing fluorescent protein. These wavelengths
coincide with low cellular auto-fluorescence. This feature makes
these proteins particularly useful in optical measurements of
action potentials as the spectrum facilitates imaging with high
signal-to-noise ratio, as well as multi-spectral imaging in
combination with other fluorescent probes.
[0132] Other optogenetic reporters may be used with methods and
systems of the invention.
[0133] Suitable optogenetic reporters include the two Arch variants
dubbed Archer1 and Archer2 reported in Flytzanis, et al., 2014,
Archaerohodopsin variants with enhanced voltage-sensitive
fluorescence in mammalian and Caenorhabditis elegans neurons, Nat
Comm 5:4894, incorporated by reference. Archer1 and Archer2 exhibit
enhanced radiance in response to 655 nm light have 3-5 times
increased fluorescence and 55-99 times reduced photocurrents
compared with Arch WT. Archer1 (D95E and T99C) and Archer2 (D95E,
T99C and A225M) may be used for voltage sensing. These mutants
exhibit high baseline fluorescence (.times.3-5 over Arch WT), large
dynamic range of sensitivity (85% DF/F and 60% DF/F per 100 mV for
Archer1 and Archer2, respectively) that is stable over long
illumination times, and fast kinetics, when imaged at .times.9
lower light intensity (880 mW mm -2 at 655 nm) than the most
recently reported Arch variants. Archer1's characteristics allow
its use to monitor rapid changes in membrane voltage throughout a
single neuron and throughout a population of neurons in vitro.
Although Archer1 has minimal pumping at wavelengths used for
fluorescence excitation (655 nm), it maintains strong proton
pumping currents at lower wavelengths (560 nm). Archer1 provides a
bi-functional tool with both voltage sensing with red light and
inhibitory capabilities with greenlight. Archer1 is capable of
detecting small voltage changes in response to sensory stimulus
[0134] Suitable optogenetic reporters include the Arch-derived
voltage sensors with trafficking signals for enhanced localization
as well as the Arch mutants dubbed Arch-EEN and Arch-EEQ reported
in Gong et al., Enhanced Archaerhodopsin fluorescent protein
voltage indicators, PLoSOne 8 (6):e66959, incorporated by
reference. Such reporters may include variants of Arch with the
double mutations D95N-D106E (Arch-EEN) and D95Q-D106E
(Arch-EEQ).
[0135] Suitable optogenetic reporters include sensors that use
fluorescence resonance energy transfer (FRET) to combine rapid
kinetics and the voltage dependence of the rhodopsin family
voltage-sensing domains with the brightness of genetically
engineered protein fluorophores. Such FRET-opsin sensors offer good
spike detection fidelity, fast kinetics, and high brightness.
FRET-opsin sensors are described in Gong et al., Imaging neural
spiking in brain tissue using FRET-opsin protein voltage sensors,
Nat Comm 5:3674, incorporated by reference. A suitable FRET-opsin
may include a fusion of a bright fluorophore to act as a FRET donor
to a Mac rhodopsin molecule to server as both the voltage sensing
domain and the FRET acceptor. Other sensors include the Accelerated
Sensor of Action Potentials (ASAP1), a voltage sensor formed by
insertion of a circularly permuted GFP into a chicken
voltage-sensitive phosphatase. St-Pierre, 2014, High-fidelity
optical reporting of neuronal electrical activity with an ultrafast
fluorescent voltage sensor, Nat Neurosci 17 (6):884, incorporated
by reference. Other suitable reporters may include the
ArcLight-derived probe dubbed Bongwoori and described in Piao et
al., 2015, Combinatorial mutagenesis of the voltage-sensing domain
enables the optical resolution of action potentials firing at 60 Hz
by a genetically encoded fluorescent sensor of membrane potential,
J Neurosci 35 (1):372-385, incorporated by reference.
[0136] 4b. Causing a Cell to Express an Optogenetic Actuator
[0137] In a preferred embodiment, the cells are transformed with an
optical voltage actuator. This can occur, for example,
simultaneously with transformation with the vector comprising the
optogenetic reporter. The far-red excitation spectrum of the QuasAr
reporters suggests that they may be paired with a blue
light-activated channelrhodopsin to achieve all-optical
electrophysiology. For spatially precise optical excitation, the
channelrhodopsin should carry current densities sufficient to
induce APs when only a subsection of a cell is excited. Preferably,
light used for imaging the reporter should not activate the
actuator, and light used for activating the actuator should not
confound the fluorescence signal of the reporter. Thus in a
preferred embodiment, an optical actuator and an optical reporter
are spectrally orthogonal to avoid crosstalk and allow for
simultaneous use. Spectrally orthogonal systems are discussed in
Carlson and Campbell, 2013, Circular permutated red fluorescent
proteins and calcium ion indicators based on mCherry, Protein Eng
Des Sel 26 (12):763-772.
[0138] Preferably, a genetically-encoded optogenetic actuator is
used. One actuator is channelrhodopsin2 H134R, an optogenetic
actuator described in Nagel, G. et al., 2005, Light activation of
channelrhodopsin-2 in excitable cells of Caenorhabditis elegans
triggers rapid behavioral responses, Curr. Biol. 15, 2279-2284.
[0139] A screen of plant genomes has identified an optogenetic
actuator, Scherffelia dubia ChR (sdChR), derived from a fresh-water
green alga first isolated from a small pond in Essex, England. See
Klapoetke et al., 2014, Independent optical excitation of distinct
neural populations, Nat Meth Advance Online Publication 1-14; see
also Melkonian & Preisig, 1986, A light and electron
microscopic study of Scherffelia dubia, a new member of the scaly
green flagellates (Prasinophyceae). Nord. J. Bot. 6:235-256, both
incorporated by reference. SdChR may offer good sensitivity and a
blue action spectrum.
[0140] An improved version of sdChR dubbed CheRiff may be used as
an optical actuator. The gene for Scherffelia dubia
Channelrhodopsin (sdChR) (selected from a screen of
channelrhodopsins for its blue excitation peak (474 nm) and its
large photocurrent relative to ChR2) is synthesized with mouse
codon optimization, a trafficking sequence from Kir2.1 is added to
improve trafficking, and the mutation E154A is introduced. CheRiff
exhibits significantly decreased crosstalk from red illumination
(to 10.5.+-.2.8 pA) allowing its use in cells along with
optogenetic reporters described herein. CheRiff shows good
expression and membrane trafficking in cultured rat hippocampal
neurons. The maximum photocurrent under saturating illumination
(488 nm, 500 mW/cm) is 2.0.+-.0.1 nA (n=10 cells), approximately
2-fold larger than the peak photocurrents of ChR2 H134R or ChIEF
(Lin et al., 2009, Characterization of engineered channelrhodopsin
variants with improved properties and kinetics, Biophys J
96:1803-1814). In neurons expressing CheRiff, whole-cell
illumination at only 22.+-.10 mW/cm induces a photocurrent of 1 nA.
Compared to ChR2 H134R and to ChIEF under standard channelrhodopsin
illumination conditions (488 nm, 500 mW/cm). At 23.degree. C.,
CheRiff reaches peak photocurrent in 4.5.+-.0.3 ms (n=10 cells).
After a 5 ms illumination pulse, the channel closing time constant
was comparable between CheRiff and ChIEF (16.+-.0.8 ms, n=9 cells,
and 15.+-.2 ms, n=6 cells, respectively, p=0.94), and faster than
ChR2 H134R (25.+-.4 ms, n=6 cells, p<0.05). Under continuous
illumination CheRiff partially desensitizes with a time constant of
400 ms, reaching a steady-state current of 1.3.+-.0.08 nA (n=10
cells). Illumination of neurons expressing CheRiff induces trains
of APs with high reliability and high repetition-rate.
