U.S. patent application number 09/819247 was filed with the patent office on 2001-11-01 for compositions and methods for identifying and targeting cancer cells of alimentary canal origin.
Invention is credited to Park, Jason, Schulz, Stephanie, Waldman, Scott A..
Application Number | 20010036635 09/819247 |
Document ID | / |
Family ID | 22708782 |
Filed Date | 2001-11-01 |
United States Patent
Application |
20010036635 |
Kind Code |
A1 |
Waldman, Scott A. ; et
al. |
November 1, 2001 |
Compositions and methods for identifying and targeting cancer cells
of alimentary canal origin
Abstract
Screening and diagnostic reagents, kits and methods for
metastatic colorectal cancer or primary and/or metastatic stomach
or esophageal cancer are disclosed. Compounds, compositions and
methods of treating patients with metastatic colorectal cancer or
stomach or esophageal cancer and for imaging metastatic colorectal
cancer or stomach or esophageal tumors in vivo are disclosed.
Compositions and methods for delivering active compounds such as
drugs, gene therapeutics and antisense compounds to metastatic
colorectal cancer or stomach or esophageal cells are disclosed.
Vaccines compositions and methods of for treating and preventing
metastatic colorectal cancer or primary and/or metastatic stomach
or esophageal cancer are disclosed.
Inventors: |
Waldman, Scott A.; (Ardmore,
PA) ; Park, Jason; (Philadelphia, PA) ;
Schulz, Stephanie; (West Chester, PA) |
Correspondence
Address: |
Mark DeLuca, Esq.
WOODCOCK WASHBURN KURTZ
MACKIEWICZ & NORRIS LLP
One Liberty Place - 46th Floor
Philadelphia
PA
19103
US
|
Family ID: |
22708782 |
Appl. No.: |
09/819247 |
Filed: |
March 27, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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60192229 |
Mar 27, 2000 |
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Current U.S.
Class: |
435/6.12 ;
424/1.11; 435/6.14; 435/7.23; 514/27; 514/34 |
Current CPC
Class: |
C12Q 2600/158 20130101;
C12Q 1/6886 20130101; A61P 35/04 20180101; C12N 15/113 20130101;
A61P 1/00 20180101; A61K 51/1075 20130101; A61K 9/127 20130101;
A61K 31/7048 20130101; A61K 39/001102 20180801; A61K 47/6871
20170801; A61K 31/7034 20130101; A61P 37/04 20180101; A61P 35/00
20180101; C07K 16/40 20130101; G01N 33/57419 20130101; G01N
33/57407 20130101; G01N 2333/988 20130101; C07K 16/3046 20130101;
G01N 33/57446 20130101 |
Class at
Publication: |
435/6 ; 435/7.23;
514/27; 514/34; 424/1.11 |
International
Class: |
C12Q 001/68; A61K
051/00; G01N 033/574; A61K 031/7048; A61K 031/7034 |
Claims
1. An in vitro method of screening an individual for metastatic
colorectal cancer cells or primary and/or metastatic stomach or
esophageal cancer cells comprising the steps of examining a sample
of extraintestinal tissue and/or body fluids from an individual to
determine whether SI is being expressed by cells in said sample
wherein expression of said SI indicates a possibility of metastatic
colorectal cancer cells or primary and/or metastatic stomach or
esophageal cancer cells in said sample.
2. The method of claim 1 wherein expression of said SI by said
cells is determined by detecting the presence of SI gene
transcription product.
3. The method of claim 1 wherein expression of said SI by said
cells is determined by polymerase chain reaction wherein said
sample is contacted with primers that selectively amplify SI gene
transcript or cDNA generated therefrom.
4. The method of claim 1 wherein expression of said SI by said
cells is determined by immunoassay wherein said sample is contacted
with antibodies that specifically bind to SI gene translation
product.
5. The method of claim 1 wherein said sample is body fluid.
6. The method of claim 1 wherein said sample is blood.
7. The method of claim 1 wherein said sample is lymphatic tissue
and/or fluid.
8. The method of claim 1 wherein said sample is a lymph node
sample.
9. The method of claim 1 wherein the individual has previously been
diagnosed with having colorectal, stomach or esophageal cancer.
10. The method of claim 1 wherein the individual has previously
been diagnosed with and treated for colorectal, stomach or
esophageal cancer
11. An in vitro method of screening an individual for metastatic
colorectal cancer cells or primary and/or metastatic stomach or
esophageal cancer cells comprising the steps of examining a sample
of extraintestinal tissue and/or body fluids from an individual to
determine whether SI gene transcription or translation product is
present in said sample wherein the presence of SI gene
transcription or translation product in said sample indicates that
the individual may have metastatic colorectal cancer cells or
primary and/or metastatic stomach or esophageal cancer cells in
said sample.
12. The method of claim 10 comprising the steps of examining a
sample of extraintestinal tissue and/or body fluids from an
individual to determine whether SI gene transcription product is
present in said sample.
13. The method of claim 12 wherein the presence of SI gene
transcription product is determined by polymerase chain reaction
wherein said sample is contacted with primers that selectively
amplify SI gene transcript or cDNA generated therefrom.
14. The method of claim 11 wherein the presence of SI gene
translation product is determined by immunoassay wherein said
sample is contacted with antibodies that specifically bind to SI
gene translation product.
15. The method of claim 11 wherein said sample is body fluid.
16. The method of claim 11 wherein said sample is blood.
17. The method of claim 11 wherein said sample is lymphatic tissue
and/or fluid.
18. The method of claim 11 wherein said sample is a lymph node
sample.
19. The method of claim 11 wherein the individual has previously
been diagnosed with having colorectal, stomach or esophageal
cancer.
20. The method of claim 11 wherein the individual has previously
been diagnosed with and treated for colorectal, stomach or
esophageal cancer
21. An in vitro method of confirming that a tumor cell removed from
a patient suspected of having colorectal, stomach or esophageal
cancer cells is a colorectal, stomach or esophageal tumor cell
comprising the step of determining whether a tumor cell expresses
SI wherein expression of SI indicates that the tumor cell is a
stomach or esophageal tumor cell.
22. The method of claim 21 wherein expression of SI by said tumor
cell is determined by detecting the presence of SI gene
transcription product.
23. The method of claim 21 wherein expression of SI by said tumor
cell is determined by polymerase chain reaction wherein mRNA from
said tumor cell or cDNA generated therefrom is contacted with
primers that selectively amplify SI gene transcript or cDNA
generated therefrom.
24. The method of claim 21 wherein expression of SI by said tumor
cell is determined by immunoassay wherein protein from said tumor
cell is contacted with antibodies that specifically bind to SI gene
translation product.
25. A method of diagnosing an individual who has stomach cancer
comprising the steps of examining a sample of stomach tissue to
detect the presence of SI transcript or translation product wherein
the presence of SI transcript or translation product in a stomach
sample indicates stomach cancer.
26. The method of claim 25 comprising the steps of examining said
sample of stomach tissue to determine whether SI gene transcription
product is present in said sample.
27. The method of claim 26 wherein the presence of SI gene
transcription product is determined by polymerase chain reaction
wherein said sample is contacted with primers that selectively
amplify SI gene transcript or cDNA generated therefrom.
28. The method of claim 26 wherein the presence of SI gene
translation product is determined by immunoassay wherein said
sample is contacted with antibodies that specifically bind to SI
gene translation product.
29. A method of diagnosing an individual who has esophageal cancer
comprising the steps of examining a sample of esophagus tissue to
detect the presence of SI transcript or translation product wherein
the presence of SI transcript or translation product in an
esophageal sample indicates esophageal cancer.
30. The method of claim 29 comprising the steps of examining said
sample of esophageal tissue to determine whether SI gene
transcription product is present in said sample.
31. The method of claim 30 wherein the presence of SI gene
transcription product is determined by polymerase chain reaction
wherein said sample is contacted with primers that selectively
amplify SI gene transcript or cDNA generated therefrom.
32. The method of claim 29 wherein the presence of SI gene
translation product is determined by immunoassay wherein said
sample is contacted with antibodies that specifically bind to SI
gene translation product.
33. A kit for diagnosing an individual who has colorectal, stomach
and/or esophageal cancer comprising either: a) a container
comprising polymerase chain reaction primers that selectively
amplify SI gene transcript or cDNA generated therefrom; and one or
more of: a container comprising a positive PCR assay control
sample, a container comprising a negative PCR assay control sample,
instructions for obtaining and/or processing a sample, instructions
for performing a PCR diagnostic assay, and photographs or
illustrations depicting a positive result and/or a negative result
of a PCR diagnostic assay; or b) a container comprising antibodies
that specifcially bind to SI gene translation product; and one or
more of: a container comprising a positive immunoassay control
sample, a container comprising a negative immunoassay control
sample, instructions for obtaining and/or processing a sample,
instructions for performing an immuno diagnostic assay, and
photographs or illustrations depicting a positive result and/or a
negative result of an immuno diagnostic assay.
34. A method of treating an individual suspected of suffering from
metastasized colorectal cancer, or primary and/or stomach or
espophageal cancer comprising the steps of administering to said
individual a therapeutically effective amount of a composition
comprising: i) an SI ligand; and, ii) an active agent.
35. The method of claim 34 wherein the SI ligand is conjugated to
the active agent.
36. The method of claim 34 wherein said an active agent is selected
from the group consisting of: methotrexate, doxorubicin,
daunorubicin, cytosinarabinoside, etoposide, 5-4 fluorouracil,
melphalan, chlorambucil, cis-platinum, vindesine, mitomycin,
bleomycin, purothionin, macromomycin, 1,4-benzoquinone derivatives,
trenimon, ricin, ricin A chain, Pseudomonas exotoxin, diphtheria
toxin, Clostridium perfringens phospholipase C, bovine pancreatic
ribonuclease, pokeweed antiviral protein, abrin, abrin A chain,
cobra venom factor, gelonin, saporin, modeccin, viscumin,
volkensin, alkaline phosphatase, nitroimidazole, metronidazole,
misonidazole, .sup.47Sc, .sup.67Cu, .sup.90Y, .sup.109Pd,
.sup.123I, .sup.125I, .sup.131I, .sup.186Re, .sup.188Re,
.sup.199Au, .sup.211At, .sup.212Pb, .sup.212B, .sup.32P and
.sup.33P, .sup.71Ge, .sup.77As, .sup.103Pb, .sup.105Rh, .sup.111Ag,
.sup.119Sb, .sup.121Sn, .sup.131Cs, .sup.143Pr, .sup.161Tb,
.sup.177Lu, .sup.191Os, .sup.193Mpt, .sup.197Hg, .sup.43K,
.sup.52Fe, .sup.57Co, .sup.67Cu, .sup.67Ga, .sup.68Ga, .sup.77Br,
.sup.81Rb/.sup.81MKr, .sup.87MSr, .sup.99MTc, .sup.111In,
.sup.113MIn, .sup.123I, .sup.125I, .sup.127Cs, .sup.129Cs,
.sup.131I, .sup.132I, .sup.197 Hg, .sup.203Pb and .sup.206Bi.
37. A method of radioimaging metastasized colorectal cancer cells
comprising the steps of administering to an individual a
composition comprising an SI ligand linked to a detectable
agent.
38. The method of claim 37 wherein said detectable agent is
selected from the group consisting of: .sup.47Sc, .sup.67Cu,
.sup.90Y, .sup.109Pd, .sup.123I, .sup.125I, .sup.131I, .sup.186Re,
.sup.188Re, .sup.199Au, .sup.211At, .sup.212Pb, .sup.212B, .sup.32P
and .sup.33P, .sup.71Ge, .sup.77As, .sup.103Pb .sup.105Rh,
.sup.111Ag, .sup.119Sb, .sup.121Sn, .sup.131Cs, .sup.143Pr,
.sup.161Tb, .sup.177Lu, .sup.191OS, .sup.193MPt, .sup.197Hg,
.sup.43K, .sup.52Fe, .sup.57Co, .sup.67Cu, .sup.67Ga, .sup.68Ga,
.sup.77Br, .sup.81Rb/.sup.81MKr, .sup.87MSr, .sup.99MTc,
.sup.111In, .sup.113MIn, .sup.123I, .sup.125I, .sup.127Cs,
.sup.129Cs, .sup.131I, .sup.132I, .sup.197Hg, .sup.203Pb and
.sup.206Bi.
Description
CROSS REFERENCE TO RELATED PATENT APPLICATIONS
[0001] This application claims priority to U.S. Provisional
Application No. 60/192,229 filed Mar. 27, 2000, which is
incorporated herein by reference.
[0002] This application is also related to U.S. Pat. No. 5,518,888,
issued May 21, 1996, U.S. Pat. No. 5,601,990 issued Feb. 11, 1997,
U.S. Pat. No. 6,060,037 issued Apr. 26, 2000, U.S. Pat. No.
5,962,220 issued Oct. 5, 1999, and U.S. Pat. No. 5,879,656 issued
Mar. 9, 1999, which are each incorporated herein by reference and
U.S. patent application Ser. No. 09/180,237 filed Mar. 12, 1997,
which is incorporated herein by reference.
FIELD OF THE INVENTION
[0003] The present invention relates to in vitro diagnostic methods
for detecting cancer cells of the alimentary canal, particularly
primary and metastatic stomach and esophageal cancer and metastatic
colorectal cancer, and to kits and reagents for performing such
methods. The present invention relates to compounds and methods for
in vivo imaging and treatment of tumors originating from the
alimentary canal, particularly primary and metastatic stomach and
esophageal tumors and metastatic colorectal tumors. The present
invention relates to methods and compositions for making and using
targeted gene therapy, antisense and drug compositions. The present
invention relates to prophylactic and therapeutic vaccines against
cancer cells of the alimentary canal, particularly primary and
metastatic stomach and esophageal cancer and metastatic colorectal
cancer and compositions and methods of making and using the
same.
BACKGROUND OF THE INVENTION
[0004] There is a need for reagents, kits and methods for
screening, diagnosing and monitoring individuals with cancer
originating from the alimentary canal, particularly primary and
metastatic stomach and esophageal cancer and metastatic colorectal
cancer. There is a need for reagents, kits and methods for
identifying and confirming that a cancer of unknown origin is
originating from the alimentary canal and for analyzing tissue and
cancer samples to identify and confirm cancer originating from the
alimentary canal and to determine the level of migration of such
cancer cells. There is a need for compositions which can
specifically target colorectal, stomach and esophageal cancer
cells. There is a need for imaging agents which can specifically
bind to colorectal, stomach and esophageal cancer cells. There is a
need for improved methods of imaging colorectal, stomach and
esophageal cancer cells. There is a need for therapeutic agents
which can specifically bind to colorectal, stomach and esophageal
cancer cells. There is a need for improved methods of treating
individuals who are suspected of suffering from primary and/or
metastatic stomach or esophageal cancer or metastatic colorectal
cancer. There is a need for vaccine composition to treat
colorectal, stomach and esophageal cancer. There is a need for
vaccine composition to treat and prevent metastasized colorectal,
stomach and esophageal cancer. There is a need for therapeutic
agents which can specifically deliver gene therapeutics, antisense
compounds and other drugs to colorectal, stomach and esophageal
cancer cells.
SUMMARY OF THE INVENTION
[0005] The invention further relates to in vitro methods of
determining whether or not an individual has cancer originating
from the alimentary canal, particularly primary and metastatic
stomach and esophageal cancer and metastatic colorectal cancer. The
present invention relates to in vitro methods of examining samples
of non-colorectal tissue and body fluids from an individual to
determine whether or not SI, which is expressed by normal colon
cells and by colorectal, stomach and esophageal tumor cells, is
being expressed by cells in samples other than colon. The presence
of SI protein or of the SI gene transcript in samples outside the
colorectal track is indicative of expression of SI and is evidence
that the individual may be suffering from metastasized colon cancer
or primary or metastatic stomach and/or esophageal cancer. In
patients suspected of suffering from colorectal cancer, the
presence of SI protein or of the SI gene transcript in samples
outside the colorectal track is supportive of the conclusion that
the individual is suffering from metastatic colorectal cancer. The
diagnosis of metastatic colorectal cancer may be made or confirmed.
In patients suspected of suffering from stomach or esophageal
cancer, the presence of SI protein or of the SI gene transcript in
samples outside the colorectal track is supportive of the
conclusion that the individual is suffering from primary and/or
metastatic stomach or esophageal cancer. The diagnosis of primary
and/or metastatic stomach or esophageal cancer may be made or
confirmed.
[0006] The invention further relates to in vitro methods of
determining whether or not tumor cells are colorectal, stomach or
esophageal in origin. The present invention relates to in vitro
methods of diagnosing whether or not an individual suffering from
cancer is suffering from colorectal, stomach or esophageal cancer.
The present invention relates to in vitro methods of examining
samples of tumors from an individual to determine whether or not SI
protein, which is expressed by colorectal, stomach or esophageal
tumor cells, is being expressed by the tumor cells. The presence of
a SI protein or of the SI gene transcript is indicative of
expression of SI and evidence that the individual may be suffering
from colorectal, stomach or esophageal cancer. In tumors which are
suspected of being colorectal, stomach or esophageal tumors, the
presence of a SI protein or of the SI gene transcript supports the
conclusion that the tumors are of colorectal, stomach or esophageal
cancer and the diagnosis of colorectal, stomach or esophageal
cancer.
[0007] The invention further relates to in vitro kits for
practicing the methods of the invention and to reagents and
compositions useful as components in such in vitro kits of the
invention.
[0008] The invention further relates to a method of imaging primary
and metastatic stomach and esophageal tumors and metastatic
colorectal tumors and to methods of treating an individual
suspected of suffering from primary and metastatic stomach and
esophageal tumors and metastatic colorectal tumors comprising the
steps of administering to said individual a pharmaceutical
compositions according to the invention, wherein the compositions
or conjugated compounds are present in an amount effective for
therapeutic or diagnostic use in humans suffering from primary
and/or metastatic stomach or esophageal tumors and metastatic
colorectal tumors cancer.