[0141] When testing for optical crosstalk between QuasArs and
CheRiff in cultured neurons, illumination sufficient to induce
high-frequency trains of APs (488 nm, 140 mW/cm) perturbed
fluorescence of QuasArs by <1%. Illumination with high intensity
red light (640 nm, 900 W/cm) induced an inward photocurrent through
CheRiff of 14.3.+-.3.1 pA, which depolarized neurons by 3.1.+-.0.2
mV (n=5 cells). ChIEF and ChR2 H134R generated similar red light
photocurrents and depolarizations. For most applications this level
of optical crosstalk is acceptable.
[0142] In some embodiments it is preferred to have an actuator
whose activation is maximal at a violet light wavelength between
400-440 nm, further to the blue than CheRiff. Violet-activated
channelrhodopsins can be simultaneously combined with
yellow-excited Ca.sup.2+ indicators (e.g. jRCaMP1a, jRGECO1a, and
R-CaMP2) and a red-excited voltage indicator, e.g. QuasAr2, for
simultaneous monitoring of Ca.sup.2+ and voltage under optical
stimulus conditions.
[0143] A preferred violet-excited channelrhodopsin actuator is
TsChR, derived from Tetraselmis striata (See Klapoetke et al.,
2014, Independent optical excitation of distinct neural
populations, Nat. Meth. 11, 338-346 (2014)). This channelrhodopsin
actuator has a blue-shifted action spectrum with a peak at 435 nm.
Another preferred violet channelrhodopsin actuator is PsChR,
derived from Platymonas subcordiformis (see Govorunova, Elena et
al., 2013, Characterization of a highly efficient blue-shifted
channelrhodopsin from the marine alga Platymonas subcordiformis, J
Biol Chem 288 (41):29911-29922). PsChr has a blue-shifted action
spectrum with a peak at 437 nm. PsChR and TsChR are advantageously
paired with red-shifted Ca.sup.2+ indicators and can be used in the
same cell or same field of view as these red-shifted Ca.sup.2+
indicators without optical crosstalk.
[0144] 4c. Vectors for Expression of Optogenetic Systems
[0145] The optogenetic reporters and actuators may be delivered in
constructs described here as optopatch constructs delivered through
the use of an expression vector. Optopatch may be taken to refer to
systems that perform functions traditionally associated with patch
clamps, but via an optical input, readout, or both as provided for
by, for example, an optical reporter or actuator. An Optopatch
construct may include a bicistronic vector for co-expression of
CheRiff-eGFP and QuasAr1- or QuasAr2-mOrange2. The QuasAr and
CheRiff constructs may be delivered separately, or a bicistronic
expression vector may be used to obtain a uniform ratio of actuator
to reporter expression levels.
[0146] The genetically encoded reporter, actuator, or both may be
delivered by any suitable expression vector using methods known in
the art. An expression vector is a specialized vector that contains
the necessary regulatory regions needed for expression of a gene of
interest in a host cell. In some embodiments the gene of interest
is operably linked to another sequence in the vector. In some
embodiments, it is preferred that the viral vectors are replication
defective, which can be achieved for example by removing all viral
nucleic acids that encode for replication. A replication defective
viral vector will still retain its infective properties and enters
the cells in a similar manner as a replicating vector, however once
admitted to the cell a replication defective viral vector does not
reproduce or multiply. The term "operably linked" means that the
regulatory sequences necessary for expression of the coding
sequence are placed in the DNA molecule in the appropriate
positions relative to the coding sequence so as to effect
expression of the coding sequence. This same definition is
sometimes applied to the arrangement of coding sequences and
transcription control elements (e.g. promoters, enhancers, and
termination elements) in an expression vector.
[0147] Many viral vectors or virus-associated vectors are known in
the art. Such vectors can be used as carriers of a nucleic acid
construct into the cell. Constructs may be integrated and packaged
into non-replicating, defective viral genomes like Adenovirus,
Adeno-associated virus (AAV), or Herpes simplex virus (HSV) or
others, including retroviral and lentiviral vectors, for infection
or transduction into cells. The vector may or may not be
incorporated into the cell's genome. The constructs may include
viral sequences for transfection, if desired. Alternatively, the
construct may be incorporated into vectors capable of episomal
replication, such as an Epstein Barr virus (EPV or EBV) vector. The
inserted material of the vectors described herein may be
operatively linked to an expression control sequence when the
expression control sequence controls and regulates the
transcription and translation of that polynucleotide sequence. In
some examples, transcription of an inserted material is under the
control of a promoter sequence (or other transcriptional regulatory
sequence) which controls the expression of the recombinant gene. In
some embodiments, a recombinant cell containing an inducible
promoter is used and exposed to a regulatory agent or stimulus by
externally applying the agent or stimulus to the cell or organism
by exposure to the appropriate environmental condition or the
operative pathogen. Inducible promoters initiate transcription only
in the presence of a regulatory agent or stimulus. Examples of
inducible promoters include the tetracycline response element and
promoters derived from the beta-interferon gene, heat shock gene,
metallothionein gene or any obtainable from steroid
hormone-responsive genes. Inducible promoters which may be used in
performing the methods of the present invention include those
regulated by hormones and hormone analogs such as progesterone,
ecdysone and glucocorticoids as well as promoters which are
regulated by tetracycline, heat shock, heavy metal ions,
interferon, and lactose operon activating compounds. See Gingrich
and Roder, 1998, Inducible gene expression in the nervous system of
transgenic mice, Annu Rev Neurosci 21:377-405. Tissue specific
expression has been well characterized in the field of gene
expression and tissue specific and inducible promoters are well
known in the art. These promoters are used to regulate the
expression of the foreign gene after it has been introduced into
the target cell. In certain embodiments, a cell-type specific
promoter or a tissue-specific promoter is used. A cell-type
specific promoter may include a leaky cell-type specific promoter,
which regulates expression of a selected nucleic acid primarily in
one cell type, but cause expression in other cells as well. For
expression of an exogenous gene specifically in neuronal cells, a
neuron-specific enolase promoter can be used. See Forss-Petter et
al., 1990, Transgenic mice expressing beta-galactosidase in mature
neurons under neuron specific enolase promoter control, Neuron 5:
187-197. For expression of an exogenous gene in dopaminergic
neurons, a tyrosine hydroxylase promoter can be used.
[0148] In some embodiments, the expression vector is a lentiviral
vector. Lentiviral vectors may include a eukaryotic promoter. The
promoter can be any inducible promoter, including synthetic
promoters, that can function as a promoter in a eukaryotic cell.
For example, the eukaryotic promoter can be, but is not limited to,
CamKII.alpha. promoter, human Synapsin promoter, ecdysone inducible
promoters, E1a inducible promoters, tetracycline inducible
promoters etc., as are well known in the art. In addition, the
lentiviral vectors used herein can further comprise a selectable
marker, which can comprise a promoter and a coding sequence for a
selectable trait. Nucleotide sequences encoding selectable markers
are well known in the art, and include those that encode gene
products conferring resistance to antibiotics or anti-metabolites,
or that supply an auxotrophic requirement. Examples of such
sequences include, but are not limited to, those that encode
thymidine kinase activity, or resistance to methotrexate,
ampicillin, kanamycin, among others. Use of lentiviral vectors is
discussed in Wardill et al., 2013, A neuron-based screening
platform for optimizing genetically-encoded calcium indicators,
PLoS One 8 (10):e77728; Dottori, et al., Neural development in
human embryonic stem cells-applications of lentiviral vectors, J
Cell Biochem 112 (8):1955-62; and Diester et al., 2011, An
optogenetic toolbox designed for primates, Nat Neurosci 14
(3):387-97. When expressed under a CaMKII.alpha. promoter in
cultured rat hippocampal neurons the Optopatch construct exhibits
high expression and good membrane trafficking of both CheRiff and
QuasAr2.
[0149] In some embodiments the viral vector is an adeno-associated
virus (AAV) vector. AAV can infect both dividing and non-dividing
cells and may incorporate its genome into that of the host cell.