[0009] The invention further relates to a method of delivering an
active agent to primary and metastatic stomach and esophageal tumor
cells and metastatic colorectal tumors cells comprising the steps
of administering to an individual who has primary and/or metastatic
stomach or esophageal tumors or metastatic colorectal cancer, a
pharmaceutical composition comprising a pharmaceutically acceptable
carrier or diluent, and an unconjugated compositions that comprises
a liposome that includes SI ligands on its surface and an active
component encapsulated therein.
[0010] The invention further relates to killed or inactivated
colorectal, stomach or esophageal tumor cells that comprise a
protein comprising at least one epitope of a SI protein; and to
vaccines comprising the same. In some embodiments, the killed or
inactivated cells or particles comprise a SI protein. In some
embodiments, the killed or inactivated cells or particles are
haptenized.
[0011] The invention further relates to methods of treating
individuals suffering from colorectal, stomach or esophageal cancer
and to methods of treating individuals susceptible colorectal,
stomach or esophageal cancer. The method of the present invention
provides administering to such individuals an effective amount of
such vaccines. The invention further relates to the use of such
vaccines as immunotherapeutics.
DESCRIPTION OF PREFERRED EMBODIMENTS
[0012] Definitions
[0013] As used herein, the term "SI" is meant to refer to the
cellular protein also known as sucrase isomaltase which is
expressed by normal colorectal cells, as well as primary and
metastasized colorectal, stomach and esophageal cancer cells.
[0014] As used herein, the term "functional fragment" as used in
the term "functional fragment of a SI gene transcript" is meant to
refer to fragments of SI gene transcript which are functional with
respect to nucleic acid molecules with full length sequences. For
example, a functional fragment may be useful as an oligonucleotide
or nucleic acid probe, a primer, an antisense oligonucleotide or
nucleic acid molecule or a coding sequence. The nucleotide sequence
encoding human SI protein is disclosed in Chantret,I et al. Ann.
Hum. Genet. 52 (Pt 1), 57-61 (1988) and GenBank Accession No. NM
001041, which are both incorporated herein by reference.
[0015] As used herein, the term "functional fragment" as used in
the term "functional fragment of a SI protein" is meant to
fragments of SI protein which function in the same manner as SI
protein with full length sequences. For example, an immunogenically
functional fragment of a SI protein comprises an epitope recognized
by an anti-SI antibody. A ligand-binding functional fragment of SI
comprises a sequence which forms a structure that can bind to a
ligand which recognizes and binds to SI protein.
[0016] As used herein, the term "epitope recognized by an anti-SI
protein antibody" refers to those epitopes specifically recognized
by an anti-SI protein antibody.
[0017] As used herein, the term "antibody" is meant to refer to
complete, intact antibodies, and Fab fragments and F(ab).sub.2
fragments thereof. Complete, intact antibodies include monoclonal
antibodies such as murine monoclonal antibodies, chimeric
antibodies and humanized antibodies.
[0018] As used herein, the term "SI ligand" is meant to refer to
compounds which specifically bind to a SI protein. Antibodies that
bind to SI are SI ligands. A SI ligand may be a protein, peptide or
a non-peptide.
[0019] As used herein, the term "active agent" is meant to refer to
compounds that are therapeutic agents or imaging agents.
[0020] As used herein, the term "radiostable" is meant to refer to
compounds which do not undergo radioactive decay; i.e. compounds
which are not radioactive.
[0021] As used herein, the term "therapeutic agent" is meant to
refer to chemotherapeutics, toxins, radiotherapeutics, targeting
agents or radiosensitizing agents.
[0022] As used herein, the term "chemotherapeutic" is meant to
refer to compounds that, when contacted with and/or incorporated
into a cell, produce an effect on the cell including causing the
death of the cell, inhibiting cell division or inducing
differentiation.
[0023] As used herein, the term "toxin" is meant to refer to
compounds that, when contacted with and/or incorporated into a
cell, produce the death of the cell.
[0024] As used herein, the term "radiotherapeutic" is meant to
refer to radionuclides which when contacted with and/or
incorporated into a cell, produce the death of the cell.
[0025] As used herein, the term "targeting agent" is meant to refer
compounds which can be bound by and or react with other compounds.
Targeting agents may be used to deliver chemotherapeutics, toxins,
enzymes, radiotherapeutics, antibodies or imaging agents to cells
that have targeting agents associated with them and/or to convert
or otherwise transform or enhance co-administered active agents. A
targeting agent may include a moiety that constitutes a first agent
that is localized to the cell which when contacted with a second
agent either is converted to a third agent which has a desired
activity or causes the conversion of the second agent into an agent
with a desired activity. The result is the localized agent
facilitates exposure of an agent with a desired activity to the
cancer cell.
[0026] As used herein, the term "radiosensitizing agent" is meant
to refer to agents which increase the susceptibility of cells to
the damaging effects of ionizing radiation. A radiosensitizing
agent permits lower doses of radiation to be administered and still
provide a therapeutically effective dose.
[0027] As used herein, the term "imaging agent" is meant to refer
to compounds which can be detected.
[0028] As used herein, the term "SI binding moiety" is meant to
refer to the portion of a conjugated compound that constitutes an
SI ligand.
[0029] As used herein, the term "active moiety" is meant to refer
to the portion of a conjugated compound that constitutes an active
agent.
[0030] As used herein, the terms "conjugated compound" and
"conjugated composition" are used interchangeably and meant to
refer to a compound which comprises a SI binding moiety and an
active moiety and which is capable of binding to SI. Conjugated
compounds according to the present invention comprise a portion
which constitutes an SI ligand and a portion which constitutes an
active agent. Thus, conjugated compounds according to the present
invention are capable of specifically binding to the SI and include
a portion which is a therapeutic agent or imaging agent. Conjugated
compositions may comprise crosslinkers and/or molecules that serve
as spacers between the moieties.
[0031] As used herein, the terms "crosslinker", "crosslinking
agent", "conjugating agent", "coupling agent", "condensation
reagent" and "bifunctional crosslinker" are used interchangeably
and are meant to refer to molecular groups which are used to attach
the SI ligand and the active agent to thus form the conjugated
compound.
[0032] As used herein, the term "colorectal cancer" is meant to
include the well-accepted medical definition that defines
colorectal cancer as a medical condition characterized by cancer of
cells of the intestinal tract below the small intestine (i.e. the
large intestine (colon), including the cecum, ascending colon,
transverse colon, descending colon, and sigmoid colon, and rectum).
Additionally, as used herein, the term "colorectal cancer" is meant
to further include medical conditions which are characterized by
cancer of cells of the duodenum and small intestine (jejunum and
ileum). The definition of colorectal cancer used herein is more
expansive than the common medical definition but is provided as
such since the cells of the duodenum and small intestine also
contain SI.
[0033] As used herein, the term "stomach cancer" is meant to
include the well-accepted medical definition that defines stomach
cancer as a medical condition characterized by cancer of cells of
the stomach.
[0034] As used herein, the term "esophageal cancer" is meant to
include the well-accepted medical definition that defines
esophageal cancer as a medical condition characterized by cancer of
cells of the esophagus.
[0035] As used herein, the term "metastasis" is meant to refer to
the process in which cancer cells originating in one organ or part
of the body relocate to another part of the body and continue to
replicate. Metastasized cells subsequently form tumors which may
further metastasize. Metastasis thus refers to the spread of cancer
from the part of the body where it originally occurs to other parts
of the body.
[0036] As used herein, the term "metastasized colorectal cancer
cells" is meant to refer to colorectal cancer cells which have
metastasized. Metastasized colorectal cancer cells localized in a
part of the body other than the duodenum, small intestine (jejunum
and ileum), large intestine (colon), including the cecum, ascending
colon, transverse colon, descending colon, and sigmoid colon, and
rectum.
[0037] As used herein, the term "metastasized stomach cancer cells"
is meant to refer to stomach cancer cells which have metastasized.
Metastasized stomach cancer cells localized in a part of the body
other than the stomach.
[0038] As used herein, the term "metastasized esophageal cancer
cells" is meant to refer to colorectal cancer cells which have
metastasized. Metastasized esophageal cancer cells localized in a
part of the body other than the esophagus.
[0039] As used herein, the term "non-colorectal sample" and
"extra-intestinal sample" are used interchangeably and meant to
refer to a sample of tissue or body fluid from a source other than
colorectal tissue. In some preferred embodiments, the
non-colorectal sample is a sample of tissue such as lymph nodes. In
some preferred embodiments, the non-colorectal sample is a sample
of extra-intestinal tissue which is an adenocarcinoma of
unconfirmed origin. In some preferred embodiments, the
non-colorectal sample is a blood sample.
[0040] As used herein, "an individual suffering from an
adenocarcinoma of unconfirmed origin" is meant to refer to an
individual who has a tumor in which the origin has not been
definitively identified.
[0041] As used herein, "an individual is suspected of being
susceptible to colorectal, stomach or esophageal cancer" is meant
to refer to an individual who is at a particular risk of developing
colorectal, stomach or esophageal cancer. Examples of individuals
at a particular risk of developing colorectal, stomach or
esophageal cancer are those whose family medical history indicates
above average incidence of colorectal, stomach or esophageal cancer
among family members and/or those who have already developed
colorectal, stomach or esophageal cancer and have been effectively
treated who therefore face a risk of relapse and recurrence.