One suitable viral vector uses recombinant adeno-associated virus
(rAAV), which is widely used for gene delivery in the CNS.
[0150] In certain embodiments, methods of the invention use a
Cre-dependent expression system. Cre-dependent expression includes
Cre-Lox recombination, a site-specific recombinase technology that
uses the enzyme Cre recombinase, which recombines a pair of short
target sequences called the Lox sequences. This system can be
implemented without inserting any extra supporting proteins or
sequences. The Cre enzyme and the original Lox site called the LoxP
sequence are derived from bacteriophage P1. Bacteriophage P1 uses
Cre-lox recombination to circularize and replicate its genomic DNA.
This recombination strategy is employed in Cre-Lox technology for
genome manipulation, which requires only the Cre recombinase and
LoxP sites. Sauer & Henderson, 1988, Site-specific DNA
recombination in mammalian cells by the Cre recombinase of
bacteriophage P1, PNAS 85:5166-70 and Sternberg & Hamilton,
1981, Bacteriophage P1 site-specific recombination. I.
Recombination between LoxP sites, J Mol Biol 150:467-86. Methods
may use a Cre recombinase-dependent viral vector for targeting
tools such as channelrhodopsin-2 (ChR2) to specific neurons with
expression levels sufficient to permit reliable photostimulation.
Optogenetic tools such as ChR2 tagged with a fluorescent protein
such as mCherry (e.g., ChR2mCherry) or any other of the tools
discussed herein are thus delivered to the cell or cells for use in
characterizing those cells.
[0151] The delivery vector may include Cre and Lox. The vector may
further optionally include a Lox-stop-Lox (LSL) cassette to prevent
expression of the transgene in the absence of Cre-mediated
recombination. In the presence of Cre recombinase, the LoxP sites
recombine, and a removable transcription termination Stop element
is deleted. Removal of the stop element may be achieved through the
use of AdenoCre, which allows control of the timing and location of
expression. Use of the LSL cassette is discussed in Jackson, et
al., 2001, Analysis of lung tumor initiation and progression using
conditional expression of oncogenic K-ras, Genes & Dev
15:3243-3248.
[0152] In certain embodiments, a construct of the invention uses a
"flip-excision" switch, or FLEX switch (FLip EXicision), to achieve
stable transgene inversion. The FLEX switch is discussed in
Schnutgen et al., 2003, A directional strategy for monitoring
Cre-mediated recombination at the cellular level in the mouse, Nat
Biotechnol 21:562-565. The FLEX switch uses two pairs of
heterotypic, antiparallel LoxP-type recombination sites which first
undergo an inversion of the coding sequence followed by excision of
two sites, leading to one of each orthogonal recombination site
oppositely oriented and incapable of further recombination. A FLEX
switch provides high efficiency and irreversibility. Thus in some
embodiments, methods use a viral vector comprising
rAAV-FLEX-rev-ChR2mCherry. Additionally or alternatively, a vector
may include FLEX and any other optogenetic tool discussed herein
(e.g., rAAV-FLEX-QuasAr, rAAV-FLEX-CheRiff). Using
rAAV-FLEX-rev-ChR2mCherry as an illustrative example, Cre-mediated
inversion of the ChR2mCherry coding sequence results in the coding
sequence being in the wrong orientation (i.e., rev-ChR2mCherry) for
transcription until Cre inverts the sequence, turning on
transcription of ChR2mCherry. FLEX switch vectors are discussed in
Atasoy et al., 2009, A FLEX switch targets channelrhodopsin-2 to
multiple cell types for imaging and long-range circuit mapping, J
Neurosci 28 (28):7025-7030.
[0153] Use of a viral vector such as Cre-Lox system with an optical
reporter, optical actuator, or both (optionally with a FLEX switch
and/or a Lox-Stop-Lox cassette) for labeling and stimulation of
neurons allows for efficient photo-stimulation with only brief
exposure (1 ms) to less than 100 .mu.W focused laser light or to
light from an optical fiber. Such Further discussion may be found
in Yizhar et al., 2011, Optogenetics in neural systems, Neuron 71
(1):9-34; Cardin et al., 2010, Targeted optogenetic stimulation and
recording of neurons in vivo using cell-type-specific expression of
Channelrhodopsin-2, Nat Protoc 5 (2):247-54; Rothermel et al.,
2013, Transgene expression in target-defined neuron populations
mediated by retrograde infection ith adeno-associated viral
vectors, J Neurosci 33 (38):195-206; and Saunders et al., 2012,
Novel recombinant adeno-associated viruses for Cre activated and
inactivated transgene expression in neurons, Front Neural Circuits
6:47.
[0154] In certain embodiments, actuators, reporters, or other
genetic material may be delivered using chemically-modified mRNA.
It may be found and exploited that certain nucleotide modifications
interfere with interactions between mRNA and toll-like receptor,
retinoid-inducible gene, or both. Exposure to mRNAs coding for the
desired product may lead to a desired level of expression of the
product in the cells. See, e.g., Kormann et al., 2011, Expression
of therapeutic proteins after delivery of chemically modified mRNA
in mice, Nat Biotech 29 (2):154-7; Zangi et al., 2013, Modified
mRNA directs the fate of heart protenitor cells and induces
vascular regeneration after myocardial infarction, Nat Biotech
31:898-907.
[0155] It may be beneficial to culture or mature the cells after
transformation with the genetically encoded optical reporter with
optional actuator. In some embodiments, the neurons are matured for
8-10 days post infection. Using microscopy and analytical methods
described herein, the cell and its action potentials may be
observed. For additional discussion, see U.S. Pub. 2013/0224756,
incorporated by reference in its entirety for all purposes.
[0156] 4d. Optogenetic Constructs and Plating Schemes for
Simultaneous Voltage and Ca2+ Measurement.
[0157] FIG. 25 presents schematic structures of optogenetic
proteins used for stimulus and detection of voltage and
intracellular Ca2+. The diagrams show proteins homologous to
CheRiff and QuasAr2. Stimulus of cells is achieved through 488 nm
LED illumination of CheRiff. The CheRiff construct is coupled to an
eGFP tag for detection of CheRiff expression. A fusion protein
called CaViar (Hou et al., 2014), consisting of QuasAr2 (Hochbaum
et al., 2014) fused to GCaMP6f (Chen et al., 2013), is used for
simultaneous voltage and Ca.sup.2+ imaging. QuasAr2 is excited via
red laser light. GCaMP6f is excited via blue laser light. Cells are
separately transduced with either CheRiff or CaViar vectors.
[0158] FIG. 26 illustrates cellular plating configurations. For
simultaneous optical stimulus and voltage imaging, CheRiff cells
(solid cyan circles) were co-mingled with CaViar cells (solid red
circles). The yellow dotted line indicates a microscope field of
view. For simultaneous optical stimulus and imaging of both
Ca.sup.2+ and membrane voltage, cells are plated to spatially
segregate CheRiff-expressing cells from CaViar-expressing cells to
avoid optical crosstalk between the pulsed blue light used to
periodically stimulate the CheRiff-expressing cells and the
continuous blue light used to image the CaViar-expressing cells.
The CheRiff-expressing cells lay outside the imaging region.
[0159] When testing for optical crosstalk between Arch-based
reporters and CheRiff in cultured cells, illumination sufficient to
induce APs (488 nm, 140 mW/cm.sup.2) perturbed fluorescence of
QuasAr reporters by <1%. Illumination with high intensity red
light (640 nm, 900 W/cm.sup.2) induced an inward photocurrent
through CheRiff of 14.3.+-.3.1 pA, which depolarized cells by
3.1.+-.0.2 mV (n=5 cells). ChIEF and ChR2 H134R generated similar
red light photocurrents and depolarizations. For most applications
this level of optical crosstalk is acceptable.