[0042] As used herein, the term "antisense composition" and
"antisense molecules" are used interchangeably and are meant to
refer to compounds that regulate transcription or translation by
hybridizing to DNA or RNA and inhibiting and/or preventing
transcription or translation from taking place. Antisense molecules
include nucleic acid molecules and derivatives and analogs thereof.
Antisense molecules hybridize to DNA or RNA in the same manner as
complementary nucleotide sequences do regardless of whether or not
the antisense molecule is a nucleic acid molecule or a derivative
or analog. Antisense molecules may inhibit or prevent transcription
or translation of genes whose expression is linked to cancer.
[0043] As used herein, the term "SI immunogen" is meant to refer to
SI protein or a fragment thereof or a protein that comprises the
same or a haptenized product thereof, cells and particles which
display at least one SI epitope, and haptenized cells and
haptenized particles which display at least one SI epitope.
[0044] As used herein, the term "recombinant expression vector" is
meant to refer to a plasmid, phage, viral particle or other vector
which, when introduced into an appropriate host, contains the
necessary genetic elements to direct expression of the coding
sequence that encodes the protein. The coding sequence is operably
linked to the necessary regulatory sequences. Expression vectors
are well known and readily available. Examples of expression
vectors include plasmids, phages, viral vectors and other nucleic
acid molecules or nucleic acid molecule containing vehicles useful
to transform host cells and facilitate expression of coding
sequences.
[0045] As used herein, the term "illegitimate transcription" is
meant to refer to the low level or background expression of
tissue-specific genes in cells from other tissues. The phenomenon
of illegitimate transcription thus provides copies of mRNA for a
tissue specific transcript in other tissues. If detection
techniques used to detect gene expression are sufficiently
sensitive to detect illegitimate transcription, the expression
level of the transcript in negative samples due to illegitimate
transcription must be discounted using controls and/or quantitative
assays and/or other means to eliminate the incidence of false
positive due to illegitimate transcription. Alternatively,
detection of evidence of SI gene expression in sample is achieved
without detecting SI gene transcript present due to illegitimate
transcription. This is accomplished using techniques which are not
sufficiently sensitive to detect the SI gene transcript present due
to illegitimate transcription which is present as background.
[0046] SI
[0047] Carcinomas derived from the colorectal cells, stomach or
esophagus express SI. The expression of SI by such tumors enables
this protein and its mRNA to be a specific biomarker for the
presence of cancer cells in extra-intestinal tissues and blood.
Indeed, this characteristic permits the detection of SI mRNA by
RT-PCR analysis to be a diagnostic test to stage patients with
colorectal, stomach or esophageal cancer and follow patients after
surgery for evidence of recurrent disease in their blood as well as
to detect colorectal, stomach and esophageal cancers. Further, the
SI may be targeted with a ligand conjugated to an active agent in
order to deliver the active agent to tumor cells in vivo.
[0048] U.S. Pat. No. 5,518,888 issued May 21, 1996 to Waldman, PCT
application PCT/US94/12232 filed Oct. 26, 1994, U.S. application
Ser. No. 08/467,920 filed Jun. 6, 1995, and U.S. application Ser.
No. 08/583,447 filed Jan. 5, 1996, which are each incorporated
herein by reference, disclose that metastasized colorectal tumors
can be targeted for delivery of active compounds by targeting ST
receptors (also referred to as guanylin cyclase C or GCC). The
presence of ST receptors on cells outside of the intestinal tract
as a marker for colorectal cancer allows for the screening,
identification and treatment of individuals with metastasized
colorectal tumors. ST receptors may also be used to target delivery
of gene therapeutics and antisense compounds to colorectal
cells.
[0049] U.S. Pat. No. 5,601,990 issued Feb. 11, 1997 to Waldman, PCT
application PCT/US94/12232 filed Oct. 26, 1994, and PCT application
PCT/US97/07467 filed May 2, 1997, which are each incorporated
herein by reference, disclose that detection of evidence of
expression of ST receptors in samples of tissue and body fluid from
outside the intestinal track indicate metastasized colorectal
cancer.
[0050] PCT application PCT/US97/07565 filed May 2, 1997, which is
incorporated herein by reference, disclose that immunogens with
epitopes that can be targeted by antibodies that react with ST
receptors can be used in vaccines compositions useful as
prophylactic and therapeutic anti-metastatic colorectal cancer
compositions.
[0051] It has been discovered that in addition to normal colon
cells, primary and metastasized colon, stomach and esophageal
carcinoma cells express SI. Normal stomach and esophageal cells do
not express SI. Thus, the present invention provides the use of SI
as a specific molecular diagnostic marker for the diagnosis,
staging, and post-operative surveillance of patients with
metastasized colon cancer and primary and metastasized stomach and
esophageal cancer.
[0052] Detection of the expression of SI employing molecular
techniques, including, but not limited to, RT-PCR, can be employed
to diagnose and stage patients, follow the development of
recurrence after surgery and/or remission, and, potentially, screen
normal people for the development of colorectal, stomach or
esophageal cancer.
[0053] The amino acid of the SI protein and the nucleotide sequence
of the SI gene transcript is disclosed in Chantret,I et al. Ann.
Hum. Genet. 52 (Pt 1), 57-61 (1988) and GenBank Accession No. NM
001041, which are incorporated herein by reference.
[0054] SI is unique in that it is only expressed in normal
intestinal cells. Mucosal cells lining the intestine are joined
together by tight junctions which form a barrier against the
passage of intestinal contents into the blood stream and components
of the blood stream into the intestinal lumen. Therefore, the
apical location of cells expressing SI results in the isolation of
such cells from the circulatory system so that they may be
considered to exist separate from the rest of the body; essentially
the "outside" of the body. Therefore, the rest of the body is
considered "outside" the intestinal tract. Compositions
administered "outside" the intestinal tract are maintained apart
and segregated from the only cells which normally express SI.
Conversely, tissue samples taken from tissue outside of the
intestinal tract do not normally contain cells which express
SI.
[0055] In individuals suffering from colorectal cancer, the cancer
cells are often derived from cells that produce and display the SI
and these cancer cells continue to produce SI. It has been observed
that SI is expressed by colorectal cancer cells. Likewise, SI is
expressed by stomach and esophageal cancer cells.
[0056] The expression of SI by colorectal tumor cells provides a
detectable target for in vitro screening, monitoring and staging as
well as a target for in vivo delivery of conjugated compositions
that comprise active agents for the imaging and treatment. SI can
also serve as targets for vaccines which may be used to protect
against metastasized colorectal cancer or to treat individiuals
with metastasized colorectal cancer.
[0057] The expression of SI by stomach and esophageal tumor cells
provides a detectable target for in vitro screening, monitoring and
staging as well as a target for in vivo delivery of conjugated
compositions that comprise active agents for the imaging and
treatment. SI can also serve as targets for vaccines which may be
used to protect against primary and metastatic stomach and
esophageal cancer or to treat individiuals with primary and
metastatic stomach and esophageal cancer.
[0058] In vitro Diagnostics
[0059] According to some embodiments of the invention,
compositions, kits and in vitro methods are provided for screening,
diagnosing and analyzing patients and patient samples to detect
evidence of SI expression by cells outside of the intestinal tract
wherein the expression of SI may be suggestive of metastasized
colorectal cancer or primary or metastatic stomach or esophageal
cancer. In patients suspected of having metastasized colorectal
cancer or primary or metastatic stomach or esophageal cancer
evidence of SI expression by cells outside of the intestinal tract
is indicative of metastasized colorectal cancer or primary or
metastatic stomach or esophageal cancer and can be used in the
diagnosis, monitoring and staging of such patients. Furthermore,
the present invention relates to methods, compositions and kits
useful in the in vitro screening, and analysis of patient and
patient samples to detect evidence of SI expression by tumor cells
outside of the intestinal tract wherein the presence of cells that
express SI suggests or confirms that a tumor is of colorectal or
stomach or esophageal cancer origin. In an additional aspect of the
invention, compositions, kits and methods are provided which are
useful to visualize metastasized colorectal cancer or primary or
metastatic stomach or esophageal cancer cells.
[0060] In vitro screening and diagnostic compositions, methods and
kits can be used in the monitoring of individuals who are in high
risk groups for colorectal, stomach or esophageal cancer such as
those who have been diagnosed with localized disease and/or
metastasized disease and/or those who are genetically linked to the
disease. In vitro screening and diagnostic compositions, methods
and kits can be used in the monitoring of individuals who are
undergoing and/or have been treated for primary colorectal, stomach
or esophageal cancer to determine if the cancer has metastasized.
In vitro screening and diagnostic compositions, methods and kits
can be used in the monitoring of individuals who are undergoing
and/or have been treated for colorectal, stomach or esophageal
cancer to determine if the cancer has been eliminated. In vitro
screening and diagnostic compositions, methods and kits can be used
in the monitoring of individuals who are otherwise susceptible,
i.e. individuals who have been identified as genetically
predisposed such as by genetic screening and/or family histories.
Advancements in the understanding of genetics and developments in
technology as well as epidemiology allow for the determination of
probability and risk assessment an individual has for developing
stomach or esophageal cancer. Using family health histories and/or
genetic screening, it is possible to estimate the probability that
a particular individual has for developing certain types of cancer
including colorectal, stomach or esophageal cancer. Those
individuals that have been identified as being predisposed to
developing a particular form of cancer can be monitored or screened
to detect evidence of colorectal, stomach or esophageal cancer.
Upon discovery of such evidence, early treatment can be undertaken
to combat the disease. Accordingly, individuals who are at risk for
developing colorectal, stomach or esophageal cancer may be
identified and samples may be isolated form such individuals. The
invention is particularly useful for monitoring individuals who
have been identified as having family medical histories which
include relatives who have suffered from colorectal, stomach or
esophageal cancer. Likewise, the invention is particularly useful
to monitor individuals who have been diagnosed as having
colorectal, stomach or esophageal cancer and, particularly those
who have been treated and had tumors removed and/or are otherwise
experiencing remission including those who have been treated for
colorectal, stomach or esophageal cancer.
[0061] In vitro screening and diagnostic compositions, methods and
kits can be used in the analysis of tumors. Expression of SI is a
marker for cell type and suggests the origin of adenocarcinoma of
unconfirmed origin may be colorectal, stomach or esophageal tumors.
Detection of SI expression can also be used to assist in an initial
diagnosis of colorectal, stomach or esophageal cancer or to confirm
such diagnosis. Tumors believed to be colorectal, stomach or
esophageal in origin can be confirmed as such using the
compositions, methods and kits of the invention.
[0062] In vitro screening and diagnostic compositions, kits and
methods of the invention can be used to analyze tissue samples from
the stomach or esophagus to identify primary stomach or esophageal
cancer.
[0063] In vitro screening and diagnostic compositions, kits and
methods of the invention can be used to analyze tissue samples from
the colon to detect the amount of invasion by primary colorectal
cancer into the intestinal tissue.
[0064] According to the invention, compounds are provided which
bind to SI gene transcript or protein. Normal tissue in the body
does not have SI transcript or protein except cells of the
intestinal tract. The expression of SI is a marker for cell type
and is useful in the identification of colorectal, stomach or
esophageal cancer in extra-intestinal samples.
[0065] In some embodiments of the invention, non-colorectal tissue
and fluid samples or tumor samples may be screened to identify the
presence or absence of SI protein. Techniques such as ELISA assays
and Western blots may be performed to determine whether SI is
present in a sample.
[0066] In some embodiments of the invention, non-colorectal tissue
and fluid samples or tumor samples may be screened to identify
whether SI are being expressed in cells outside of the colorectal
tract by detecting the presence or absence of SI gene transcript.
The presence of SI gene transcript or cDNA generated therefrom can
be determined using techniques such as PCR amplification, branched
oligonucleotide technology, Northern Blots (mRNA), Southern Blots
(cDNA), or oligonucleotide hybridization.
[0067] In some embodiments of the invention, cells of
non-colorectal tissue samples or tumor samples may be examined to
identify the presence or absence of SI proteins. Techniques such as
immunohistochemistry blots may be performed on tissue sections to
determine whether SI are present in a sample.
[0068] In some embodiments of the invention, cells of
non-colorectal tissue samples or tumor samples may be examined to
determine whether SI are being expressed in cells outside of the
colorectal tract by detecting the presence or absence of the SI
gene transcript. The presence of the SI gene transcript or cDNA
generated therefrom in cells from tissue sections can be determined
using techniques such as in situ hybridization.
[0069] The presence of SI in non-colorectal tissue and fluid
samples or on cells from non-colorectal tissue samples suggests
possible stomach or esophageal cancer. The presence of SI in a
tumor sample or on tumor cells suggests that the tumor may be
colorectal, stomach or esophageal in origin. The presence of the SI
gene transcript in non-colorectal tissue and fluid samples or in
cells from non-colorectal tissue samples suggests possible
colorectal, stomach or esophageal cancer. The presence of the SI
gene transcript in tumor samples and tumor cells suggests that the
tumor may be colorectal, stomach or esophageal in origin.
[0070] Samples may be obtained from resected tissue or biopsy
material including needle biopsy. Tissue section preparation for
surgical pathology may be frozen and prepared using standard
techniques. Immunohistochemistry and in situ hybridization binding
assays on tissue sections are performed in fixed cells.
Extra-intestinal samples may be homogenized by standard techniques
such as sonication, mechanical disruption or chemical lysis such as
detergent lysis. It is also contemplated that tumor samples in body
fluids such as blood, urine, lymph fluid, cerebral spinal fluid,
amniotic fluid, vaginal fluid, semen and stool samples may also be
screened to determine if such tumors are colorectal, stomach or
espophageal in origin.
[0071] Non-colorectal tissue samples may be obtained from any
tissue except those of the colorectal tract, i.e. the intestinal
tract below the small intestine (i.e. the large intestine (colon),
including the cecum, ascending colon, transverse colon, descending
colon, and sigmoid colon, and rectum) and additionally the duodenum
and small intestine (jejunum and ileum). The normal cells of all
tissue except those of the colorectal tract do not express SI. Thus
if SI protein or the SI gene transcript are detected in
non-colorectal samples, the possible presence of colorectal,
stomach or esophageal cancer cells is suggested. In some preferred
embodiments, the tissue samples are lymph nodes.
[0072] Tissue samples may be obtained by standard surgical
techniques including use of biopsy needles. One skilled in the art
would readily appreciate the variety of test samples that may be
examined for SI and recognize methods of obtaining tissue
samples.
[0073] Tissue samples may be homogenized or otherwise prepared for
screening for the presence of SI by well known techniques such as
sonication, mechanical disruption, chemical lysis such as detergent
lysis or combinations thereof.
[0074] Examples of body fluid samples include blood, urine, lymph
fluid, cerebral spinal fluid, amniotic fluid, vaginal fluid and
semen. In some preferred embodiments, blood is used as a sample of
body fluid. Cells may be isolated from fluid sample such as
centrifugation. One skilled in the art would readily appreciate the
variety of test samples that may be examined for SI. Test samples
may be obtained by such methods as withdrawing fluid with a syringe
or by a swab. One skilled in the art would readily recognize other
methods of obtaining test samples.
[0075] In an assay using a blood sample, the blood plasma may be
separated from the blood cells. The blood plasma may be screened
for SI including truncated proteins which are released into the
blood when one or more SI are cleaved from or sloughed off from
tumor cells. In some embodiments, blood cell fractions are screened
for the presence of colorectal, stomach or esophageal tumor cells.
In some embodiments, lymphocytes present in the blood cell fraction
are screened by lysing the cells and detecting the presence of SI
protein or the SI gene transcript which may be present as a result
of the presence of any stomach or esophageal tumor cells that may
have been engulfed by the blood cell. In some preferred
embodiments, CD34+ cells are removed prior to isolation of mRNA
from samples using commercially available immuno-columns.
[0076] Aspects of the present invention include various methods of
determining whether a sample contains cells that express SI by
nucleotide sequence-based molecular analysis to detect the SI gene
transcript. Several different methods are available for doing so
including those using Polymerase Chain Reaction (PCR) technology,
branched oligonucleotide technology, Northern blot technology,
oligonucleotide hybridization technology, and in situ hybridization
technology.
[0077] The invention relates to oligonucleotide probes and primers
used in the methods of identifying the SI gene transcript and to
diagnostic kits which comprise such components.
[0078] The mRNA sequence-based methods for detect the SI gene
transcript include but are not limited to polymerase chain reaction
technology, branched oligonucleotide technology, Northern and
Southern blot technology, in situ hybridization technology and
oligonucleotide hybridization technology.
[0079] The methods described herein are meant to exemplify how the
present invention may be practiced and are not meant to limit the
scope of invention. It is contemplated that other sequence-based
methodology for detecting the presence of the SI gene transcript in
non-colorectal samples may be employed according to the
invention.
[0080] A preferred method to detecting the SI gene transcript in
genetic material derived from non-colorectal samples uses
polymerase chain reaction (PCR) technology. PCR technology is
practiced routinely by those having ordinary skill in the art and
its uses in diagnostics are well known and accepted. Methods for
practicing PCR technology are disclosed in "PCR Protocols: A Guide
to Methods and Applications", Innis, M. A., et al. Eds. Academic
Press, Inc. San Diego, Calif. (1990) which is incorporated herein
by reference. Applications of PCR technology are disclosed in
"Polymerase Chain Reaction" Erlich, H. A., et al., Eds. Cold Spring
Harbor Press, Cold Spring Harbor, N.Y. (1989) which is incorporated
herein by reference. U.S. Pat. No. 4,683,202, U.S. Pat. No.
4,683,195, U.S. Pat. No. 4,965,188 and U.S. Pat. No. 5,075,216,
which are each incorporated herein by reference describe methods of
performing PCR. PCR may be routinely practiced using Perkin Elmer
Cetus GENE AMP RNA PCR kit, Part No. N808-0017.