[0160] 4e. Multimodal Sensing/Multiplexing
[0161] Membrane potential is only one of several mechanisms of
signaling within cells. One may correlate changes in membrane
potential with changes in concentration of other species, such as
Ca.sup.2+, H.sup.+ (i.e. pH), Na.sup.+, ATP, cAMP, NADH. We
constructed fusions of Arch with pHluorin (a fluorescent pH
indicator) and GCaMP6f (a fluorescent Ca.sup.2+ indicator). The
fusion of an Arch-based voltage indicator and a genetically encoded
Ca.sup.2+ indicator is called CaViar (See Hou et al., 2014,
Simultaneous mapping of membrane voltage and calcium in zebrafish
heart in vivo reveals chamber-specific developmental transitions in
ionic currents, Frontiers in physiology 5). One can also use
fusions with other protein-based fluorescent indicators to enable
other forms of multimodal imaging using the concept as taught
herein. Concentration of ions such as sodium, potassium, chloride,
and calcium can be simultaneously measured when the nucleic acid
encoding the microbial rhodopsin is operably linked to or fused
with an additional fluorescent analyte sensitive indicator; or when
the microbial rhodopsin and the additional fluorescent analyte
sensitive indicator are co-expressed in the same cell.
[0162] It is often desirable to achieve simultaneous optical
stimulation of a cell, calcium imaging, and voltage imaging. To
achieve all three modalities in the same cell, the invention
provides for a violet-excited Channelrhodopsin actuator (psChR or
TsChR); a red-shifted genetically encoded calcium indicator; and a
far red Arch-derived voltage indicator. Red-shifted genetically
encoded calcium indicators include R-GECO1 (See Zhao, Yongxin, et
al. "An expanded palette of genetically encoded Ca.sup.2+
indicators." Science 333.6051 (2011): 1888-1891 and Wu, Jiahui, et
al. "Improved orange and red Ca.sup.2+ indicators and photophysical
considerations for optogenetic applications." ACS chemical
neuroscience 4.6 (2013): 963-972, both incorporated by reference),
R-CaMP2 (See Inoue, Masatoshi, et al. "Rational design of a
high-affinity, fast, red calcium indicator R-CaMP2." Nature methods
12.1 (2015): 64-70, incorporated by reference), jRCaMP1a (Addgene
plasmid 61562), and jRGECO1a (Addgene plasmid 61563). These calcium
indicators are excited by wavelengths between 540 and 560 nm, and
emit at wavelengths between 570 and 620 nm, thereby permitting
spectral separation from the violet-excited channelrhodopsin
actuator and the Arch-based voltage indicator.
[0163] One can combine imaging of voltage indicating proteins with
other structural and functional imaging, of e.g. pH, calcium, or
ATP. One may also combine imaging of voltage indicating proteins
with optogenetic control of membrane potential using e.g.
channelrhodopsin, halorhodopsin, and Archaerhodopsin. If optical
measurement and control are combined, one can perform all-optical
electrophysiology to probe the dynamic electrical response of any
membrane.
[0164] The invention provides high-throughput methods of
characterizing cells. Robotics and custom software may be used for
screening large libraries or large numbers of conditions which are
typically encountered in high throughput drug screening
methods.
[0165] 4f Optical Readout
[0166] Embodiments of the invention provide for spatial separation
of stimulating cells and reporter cells. Expression of
channelrhodopsin-based light-gated ion channels provides a means to
achieve optical stimulus. However, the blue light used to activate
these channels may overlap spectrally with the light used to image
most small-molecule and genetically encoded fluorescent reporters
of physiological activity (e.g. gCaMP Ca.sup.2+ indicators,
Percival ATP indicators, pHluorin pH indicators, VF2.1.C1
voltage-sensitive dyes). Also, the light used to image these
reporters may lead to off-target activation of all known
channelrhodopsin actuators. Ideally, one would like to optically
stimulate a cell culture while maintaining freedom to record from
fluorescent reporters of any color, without optical crosstalk
between the stimulus and the physiological measurement. Methods of
the invention allow a cellular culture to be optically stimulated
while also using fluorescent reporters of any color, without
optical crosstalk between the stimulus and the physiological
measurement through the spatial separation of actuator cells and
reporter cells.
[0167] One solution presented here comprises expressing
channelrhodopsin actuators in one set of hiPSC-derived cells, and
expressing reporters (e.g. CaViar dual-function Ca.sup.2+ and
voltage reporter) in another set of cells. Flashes of blue light
are delivered to the actuator cells, while continuous blue light is
used to monitor the reporter cells. The actuator cells stimulate
the reporter cells through synapses. A key challenge is to identify
and target the stimulus and the measurement light beams to the
appropriate corresponding cells. Methods of the invention provide
at least two embodiments of the solution to the problem of
targeting separate stimulus and measurement light beams to the
appropriate cells: a first approach based on spatial segregation
and a second approach based on image processing and patterned
illumination.
[0168] 4g. Spatial Segregation
[0169] In a first embodiment using spatial segregation, light is
targeted to the actuator cells using spatial segregation of
actuator and reporter-expressing cells.
[0170] Cells are independently infected with actuator and reporter
and are re-plated in distinct but electrically contiguous regions.
Optical stimulus is delivered only to regions of the dish with
cells expressing the actuator, and sensor measurements using any
wavelength of light are recorded in regions of the dish away from
cells expressing the actuator. In one instance, the actuator is
CheRiff, and the sensor is CaViar in human iPSC-derived
neurons.
[0171] FIG. 27 shows cells expressing CheRiff plated in an annular
region, 10 mm outer diameter, .about.8 mm diameter. The inner
radius is set by a disk of polydimethyl siloxane (PDMS) adhered to
the coverslip and the outer diameter is set by the edge of the
chamber. The PDMS disk is then removed and cells expressing CaViar
are plated throughout. Stimulus is controlled by a blue LED whose
illumination is confined to a small region of the actuating cells.
Voltage and calcium imaging are achieved with a red and blue laser,
respectively, in a region free of CheRiff-expressing cells.
[0172] 4h. Patterned Illumination
[0173] In a second embodiment using patterned illumination, light
is targeted to the actuator cells using image processing and
patterned illumination to separately target intermingled actuator-
and reporter-expressing cells.
[0174] For image processing and patterned illumination, cells
expressing either actuator or reporters are randomly intermixed. In
one embodiment, cells are initially plated separately and caused to
express either the actuator or the reporter. The cells are then
lifted from their respective dishes, mixed, and co-plated onto the
imaging dish. In another embodiment, cells are plated directly in
the imaging chamber, and doubly infected with lentivirus encoding
Cre-On actuator and a Cre-Off reporter. The cells are then infected
sparsely with lentivirus encoding the Cre protein, so that in a
sparse subset of cells the actuator is switched on and the reporter
is switched off.
[0175] Cells expressing the actuator are identified via a
recognizable marker, e.g. a fluorescent protein, or by their
absence of fluorescence transients indicating presence of a
reporter. Optical stimulus is achieved by spatially patterning the
excitation light using a digital micromirror device (DMD) to
project flashes onto only those cells expressing the actuator.
[0176] FIG. 5 diagrams an optical imaging apparatus 501 for
patterned illumination. A 488 nm blue laser beam is modulated in
intensity by an acousto-optic modulator (not shown), and then
reflected off a digital micromirror device (DMD) 505. The DMD
imparted a spatial pattern on the blue laser beam (used for CheRiff
excitation) on its way into the microscope. The micromirrors are
re-imaged onto the sample 509, leading to an arbitrary user-defined
spatio-temporal pattern of illumination at the sample. Simultaneous
whole-field illumination with 640 nm red light excites fluorescence
of the reporter.
[0177] The fluorescent protein serving as a recognizable marker of
the cells expressing the actuator is imaged to determine a pattern
of those actuator cells. The digital coordinates of that image are
used to control the DMD 505 so that the DMD 505 directs the blue
488 nm light only onto the actuator cells. Due to the precision of
the patterned illumination provided by the DMD 505, the cells
expressing the reporter are not exposed to the 488 nm light. Cells
expressing the reporter are imaged under continuous illumination,
with the 640 nm light targeted via the DMD to illuminate only those
cells expressing the reporter, and optionally continuous
illumination at a wavelength of 488 nm to illuminate an additional
reporter such as a GCaMP calcium indicator.
[0178] By the patterned illumination method, flashes of blue light
are delivered to the actuator cells, while continuous red and/or
blue light is used to monitor the reporter cells. The actuator
cells stimulate the reporter cells (e.g., across synapses).
Preferably, the actuator cells comprise a first set of
hiPSC-derived neurons expressing channelrhodopsin actuators and the
reporter cells comprise a second set of hiPSC-derived neurons
expressing reporters (e.g. QuasAr2 or CaViar dual-function
Ca.sup.2+ and voltage reporter).
[0179] The foregoing (i) spatial segregation and (ii) patterned
illumination methods provide for optical detection of changes in
membrane potential, [Ca.sup.2+], or both, in optically stimulated
neurons. The described methods and techniques herein provide for
the optical detection of the effects of compounds on cells such as
cells with disease genotypes. Such detection allows for evaluating
the effect of a compound or other stimulus on the phenotype of such
cells.
[0180] 4i. Preparation of Plates for Voltage Imaging
[0181] MatTek dishes (MatTek corp.; 10 mm glass diameter, #1.5) are
coated with 10 .mu.g/mL fibronectin (Sigma-Aldrich) in 0.1% gelatin
overnight at 4.degree. C. Trypsinized CaViar and CheRiff-expressing
cells are first mixed at a ratio of 5:1 CaViar:CheRiff, and then
pelleted. The combined cells are re-suspended in 2.1 mL of
maintenance medium and plated at a density of 2.5.times.10.sup.4
cells/cm.sup.2 in 100 .mu.L of plating medium to cover the entire
glass surface. Cells are kept at 37.degree. C. in 5% CO.sub.2
overnight to adhere to the glass. Maintenance medium (1.0 mL) is
added to each dish and the cells are fed every 48 hours by removing
750 .mu.L of medium from the dish and replacing with 750 .mu.L
fresh maintenance medium.
[0182] Preparation of Plates for Simultaneous Voltage and Calcium
Imaging
[0183] For simultaneous voltage and calcium imaging, MatTek dishes
(10 mm glass diameter) are prepared to segregate CheRiff-expressing
cells from CaViar-expressing cells. This allows simultaneous
calcium imaging and CheRiff stimulus, both with blue light, without
optical crosstalk between the two functions. In certain
embodiments, 8 mm-diameter polydimethylsiloxane (PDMS) discs are
treated with a solution of 10 .mu.g/mL fibronectin in 0.1% gelatin
on one side for 10 minutes at room temperature. The coated discs
are then dried and then pressed onto the MatTek dish glass surface,
slightly offset to one side. The remaining exposed area of the
glass is then coated with 10 .mu.g/mL fibronectin in 0.1% gelatin.
Cells expressing the CheRiff are trypsinized according to the
manufacturer's protocol and re-suspended in 50 .mu.L of maintenance
medium per dish. For plating, 50 .mu.L of the CheRiff cells are
then added to the exposed portion of the glass surface and allowed
to sit for 40 minutes at 37.degree. C. in 5% CO.sub.2 to allow the
cells to adhere. The PDMS discs are then removed, the glass surface
washed with 150 .mu.L of maintenance media medium and the remaining
volume aspirated. Trypsinized CaViar cells are then re-suspended in
100 .mu.L of maintenance medium per dish and plated at a density of
2.0.times.10.sup.4 cells/cm.sup.2 in 100 .mu.L to cover the entire
glass surface. Cells are kept at 37.degree. C. in 5% CO.sub.2
overnight to adhere to the glass. 1.00 mL of maintenance medium is
added to each dish and the cells were fed every 48 hours by
removing 750 .mu.L of media from the dish and adding 750 .mu.L
fresh maintenance medium.
[0184] 5. Imaging Activity Assay
[0185] 5a. Capturing Images
[0186] Methods of the invention may include stimulating the cells
that are to be observed. Stimulation may be direct or indirect
(e.g., optical stimulation of an optical actuator or stimulating an
upstream cell in synaptic communication with the cell(s) to be
observed). Stimulation may be optical, electrical, chemical, or by
any other suitable method. Stimulation may involve any pattern of a
stimulation including, for example, regular, periodic pulses,
single pulses, irregular patterns, or any suitable pattern. Methods
may include varying optical stimulation patterns in space or time
to highlight particular aspects of cellular function. For example,
a pulse pattern may have an increasing frequency. In certain
embodiments, imaging includes stimulating a neuron that expresses
an optical actuator using pulses of light.
[0187] A neuron expressing an Optopatch construct may be exposed to
whole-field illumination with pulses of blue light (10 ms, 25
mW/cm) to stimulate CheRiff, and simultaneous constant illumination
with red light (800 W/cm) to excite fluorescence of QuasAr2. The
fluorescence of QuasAr2 may be imaged at a 1 kHz frame rate. Key
parameters include temporal precision with which single spikes can
be elicited and recorded, signal-to-noise ratio (SNR) in
fluorescence traces, and long-term stability of the reporter
signal. Methods provided herein may be found to optimize those
parameters. Further discussion may be found in Foust et al., 2010,
Action potentials initiate in the axon initial segment and
propagate through axon collaterals reliably in cerebellar Purkinje
neurons, J. Neurosci 30:6891-6902; and Popovic et al., 2011, The
spatio-temporal characteristics of action potential initiation in
layer 5 pyramidal neurons: a voltage imaging study, J. Physiol.
589:4167-4187.
[0188] In some embodiments, measurements are made using a
low-magnification microscope that images a 1.2.times.3.3 mm field
of view with 3 .mu.m spatial resolution and 2 ms temporal
resolution. In other embodiments, measurements are made using a
high-magnification microscope that images a 100 .mu.m field of view
with 0.8 .mu.m spatial resolution and 1 ms temporal resolution. A
suitable instrument is an inverted fluorescence microscope, similar
to the one described in the Supplementary Material to Kralj et al.,
2012, Optical recording of action potentials in mammalian neurons
using a microbial rhodopsin, Nat. Methods 9:90-95. Briefly,
illumination from a red laser 640 nm, 140 mW (Coherent Obis 637-140
LX), is expanded and focused onto the back-focal plane of a
60.times. oil immersion objective, numerical aperture 1.45 (Olympus
1-U2B616).
[0189] FIG. 5 gives a functional diagram of components of an
optical imaging apparatus 501 according to certain embodiments. A
488 nm blue laser beam is modulated in intensity by an
acousto-optic modulator (not shown), and then reflected off a
digital micromirror device (DMD) 505. The DMD imparted a spatial
pattern on the blue laser beam (used for CheRiff excitation) on its
way into the microscope. The micromirrors were re-imaged onto the
sample 509, leading to an arbitrary user-defined spatiotemporal
pattern of illumination at the sample. Simultaneous whole-field
illumination with 640 nm red light excites fluorescence of the
QuasAr reporter.
[0190] With the inverted fluorescence microscope, illumination from
a blue laser 488 nm 50 mW (Omicron PhoxX) is sent through an
acousto-optic modulator (AOM; Gooch and Housego 48058-2.5-0.55-5W)
for rapid control over the blue intensity. The beam is then
expanded and modulated by DMD 505 with 608.times.684 pixels (Texas
Instruments LightCrafter). The DMD is controlled via custom
software (Matlab) through a TCP/IP protocol. The DMD chip is
re-imaged through the objective onto the sample, with the blue and
red beams merging via a dichroic minor. Each pixel of the DMD
corresponds to 0.65 .mu.m in the sample plane. A 532 nm laser is
combined with the red and blue beams for imaging of mOrange2.