[0081] PCR technology allows for the rapid generation of multiple
copies of DNA sequences by providing 5' and 3' primers that
hybridize to sequences present in an RNA or DNA molecule, and
further providing free nucleotides and an enzyme which fills in the
complementary bases to the nucleotide sequence between the primers
with the free nucleotides to produce a complementary strand of DNA.
The enzyme will fill in the complementary sequences adjacent to the
primers. If both the 5' primer and 3' primer hybridize to
nucleotide sequences on the same small fragment of nucleic acid,
exponential amplification of a specific double-stranded size
product results. If only a single primer hybridizes to the nucleic
acid fragment, linear amplification produces single-stranded
products of variable length.
[0082] PCR primers can be designed routinely by those having
ordinary skill in the art using sequence information. The
nucleotide sequence of the SI gene transcript is set forth in SEQ
ID NO:1. To perform this method, RNA is extracted from cells in a
sample and tested or used to make cDNA using well known methods and
readily available starting materials. Those having ordinary skill
in the art can readily prepare PCR primers. A set of primers
generally contains two primers. When performing PCR on extracted
mRNA or cDNA generated therefrom, if the SI gene transcript or cDNA
generated therefrom is present, multiple copies of the MRNA or cDNA
will be made. If it is not present, PCR will not generate a
discrete detectable product. Primers are generally 8-50
nucleotides, preferably about 15-35 nucleotides, more preferably
18-28 nucleotides, which are identical or complementary to and
therefor hybridize to the SI gene transcript or cDNA generated
therefrom. In preferred embodiments, the primers are each 15-35
nucleotide, more preferably 18-28 nucleotide fragments of SEQ ID
NO:1. The primer must hybridize to the sequence to be amplified.
Typical primers are 18-28 nucleotides in length and are generally
have 50% to 60% G+C composition. The entire primer is preferably
complementary to the sequence it must hybridize to. Preferably,
primers generate PCR products 100 base pairs to 2000 base pairs.
However, it is possible to generate products of 50 to up to 10 kb
and more. If MRNA is used as a template, the primers must hybridize
to mRNA sequences. If cDNA is used as a template, the primers must
hybridize to cDNA sequences.
[0083] The mRNA or cDNA is combined with the primers, free
nucleotides and enzyme following standard PCR protocols. The
mixture undergoes a series of temperature changes. If the SI gene
transcript or cDNA generated therefrom is present, that is, if both
primers hybridize to sequences on the same molecule, the molecule
comprising the primers and the intervening complementary sequences
will be exponentially amplified. The amplified DNA can be easily
detected by a variety of well known means. If no SI gene transcript
or cDNA generated therefrom is present, no PCR product will be
exponentially amplified. The PCR technology therefore provides an
extremely easy, straightforward and reliable method of detecting
the SI gene transcript in a sample.
[0084] PCR product may be detected by several well known means. The
preferred method for detecting the presence of amplified DNA is to
separate the PCR reaction material by gel electrophoresis and stain
the gel with ethidium bromide in order to visual the amplified DNA
if present. A size standard of the expected size of the amplified
DNA is preferably run on the gel as a control.
[0085] In some instances, such as when unusually small amounts of
RNA are recovered and only small amounts of cDNA are generated
therefrom, it is desirable or necessary to perform a PCR reaction
on the first PCR reaction product. That is, if difficult to detect
quantities of amplified DNA are produced by the first reaction, a
second PCR can be performed to make multiple copies of DNA
sequences of the first amplified DNA. A nested set of primers are
used in the second PCR reaction. The nested set of primers
hybridize to sequences downstream of the 5' primer and upstream of
the 3' primer used in the first reaction.
[0086] The present invention includes oligonucleotide which are
useful as primers for performing PCR methods to amplify the SI gene
transcript or cDNA generated therefrom.
[0087] According to the invention, diagnostic kits can be assembled
which are useful to practice methods of detecting the presence of
the SI gene transcript or cDNA generated therefrom in
non-colorectal samples. Such diagnostic kits comprise
oligonucleotide which are useful as primers for performing PCR
methods. It is preferred that diagnostic kits according to the
present invention comprise a container comprising a size marker to
be run as a standard on a gel used to detect the presence of
amplified DNA. The size marker is the same size as the DNA
generated by the primers in the presence of the SI gene transcript
or cDNA generated therefrom. Additional components in some kits
include instructions for carrying out the assay. Additionally the
kit may optionally comprise depictions or photographs that
represent the appearance of positive and negative results. Positive
and negative controls may also be provided.
[0088] PCR assays are useful for detecting the SI gene transcript
in homogenized tissue samples and cells in body fluid samples. It
is contemplated that PCR on the plasma portion of a fluid sample
could be used to detect the SI gene transcript.
[0089] Another method of determining whether a sample contains
cells expressing SI is by branched chain oligonucleotide
hybridization analysis of mRNA extracted from a sample. Branched
chain oligonucleotide hybridization may be performed as described
in U.S. Pat. No. 5,597,909, U.S. Pat. No. 5,437,977 and U.S. Pat.
No. 5,430,138, which are each incorporated herein by reference.
Reagents may be designed following the teachings of those patents
and that sequence of the SI gene transcript.
[0090] Another method of determining whether a sample contains
cells expressing SI is by Northern Blot analysis of mRNA extracted
from a non-colorectal sample. The techniques for performing
Northern blot analyses are well known by those having ordinary
skill in the art and are described in Sambrook, J. et al., (1989)
Molecular Cloning: A Laboratory Manual, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y. mRNA extraction,
electrophoretic separation of the MRNA, blotting, probe preparation
and hybridization are all well known techniques that can be
routinely performed using readily available starting material.
[0091] The mRNA is extracted using poly dT columns and the material
is separated by electrophoresis and, for example, transferred to
nitrocellulose paper. Labeled probes made from an isolated specific
fragment or fragments can be used to visualize the presence of a
complementary fragment fixed to the paper. Probes useful to
identify mRNA in a Northern Blot have a nucleotide sequence that is
complementary to the SI gene transcript. Those having ordinary
skill in the art could use the sequence information in SEQ ID NO:1
to design such probes or to isolate and clone the SI gene
transcript or cDNA generated therefrom to be used as a probe. Such
probes are at least 15 nucleotides, preferably 30-200, more
preferably 40-100 nucleotide fragments and may be the entire SI
gene transcript.
[0092] According to the invention, diagnostic kits can be assembled
which are useful to practice methods of detecting the presence of
the SI gene transcript in non-colorectal samples by Northern blot
analysis. Such diagnostic kits comprise oligonucleotide which are
useful as probes for hybridizing to the mRNA. The probes may be
radiolabeled. It is preferred that diagnostic kits according to the
present invention comprise a container comprising a size marker to
be run as a standard on a gel. It is preferred that diagnostic kits
according to the present invention comprise a container comprising
a positive control which will hybridize to the probe. Additional
components in some kits include instructions for carrying out the
assay. Additionally the kit may optionally comprise depictions or
photographs that represent the appearance of positive and negative
results.
[0093] Northern blot analysis is useful for detecting the SI gene
transcript in homogenized tissue samples and cells in body fluid
samples. It is contemplated that PCR on the plasma portion of a
fluid sample could be used to detect the SI gene transcript.
[0094] Another method of detecting the presence of the SI gene
transcript by oligonucleotide hybridization technology.
Oligonucleotide hybridization technology is well known to those
having ordinary skill in the art. Briefly, detectable probes which
contain a specific nucleotide sequence that will hybridize to
nucleotide sequence of the SI gene transcript. RNA or cDNA made
from RNA from a sample is fixed, usually to filter paper or the
like. The probes are added and maintained under conditions that
permit hybridization only if the probes fully complement the fixed
genetic material. The conditions are sufficiently stringent to wash
off probes in which only a portion of the probe hybridizes to the
fixed material. Detection of the probe on the washed filter
indicate complementary sequences.
[0095] Probes useful in oligonucleotide assays at least 18
nucleotides of complementary DNA and may be as large as a complete
complementary sequence to the SI gene transcript. In some preferred
embodiments the probes of the invention are 30-200 nucleotides,
preferably 40-100 nucleotides.
[0096] One having ordinary skill in the art, using the sequence
information disclosed in SEQ ID NO:1 can design probes useful in
the invention. Hybridization conditions can be routinely optimized
to minimize background signal by non-fully complementary
hybridization. In some preferred embodiments, the probes are full
length clones. Probes are at least 15 nucleotides, preferably
30-200, more preferably 40-100 nucleotide fragments and may be the
entire SI gene transcript.
[0097] The present invention includes labeled oligonucleotide which
are useful as probes for performing oligonucleotide hybridization.
The labeled probes of the present invention are labeled with
radiolabeled nucleotides or are otherwise detectable by readily
available nonradioactive detection systems.
[0098] According to the invention, diagnostic kits can be assembled
which are useful to practice oligonucleotide hybridization methods
of the invention. Such diagnostic kits comprise a labeled
oligonucleotide which encodes portions of the SI gene transcript.