Software is written to map DMD coordinates to camera coordinates,
enabling precise optical targeting of any point in the sample.
[0191] To achieve precise optical stimulation of user-defined
regions of a neuron, pixels on DMD 505 are mapped to pixels on the
camera. The DMD projects an array of dots of known dimensions onto
the sample. The camera acquires an image of the fluorescence.
Custom software locates the centers of the dots in the image, and
creates an affine transformation to map DMD coordinates onto camera
pixel coordinates.
[0192] A dual-band dichroic filter (Chroma zt532/635rpc) separates
reporter (e.g., Arch) from excitation light. A 531/40 nm bandpass
filter (Semrock FF01-531/40-25) may be used for eGFP imaging; a
710/100 nm bandpass filter (Chroma, HHQ710/100) for Arch imaging;
and a quad-band emission filter (Chroma ZET405/488/532/642m) for
mOrange2 imaging and pre-measurement calibrations. A variable-zoom
camera lens (Sigma 18-200 mm f/3.5-6.3 II DC) is used to image the
sample onto an EMCCD camera (Andor iXon+DU-860), with 128.times.128
pixels. Images may be first acquired at full resolution
(128.times.128 pixels). Data is then acquired with 2.times.2 pixel
binning to achieve a frame rate of 1,000 frames/s. For runs with
infrequent stimulation (once every 5 s), the red illumination is
only on from 1 s before stimulation to 50 ms after stimulation to
minimize photobleaching. Cumulative red light exposure may be
limited to <5 min. per neuron.
[0193] Low magnification wide-field imaging is performed with a
custom microscope system based around a 2.times., NA 0.5 objective
(Olympus MVX-2). Illumination is provided by six lasers 640 nm, 500
mW (Dragon Lasers 635M500), combined in three groups of two.
Illumination is coupled into the sample using a custom fused silica
prism, without passing through the objective. Fluorescence is
collected by the objective, passed through an emission filter, and
imaged onto a scientific CMOS camera (Hamamatsu Orca Flash 4.0).
Blue illumination for channelrhodopsin stimulation is provided by a
473 nm, 1 W laser (Dragon Lasers), modulated in intensity by an AOM
and spatially by a DMD (Digital Light Innovations DLi4130-ALP HS).
The DMD is re-imaged onto the sample via the 2.times. objective.
During a run, neurons may be imaged using wide-field illumination
at 488 nm and eGFP fluorescence. A user may select regions of
interest on the image of the neuron, and specify a time course for
the illumination in each region. The software maps the
user-selected pixels onto DMD coordinates and delivers the
illumination instructions to the DMD.
[0194] The inverted fluorescence micro-imaging system records
optically from numerous (e.g., 50) expressing cells or cell
clusters in a single field of view. The system may be used to
characterize optically evoked firing patterns and AP waveforms in
neurons expressing an Optopatch construct. Each field of view is
exposed to whole-field pulses of blue light to evoke activity
(e.g., 0.5 s, repeated every 6 s, nine intensities increasing from
0 to 10 mW/cm). Reporter fluorescence such as from QuasAr may be
simultaneously monitored with whole-field excitation at 640 nm, 100
W/cm.
[0195] FIG. 6 illustrates a pulse sequence of red and blue light
used to record action potentials under increasing optical
stimulation. In some embodiments, neurons are imaged on a high
resolution microscope with 640 nm laser (600 W/cm) for voltage
imaging. In certain embodiments, neurons are imaged on a high
resolution microscope with 640 nm laser (600 W/cm) for voltage
imaging and excited with a 488 nm laser (20-200 mW/cm). Distinct
firing patterns can be observed (e.g., fast adapting and
slow-adapting spike trains). System measurements can detect rare
electrophysiological phenotypes that might be missed in a manual
patch clamp measurement. Specifically, the cells' response to
stimulation (e.g., optical actuation) may be observed. Instruments
suitable for use or modification for use with methods of the
invention are discussed in U.S. Pub. 2013/0170026 to Cohen,
incorporated by reference.
[0196] Using the described methods, populations of cells may be
measured. For example, both diseased and corrected (e.g., by zinc
finger domains) motor neurons may be measured. A cell's
characteristic signature such as a neural response as revealed by a
spike train may be observed.
[0197] 5b. Extracting Fluorescence from Movies
[0198] Fluorescence values are extracted from raw movies by any
suitable method. One method uses the maximum likelihood pixel
weighting algorithm described in Kralj et al., 2012, Optical
recording of action potentials in mammalian neurons using a
microbial rhodopsin, Nat Methods 9:90-95. Briefly, the fluorescence
at each pixel is correlated with the whole-field average
fluorescence. Pixels that showed stronger correlation to the mean
are preferentially weighted. This algorithm automatically finds the
pixels carrying the most information, and de-emphasizes background
pixels.
[0199] In movies containing multiple cells, fluorescence from each
cell is extracted via methods known in the art such as Mukamel,
Eran A., Axel Nimmerjahn, and Mark J. Schnitzer. "Automated
analysis of cellular signals from large-scale calcium imaging
data." Neuron 63.6 (2009): 747-760, or Maruyama, Ryuichi, et al.
"Detecting cells using non-negative matrix factorization on calcium
imaging data." Neural Networks 55 (2014): 11-19. These methods use
the spatial and temporal correlation properties of action potential
firing events to identify clusters of pixels whose intensities
co-vary, and associate such clusters with individual cells.
[0200] Alternatively, a user defines a region comprising the cell
body and adjacent neurites, and calculates fluorescence from the
unweighted mean of pixel values within this region. With the
improved trafficking of the QuasAr mutants compared to Arch, these
two approaches give similar results. In low-magnification images,
direct averaging and the maximum likelihood pixel weighting
approaches may be found to provide optimum signal-to-noise
ratios.
[0201] 6. Signal Processing
[0202] 6a. Signal Processing with Independent Component Analysis to
Associate Signals with Cells
[0203] An image or movie may contain multiple cells in any given
field of view, frame, or image. In images containing multiple
neurons, the segmentation is performed semi-automatically using an
independent components analysis (ICA) based approach modified from
that of Mukamel, et al., 2009, Automated analysis of cellular
signals from large-scale calcium imaging data, Neuron 63:747-760.
The ICA analysis can isolate the image signal of an individual cell
from within an image.
[0204] FIG. 7-FIG. 10 illustrate the isolation of individual cells
in a field of view. Individual cells are isolated in a field of
view using an independent component analysis.
[0205] FIG. 7 shows an image that contains five neurons whose
images overlap with each other. The fluorescence signal at each
pixel is an admixture of the signals from each of the neurons
underlying that pixel.
[0206] As shown in FIG. 8, the statistical technique of independent
components analysis finds clusters of pixels whose intensity is
correlated within a cluster, and maximally statistically
independent between clusters. These clusters correspond to images
of individual cells comprising the aggregate image of FIG. 7.
[0207] From the pseudo-inverse of the set of images shown in FIG. 8
are calculated spatial filters with which to extract the
fluorescence intensity time-traces for each cell. Filters are
created by setting all pixel weights to zero, except for those in
one of the image segments. These pixels are assigned the same
weight they had in the original ICA spatial filter.
[0208] In FIG. 9, by applying the segmented spatial filters to the
movie data, the ICA time course has been broken into distinct
contributions from each cell. Segmentation may reveal that the
activities of the cells are strongly correlated, as expected for
cells found together by ICA. In this case, the spike trains from
the image segments are similar but show a progress over time as the
cells signal one another.
[0209] FIG. 10 shows the individual filters used to map (and color
code) individual cells from the original image.
[0210] 6b. Signal Processing via Sub-Nyquist Action Potential
Timing (SNAPT)
[0211] For individual cells, action potentials can be identified as
spike trains represented by the timing at which an interpolated
action potential crosses a threshold at each pixel in the image.
Identifying the spike train may be aided by first processing the
data to remove noise, normalize signals, improve SNR, other
pre-processing steps, or combinations thereof. Action potential
signals may first be processed by removing photobleaching,
subtracting a median filtered trace, and isolating data above a
noise threshold. The spike train may then be identified using an
algorithm based on sub-Nyquist action potential timing such as an
algorithm based on the interpolation approach of Foust, et al.,
2010, Action potentials initiate in the axon initial segment and
propagate through axon collaterals reliably in cerebellar Purkinje
neurons. J. Neurosci 30, 6891-6902 and Popovic et al, 2011, The
spatio-temporal characteristics of action potential initiation in
layer 5 pyramidal neurons: a voltage imaging study. J. Physiol.
589, 4167-4187.
[0212] A sub-Nyquist action potential timing (SNAPT) algorithm
highlights subcellular timing differences in AP initiation. For
example, the algorithm may be applied for neurons expressing
Optopatch1, containing a voltage reporter such as QuasAr1. Either
the soma or a small dendritic region is stimulated. The timing and
location of the ensuing APs is monitored.
[0213] FIG. 11 shows a patterned optical excitation being used to
induce action potentials. Movies of individual action potentials
are acquired (e.g., at 1,000 frames/s), temporally registered, and
averaged.
[0214] The first step in the temporal registration of spike movies
is to determine the spike times. Determination of spike times is
performed iteratively. A simple threshold-and-maximum procedure is
applied to F(t) to determine approximate spike times, {T0}.
Waveforms in a brief window bracketing each spike are averaged
together to produce a preliminary spike kernel K0(t). A
cross-correlation of K0(t) with the original intensity trace F(t)
is calculated. Whereas the timing of maxima in F(t) is subject to
errors from single-frame noise, the peaks in the cross-correlation,
located at times {T}, are a robust measure of spike timing. A movie
showing the mean AP propagation may be constructed by averaging
movies in brief windows bracketing spike times {T}. Typically
100-300 APs are included in this average. The AP movie has high
signal-to-noise ratio. A reference movie of an action potential is
thus created by averaging the temporally registered movies (e.g.,
hundreds of movies) of single APs. Each frame of the movie is then
corrected by dividing by this baseline.
[0215] Spatial and temporal linear filters may further decrease the
noise in AP movie. A spatial filter may include convolution with a
Gaussian kernel, typically with a standard deviation of 1 pixel. A
temporal filter may be based upon Principal Components Analysis
(PCA) of the set of single-pixel time traces. The time trace at
each pixel is expressed in the basis of PCA eigenvectors. Typically
the first 5 eigenvectors are sufficient to account for >99% of
the pixel-to-pixel variability in AP waveforms, and thus the PCA
Eigen-decomposition is truncated after 5 terms. The remaining
eigenvectors represented uncorrelated shot noise.
[0216] FIG. 12 shows eigenvectors resulting from a principal
component analysis (PCA) smoothing operation performed to address
noise. Photobleaching or other such non-specific background
fluorescence may be addressed by these means.
[0217] FIG. 13 shows a relation between cumulative variance and
eigenvector number. FIG. 14 gives a comparison of action potential
waveforms before and after the spatial and PCA smoothing
operations.
[0218] A smoothly varying spline function may be interpolated
between the discretely sampled fluorescence measurements at each
pixel in this smoothed reference AP movie. The timing at each pixel
with which the interpolated AP crosses a user-selected threshold
may be inferred with sub-exposure precision. The user sets a
threshold depolarization to track (represented as a fraction of the
maximum fluorescence transient), and a sign for dV/dt (indicating
rising or falling edge. The filtered data is fit with a quadratic
spline interpolation and the time of threshold crossing is
calculated for each pixel.
[0219] FIG. 15 shows an action potential timing map. The timing map
may be converted into a high temporal resolution SNAPT movie by
highlighting each pixel in a Gaussian time course centered on the
local AP timing. The SNAPT fits are converted into movies showing
AP propagation as follows. Each pixel is kept dark except for a
brief flash timed to coincide with the timing of the user-selected
AP feature at that pixel. The flash followed a Gaussian
time-course, with amplitude equal to the local AP amplitude, and
duration equal to the cell-average time resolution, .sigma.. Frame
times in the SNAPT movies are selected to be .about.2-fold shorter
than .sigma.. Converting the timing map into a SNAPT movie is for
visualization; propagation information is in the timing map.
[0220] FIG. 16 shows the accuracy of timing extracted by the SNAPT
algorithm for voltage at a soma via comparison to a simultaneous
patch clamp recording. FIG. 17 gives an image of eGFP fluorescence,
indicating CheRiff distribution.
[0221] FIG. 18 presents frames from a SNAPT movie formed by mapping
the timing information from FIG. 16 onto a high spatial resolution
image from FIG. 17. In FIG. 17, the white arrows mark the zone of
action potential initiation in the presumed axon initial segment
(AIS). FIGS. 16-18 demonstrate that methods of the invention can
provide high resolution spatial and temporal signatures of cells
expressing an optical reporter of neural activity.
[0222] After acquiring Optopatch data, cells may be fixed and
stained for ankyrin-G, a marker of the AIS. Correlation of the
SNAPT movies with the immunostaining images establish that the AP
initiated at the distal end of the AIS. The SNAPT technique does
not rely on an assumed AP waveform; it is compatible with APs that
change shape within or between cells.
[0223] The SNAPT movies show AP initiation from the soma in single
neurites in measured cells. The described methods are useful to
reveal latencies between AP initiation at the AIS and arrival in
the soma of 320.+-.220 .mu.s, where AP timing is measured at 50%
maximum depolarization on the rising edge. Thus Optopatch can
resolve functionally significant subcellular details of AP
propagation. Discussion of signal processing may be found in Mattis
et al., 2011, Principles for applying optogenetic tools derived
from direct comparative analysis of microbial opsins, Nat. Meth.
9:159-172; and Mukamel et al., 2009, Automated analysis of cellular
signals from large-scale calcium imaging data, Neuron 63
(6):747-760.
[0224] Methods of the invention are used to obtain a signature from
the observed cell or cells tending to characterize a physiological
parameter of the cell. The measured signature can include any
suitable electrophysiology parameter such as, for example, activity
at baseline, activity under different stimulus strengths, tonic vs.
phasic firing patterns, changes in AP waveform, others, or a
combination thereof. Measurements can include different modalities,
stimulation protocols, or analysis protocols. Exemplarily
modalities for measurement include voltage, calcium, ATP, or
combinations thereof. Exemplary stimulation protocols can be
employed to measure excitability, to measure synaptic transmission,
to test the response to modulatory chemicals, others, and
combinations thereof. Methods of invention may employ various
analysis protocols to measure: spike frequency under different
stimulus types, action potential waveform, spiking patterns,
resting potential, spike peak amplitude, others, or combinations
thereof.
[0225] In certain embodiments, the imaging methods are applied to
obtain a signature mean probability of spike for cells from the
patient and may also be used to obtain a signature from a control
line of cells such as a wild-type control (which may be produced by
genome editing as described above so that the control and the
wild-type are isogenic but for a single site). The observed
signature can be compared to a control signature and a difference
between the observed signature and the expected signature
corresponds to a positive diagnosis of the condition.
[0226] FIG. 19 shows a mean probability of spike of wild-type (WT)
and mutant (SOD1) cells. Cellular excitability was measured by
probability of spiking during each blue light stimulation, and
during no stimulation (spontaneous firing).
[0227] 7. Diagnosis
[0228] FIG. 19 illustrates an output from measuring action
potentials in cells affected by a mutation and control cells
isogenic but for the mutation. In the illustrated example, a
patient known to have SOD1A4V is studied and the bottom trace is
obtained from cells of that patient's genotype. The top trace
labeled "WT" refers to cells from that patient that were edited to
be SOD1V4A and thus wild-type at the locus of the patient's known
mutation but otherwise to provide the genetic context present in
the patient. A clinician may diagnosis a neurodegenerative disease
based on a signature spike train manifest by the patient's cells.