It is preferred that labeled probes of the oligonucleotide
diagnostic kits according to the present invention are labeled with
a radionucleotide. The oligonucleotide hybridization-based
diagnostic kits according to the invention preferably comprise DNA
samples that represent positive and negative controls. A positive
control DNA sample is one that comprises a nucleic acid molecule
which has a nucleotide sequence that is fully complementary to the
probes of the kit such that the probes will hybridize to the
molecule under assay conditions. A negative control DNA sample is
one that comprises at least one nucleic acid molecule, the
nucleotide sequence of which is partially complementary to the
sequences of the probe of the kit. Under assay conditions, the
probe will not hybridize to the negative control DNA sample.
Additional components in some kits include instructions for
carrying out the assay. Additionally the kit may optionally
comprise depictions or photographs that represent the appearance of
positive and negative results.
[0099] Oligonucleotide hybridization techniques are useful for
detecting the SI gene transcript in homogenized tissue samples and
cells in body fluid samples. It is contemplated that PCR on the
plasma portion of a fluid sample could be used to detect the SI
gene transcript.
[0100] The present invention relates to in vitro kits for
evaluating samples of tumors to determine whether or not they are
colorectal, stomach or esophageal in origin and to reagents and
compositions useful to practice the same. In some embodiments of
the invention, tumor samples may be isolated from individuals
undergoing or recovery from surgery to remove tumors in the
colorectal, stomach or esophagus, tumors in other organs or biopsy
material. The tumor sample is analyzed to identify the presence or
absence of the SI gene transcript. Techniques such as
immunohistochemistry assays may be performed to determine whether
SI are present in cells in the tumor sample. The presence of mRNA
that encodes the SI protein or cDNA generated therefrom can be
determined using techniques such as in situ hybridization,
immunohistochemistry and in situ ST binding assay.
[0101] In situ hybridization technology is well known by those
having ordinary skill in the art. Briefly, cells are fixed and
detectable probes which contain a specific nucleotide sequence are
added to the fixed cells. If the cells contain complementary
nucleotide sequences, the probes, which can be detected, will
hybridize to them.
[0102] Probes useful in oligonucleotide assays at least 18
nucleotides of complementary DNA and may be as large as a complete
complementary sequence to the SI gene transcript. In some preferred
embodiments the probes of the invention are 30-200 nucleotides,
preferably 40-100 nucleotides.
[0103] One having ordinary skill in the art, using the sequence
information set forth in SEQ ID NO:1 can design probes useful in in
situ hybridization technology to identify cells that express SI.
Probes preferably hybridizes to a nucleotide sequence that
corresponds to the SI gene transcript. Hybridization conditions can
be routinely optimized to minimize background signal by non-fully
complementary hybridization. Probes preferably hybridize to the
full length SI gene transcript. Probes are at least 15 nucleotides,
preferably 30-200, more preferably 40-100 nucleotide fragments and
may be the SI gene transcript, more preferably 18-28 nucleotide
fragments of the SI gene transcript.
[0104] The probes are fully complementary and do not hybridize well
to partially complementary sequences. For in situ hybridization
according to the invention, it is preferred that the probes are
detectable by fluorescence. A common procedure is to label probe
with biotin-modified nucleotide and then detect with fluorescently
tagged avidin. Hence, probe does not itself have to be labeled with
florescent but can be subsequently detected with florescent
marker.
[0105] The present invention includes labeled oligonucleotide which
are useful as probes for performing oligonucleotide hybridization.
That is, they are fully complementary with mRNA sequences but not
genomic sequences. The labeled probes of the present invention are
labeled with radiolabeled nucleotides or are otherwise detectable
by readily available nonradioactive detection systems.
[0106] The present invention relates to probes useful for in situ
hybridization to identify cells that express SI.
[0107] Cells are fixed and the probes are added to the genetic
material. Probes will hybridize to the complementary nucleic acid
sequences present in the sample. Using a fluorescent microscope,
the probes can be visualized by their fluorescent markers.
[0108] According to the invention, diagnostic kits can be assembled
which are useful to practice in situ hybridization methods of the
invention are fully complementary with mRNA sequences but not
genomic sequences. For example, the mRNA sequence includes
different exon sequences. It is preferred that labeled probes of
the in situ diagnostic kits according to the present invention are
labeled with a fluorescent marker.
[0109] Immunohistochemistry techniques may be used to identify and
essentially stain cells with SI. Such "staining" allows for
analysis of metastatic migration. Anti-SI antibodies such as those
described above of contacted with fixed cells and the SI present in
the cells reacts with the antibodies. The antibodies are detectably
labeled or detected using labeled second antibody or protein A to
stain the cells.
[0110] The techniques described herein for evaluating tumor
sections can also be used to analyze tissue sections for samples of
lymph nodes as well as other tissues to identify the presence of
cells that express SI. The samples can be prepared and "stained" to
detect expression of SI.
[0111] Immunoassay methods may be used in the diagnosis of
individuals suffering from colorectal, stomach or esophageal cancer
by detecting presence of SI in sample of non-colorectal tissue or
body fluid from an individuals suspected of having or being
susceptible to colorectal, stomach or esophageal cancer using
antibodies which were produced in response to exposure to such SI
protein. Moreover, immunoassay methods may be used to identify
individuals suffering from colorectal, stomach or esophageal cancer
by detecting presence of SI in sample of tumor using antibodies
which were produced in response to exposure to such SI protein.
[0112] The antibodies are preferably monoclonal antibodies. The
antibodies are preferably raised against SI made in human cells.
Immunoassays are well known and there design may be routinely
undertaken by those having ordinary skill in the art. Those having
ordinary skill in the art can produce monoclonal antibodies which
specifically bind to SI and are useful in methods and kits of the
invention using standard techniques and readily available starting
materials. The techniques for producing monoclonal antibodies are
outlined in Harlow, E. and D. Lane, (1988) ANTIBODIES: A Laboratory
Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor N.Y.,
which is incorporated herein by reference, provide detailed
guidance for the production of hybridomas and monoclonal antibodies
which specifically bind to target proteins. It is within the scope
of the present invention to include Fabs, recombinant Fabs,
F(Ab)2s, recombinant F(Ab)2s which specifically bind to SI
translation products in place of antibodies.
[0113] Briefly, SI protein is injected into mice. The spleen of the
mouse is removed, the spleen cells are isolated and fused with
immortalized mouse cells. The hybrid cells, or hybridomas, are
cultured and those cells which secrete antibodies are selected. The
antibodies are analyzed and, if found to specifically bind to the
SI, the hybridoma which produces them is cultured to produce a
continuous supply of anti-SI specific antibodies.
[0114] The antibodies are preferably monoclonal antibodies. The
antibodies are preferably raised against SI made in human
cells.
[0115] The means to detect the presence of a protein in a test
sample are routine and one having ordinary skill in the art can
detect the presence or absence of a protein or an antibody using
well known methods. One well known method of detecting the presence
of a protein is an immunoassay. One having ordinary skill in the
art can readily appreciate the multitude of ways to practice an
immunoassay to detect the presence of a SI protein in a sample.
[0116] According to some embodiments, immunoassays comprise
allowing proteins in the sample to bind a solid phase support such
as a plastic surface. Detectable antibodies are then added which
selectively binding to the SI. Detection of the detectable antibody
indicates the presence of SI. The detectable antibody may be a
labeled or an unlabeled antibody. Unlabeled antibody may be
detected using a second, labeled antibody that specifically binds
to the first antibody or a second, unlabeled antibody which can be
detected using labeled protein A, a protein that complexes with
antibodies. Various immunoassay procedures are described in
Immunoassays for the 80's, A. Voller et al., Eds., University Park,
1981, which is incorporated herein by reference.
[0117] Simple immunoassays may be performed in which a solid phase
support is contacted with the test sample. Any proteins present in
the test sample bind the solid phase support and can be detected by
a specific, detectable antibody preparation. Such a technique is
the essence of the dot blot, Western blot and other such similar
assays.
[0118] Other immunoassays may be more complicated but actually
provide excellent results. Typical and preferred immunometric
assays include "forward" assays for the detection of a protein in
which a first anti-protein antibody bound to a solid phase support
is contacted with the test sample. After a suitable incubation
period, the solid phase support is washed to remove unbound
protein. A second, distinct anti-protein antibody is then added
which is specific for a portion of the specific protein not
recognized by the first antibody. The second antibody is preferably
detectable. After a second incubation period to permit the
detectable antibody to complex with the specific protein bound to
the solid phase support through the first antibody, the solid phase
support is washed a second time to remove the unbound detectable
antibody. Alternatively, the second antibody may not be detectable.
In this case, a third detectable antibody, which binds the second
antibody is added to the system. This type of "forward sandwich"
assay may be a simple yes/no assay to determine whether binding has
occurred or may be made quantitative by comparing the amount of
detectable antibody with that obtained in a control. Such
"two-site" or "sandwich" assays are described by Wide, Radioimmune
Assay Method, Kirkham, Ed., E. & S. Livingstone, Edinburgh,
1970, pp. 199-206, which is incorporated herein by reference.
[0119] Other types of immunometric assays are the so-called
"simultaneous" and "reverse" assays. A simultaneous assay involves
a single incubation step wherein the first antibody bound to the
solid phase support, the second, detectable antibody and the test
sample are added at the same time. After the incubation is
completed, the solid phase support is washed to remove unbound
proteins. The presence of detectable antibody associated with the
solid support is then determined as it would be in a conventional
"forward sandwich" assay. The simultaneous assay may also be
adapted in a similar manner for the detection of antibodies in a
test sample.