Here, a difference between the signature observed in the patient's
cells and the control signature may be correlated to a positive
diagnosis of a neurodegenerative disease.
[0229] Any suitable method of correlating the patient's signature
to a diagnosis may be used. For example, in some embodiments,
visual inspection of a signature may be used. In certain
embodiments, a computer system may be used to automatically
evaluate that an observed signature of the test cells satisfies
predetermined criteria for a diagnosis. Any suitable criteria can
be used. For example, a computer system may integrate under the
spike train for both the test cells and the control cells over a
range of time of at least a few thousand ms and compare a
difference between the results. Any suitable difference between the
observed and expected signals can be used, for example, the
difference may include a modified probability of a voltage spike in
response to the stimulation of the cell relative to a control. In
certain embodiments (e.g., FIG. 19) the difference between the
observed signal and the expected signal comprises a decreased
probability of a voltage spike in response to the stimulation of
the cell relative to a control and an increased probability of a
voltage spike during periods of no stimulation of the cell relative
to a control. In one embodiment, systems and methods of the
invention detect a decreased probability of a voltage spike in
response to the stimulation of the cell relative to a control.
[0230] To give one example, a difference of at least 5% can be
reported as indicative of an increased risk or diagnosis of a
condition. In another example, a computer system can analyze a
probability of spike at a certain time point (e.g., 5500 ms) and
look for a statistically significant difference. In another
example, a computer system can be programed to first identify a
maximal point in the WT spike train (control signature) and then
compare a probability at that point in the control signature to a
probability in the patient's test signature at the same point and
look for a reportable difference (e.g., at least 5% different). One
of skill in the art will recognize that any suitable criterion can
be used in the comparison of the test signature to the control
signature. In certain embodiments, a computer system is trained by
machine learning (e.g., numerous instances of known healthy and
known diseased are input and a computer system measures an average
difference between those or an average signature pattern of a
disease signature). Where the computer system stores a signature
pattern for a disease phenotype, a diagnosis is supported when the
computer system finds a match between the test signature and the
control signature (e.g., <5% different or less than 1% different
at some point or as integrated over a distance). While obtaining a
control signature from a genome-edited cell line from the patient
has been discussed, one of skill in the art will recognize that the
control signature can be a template or documented control signature
stored in computer system of the invention.
[0231] In certain embodiments, observation of a signature from a
cell is used in a diagnosis strategy in which the observed
signature phenotype contributes to arriving at a final diagnosis.
For example, with certain disease of the nervous system such as
ALS, different neuron types may be affected differently. In some
embodiments, a diagnostic method includes comparing different
neuron types from the same patient to diagnose a sub-type specific
disease.
[0232] 8. Additional Methods
[0233] Methods of the invention may include the use of tool/test
compounds or other interventional tools applied to the observed
cell or cells. Application of test compounds can reveal effects of
those compounds on cellular electrophysiology. Use of a tool
compounds can achieve greater specificity in diagnosis or for
determining disease mechanisms, e.g. by blocking certain ion
channels. By quantifying the impact of the compound, one can
quantify the level of that channel in the cell.
[0234] With a tool or test compound, a cell may be caused to
express an optical reporter of neural or electrical activity and
may also be exposed to a compound such as a drug. A signature of
the cell can be observed before, during, or after testing the
compound. Any combination of different cells and cell types can be
exposed to one or any combination of compounds, including different
test compound controls. Multi-well plates, multi-locus spotting on
slides, or other multi-compartment lab tools can be used to
cross-test any combination of compounds and cell types.
[0235] In certain embodiments, tool compounds are added to cells
and their effect on the cells is observed to distinguish possible
diseases or causes or mechanisms of diseases. For example, where
two or more cells in synaptic connection with one another are
observed, extrinsic stimulation of an upstream cell should manifest
as an action potential in a downstream cell. A compound that is
known to inhibit neurotransmitter reuptake may be revealed to work
on only certain neural subtypes thus indicating a specific disease
pattern.
[0236] In some embodiments, methods of the invention are used to
detect, measure, or evaluate synaptic transmission. A signature may
be observed for a cell other than the cell to which direct
stimulation was applied. In fact, using the signal processing
algorithms discussed herein, synaptic transmission among a
plurality of cells may be detected thus revealing patterns of
neural connection. Establishing an assay that successfully detects
firing of a downstream neuron upon stimulation of an upstream
neuron can reveal, where the subject cell to be observed fails to
fire upon stimulation of an upstream neuron, a disease or condition
characterized by a failure of synaptic transmission.
[0237] Test compounds can be evaluated as candidate therapies to
determine suitability of a treatment prior to application to
patient. E.g. one can test epilepsy drugs to find the one that
reverts the firing pattern back to wild-type. In some embodiments,
the invention provides systems and methods for identifying possible
therapies for a patient by testing compounds, which systems and
methods may be employed as personalized medicine. Due to the nature
of the assays described herein, it may be possible to evaluate the
effects of candidate therapeutic compounds on a per-patient basis
thus providing a tool for truly personalized medicine. For example,
an assay as described herein may reveal that a patient suffering
from a certain disease has neurons or neural subtypes that exhibit
a disease-type physiological phenotype under the assays described
herein. One or a number of different compounds may be applied to
those neurons or neural subtypes. Cells that are exposed to one of
those different compounds (or a combination of compounds) may
exhibit a change in physiological phenotype from disease-type to
normal. The compound or combination of compounds that affects the
change in phenotype from disease-type to normal is thus identified
as a candidate treatment compound for that patient.
[0238] 9. Systems of the Invention
[0239] FIG. 20 presents a system 1101 useful for performing methods
of the invention. Results from a lab (e.g., transformed, converted
patient cells) are loaded into imaging instrument 501. Imaging
instrument 501 is operably coupled to an analysis system 1119,
which may be a PC computer or other device that includes a
processor 125 coupled to a memory 127. A user may access system
1101 via PC 1135, which also includes a processor 125 coupled to a
memory 127. Analytical methods described herein may be performed by
any one or more processor 125 such as may be in analysis system
1119, PC 1135, or server 1139, which may be provided as part of
system 1101. Server 1139 includes a processor 125 coupled to a
memory 127 and may also include optional storage system 1143. Any
of the computing device of system 1101 may be communicably coupled
to one another via network 1131. Any, each, or all of analysis
system 1119, PC 1135, and server 1139 will generally be a computer.
A computer will generally include a processor 125 coupled to a
memory 127 and at least one input/output device.
[0240] A processor 125 will generally be a silicon chip
microprocessor such as one of the ones sold by Intel or AMD.
[0241] Memory 127 may refer to any tangible, non-transitory memory
or computer readable medium capable of storing data or
instructions, which--when executed by a processer 125--cause
components of system 1101 to perform methods described herein.
[0242] Typical input/output devices may include one or more of a
monitor, keyboard, mouse, pointing device, network card, Wi-Fi
card, cellular modem, modem, disk drive, USB port, others, and
combinations thereof.
[0243] Generally, network 1131 will include hardware such as
switches, routers, hubs, cell towers, satellites, landlines, and
other hardware such as makes up the Internet.
INCORPORATION BY REFERENCE
[0244] References and citations to other documents, such as
patents, patent applications, patent publications, journals, books,
papers, web contents, have been made throughout this disclosure.
All such documents are hereby incorporated herein by reference in
their entirety for all purposes.
Equivalents
[0245] Various modifications of the invention and many further
embodiments thereof, in addition to those shown and described
herein, will become apparent to those skilled in the art from the
full contents of this document, including references to the
scientific and patent literature cited herein. The subject matter
herein contains important information, exemplification and guidance
that can be adapted to the practice of this invention in its
various embodiments and equivalents thereof.
* * * * *