[0120] The "reverse" assay comprises the stepwise addition of a
solution of detectable antibody to the test sample followed by an
incubation period and the addition of antibody bound to a solid
phase support after an additional incubation period. The solid
phase support is washed in conventional fashion to remove unbound
protein/antibody complexes and unreacted detectable antibody. The
determination of detectable antibody associated with the solid
phase support is then determined as in the "simultaneous" and
"forward" assays. The reverse assay may also be adapted in a
similar manner for the detection of antibodies in a test
sample.
[0121] The first component of the immunometric assay may be added
to nitrocellulose or other solid phase support which is capable of
immobilizing proteins. The first component for determining the
presence of SI in a test sample is an anti-SI antibody. By "solid
phase support" or "support" is intended any material capable of
binding proteins. Well-known solid phase supports include glass,
polystyrene, polypropylene, polyethylene, dextran, nylon, amylases,
natural and modified celluloses, polyacrylamides, agaroses, and
magnetite. The nature of the support can be either soluble to some
extent or insoluble for the purposes of the present invention. The
support configuration may be spherical, as in a bead, or
cylindrical, as in the inside surface of a test tube or the
external surface of a rod. Alternatively, the surface may be flat
such as a sheet, test strip, etc. Those skilled in the art will
know many other suitable "solid phase supports" for binding
proteins or will be able to ascertain the same by use of routine
experimentation. A preferred solid phase support is a 96-well
microtiter plate.
[0122] To detect the presence of SI, detectable anti-SI antibodies
are used. Several methods are well known for the detection of
antibodies.
[0123] One method in which the antibodies can be detectably labeled
is by linking the antibodies to an enzyme and subsequently using
the antibodies in an enzyme immunoassay (EIA) or enzyme-linked
immunosorbent assay (ELISA), such as a capture ELISA. The enzyme,
when subsequently exposed to its substrate, reacts with the
substrate and generates a chemical moiety which can be detected,
for example, by spectrophotometric, fluorometric or visual means.
Enzymes which can be used to detectably label antibodies include,
but are not limited to malate dehydrogenase, staphylococcal
nuclease, delta-5-steroid isomerase, yeast alcohol dehydrogenase,
alpha-glycerophosphate dehydrogenase, triose phosphate isomerase,
horseradish peroxidase, alkaline phosphatase, asparaginase, glucose
oxidase, beta-galactosidase, ribonuclease, urease, catalase,
glucose-6-phosphate dehydrogenase, glucoamylase and
acetylcholinesterase. One skilled in the art would readily
recognize other enzymes which may also be used.
[0124] Another method in which antibodies can be detectably labeled
is through radioactive isotopes and subsequent use in a
radioimmunoassay (RIA) (see, for example, Work, T. S. et al.,
Laboratory Techniques and Biochemistry in Molecular Biology, North
Holland Publishing Company, N.Y., 1978, which is incorporated
herein by reference). The radioactive isotope can be detected by
such means as the use of a gamma counter or a scintillation counter
or by autoradiography. Isotopes which are particularly useful for
the purpose of the present invention are .sup.3H, .sup.125I,
.sup.131I, .sup.35S, and .sup.14C. Preferably .sup.125I is the
isotope. One skilled in the art would readily recognize other
radioisotopes which may also be used.
[0125] It is also possible to label the antibody with a fluorescent
compound. When the fluorescent-labeled antibody is exposed to light
of the proper wave length, its presence can be detected due to its
fluorescence. Among the most commonly used fluorescent labeling
compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin,
phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine. One
skilled in the art would readily recognize other fluorescent
compounds which may also be used.
[0126] Antibodies can also be detectably labeled using
fluorescence-emitting metals such as .sup.152Eu, or others of the
lanthanide series. These metals can be attached to the
protein-specific antibody using such metal chelating groups as
diethylenetriaminepentaacet- ic acid (DTPA) or
ethylenediamine-tetraacetic acid (EDTA). One skilled in the art
would readily recognize other fluorescence-emitting metals as well
as other metal chelating groups which may also be used.
[0127] Antibody can also be detectably labeled by coupling to a
chemiluminescent compound. The presence of the
chemiluminescent-labeled antibody is determined by detecting the
presence of luminescence that arises during the course of a
chemical reaction. Examples of particularly useful chemoluminescent
labeling compounds are luminol, isoluminol, theromatic acridinium
ester, imidazole, acridinium salt and oxalate ester. One skilled in
the art would readily recognize other chemiluminescent compounds
which may also be used.
[0128] Likewise, a bioluminescent compound may be used to label
antibodies. Bioluminescence is a type of chemiluminescence found in
biological systems in which a catalytic protein increases the
efficiency of the chemiluminescent reaction. The presence of a
bioluminescent protein is determined by detecting the presence of
luminescence. Important bioluminescent compounds for purposes of
labeling are luciferin, luciferase and aequorin. One skilled in the
art would readily recognize other bioluminescent compounds which
may also be used.
[0129] Detection of the protein-specific antibody, fragment or
derivative may be accomplished by a scintillation counter if, for
example, the detectable label is a radioactive gamma emitter.
Alternatively, detection may be accomplished by a fluorometer if,
for example, the label is a fluorescent material. In the case of an
enzyme label, the detection can be accomplished by colorometric
methods which employ a substrate for the enzyme. Detection may also
be accomplished by visual comparison of the extent of enzymatic
reaction of a substrate in comparison with similarly prepared
standards. One skilled in the art would readily recognize other
appropriate methods of detection which may also be used.
[0130] The binding activity of a given lot of antibodies may be
determined according to well known methods. Those skilled in the
art will be able to determine operative and optimal assay
conditions for each determination by employing routine
experimentation.
[0131] Positive and negative controls may be performed in which
known amounts of SI proteins and no SI protein, respectively, are
added to assays being performed in parallel with the test assay.
One skilled in the art would have the necessary knowledge to
perform the appropriate controls. In addition, the kit may comprise
instructions for performing the assay. Additionally the kit may
optionally comprise depictions or photographs that represent the
appearance of positive and negative results.
[0132] SI may be produced as a reagent for positive controls
routinely. One skilled in the art would appreciate the different
manners in which the SI protein may be produced and isolated.
[0133] Antibody composition refers to the antibody or antibodies
required for the detection of the protein. For example, the
antibody composition used for the detection of a SI in a test
sample comprises a first antibody that binds to the SI as well as a
second or third detectable antibody that binds the first or second
antibody, respectively.
[0134] To examine a test sample for the presence of a SI, a
standard immunometric assay such as the one described below may be
performed. A first anti-SI antibody, which recognizes a specific
portion of SI, is added to a 96-well microtiter plate in a volume
of buffer. The plate is incubated for a period of time sufficient
for binding to occur and subsequently washed with PBS to remove
unbound antibody. The plate is then blocked with a PBS/BSA solution
to prevent sample proteins from non-specifically binding the
microtiter plate. Test sample are subsequently added to the wells
and the plate is incubated for a period of time sufficient for
binding to occur. The wells are washed with PBS to remove unbound
protein. Labeled anti-SI antibodies, which recognize portions of SI
not recognized by the first antibody, are added to the wells. The
plate is incubated for a period of time sufficient for binding to
occur and subsequently washed with PBS to remove unbound, labeled
anti-SI antibody. The amount of labeled and bound anti-SI antibody
is subsequently determined by standard techniques.
[0135] Kits which are useful for the detection of SI in a test
sample comprise a container comprising anti-SI antibodies and a
container or containers comprising controls. Controls include one
control sample which does not contain SI and/or another control
sample which contained the SI. The anti-SI antibodies used in the
kit are detectable such as being detectably labeled. If the
detectable anti-SI antibody is not labeled, it may be detected by
second antibodies or protein A for example which may also be
provided in some kits in separate containers. Additional components
in some kits include solid support, buffer, and instructions for
carrying out the assay. Additionally the kit may optionally
comprise depictions or photographs that represent the appearance of
positive and negative results.
[0136] The immunoassay is useful for detecting SI in homogenized
tissue samples and body fluid samples including the plasma portion
or cells in the fluid sample.
[0137] Western Blots may be useful in assisting the diagnosis os
individuals suffering from stomach or esophageal cancer by
detecting presence of SI of non-colorectal tissue or body fluid.
Western blots may also be used to detect presence of SI in sample
of tumor from an individual suffering from cancer. Western blots
use detectable anti-SI-antibodies to bind to any SI present in a
sample and thus indicate the presence of the receptor in the
sample.
[0138] Western blot techniques, which are described in Sambrook, J.
et al., (1989) Molecular Cloning: A Laboratory Manual, Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y., which is
incorporated herein by reference, are similar to immunoassays with
the essential difference being that prior to exposing the sample to
the antibodies, the proteins in the samples are separated by gel
electrophoresis and the separated proteins are then probed with
antibodies. In some preferred embodiments, the matrix is an
SDS-PAGE gel matrix and the separated proteins in the matrix are
transferred to a carrier such as filter paper prior to probing with
antibodies. Anti-SI antibodies described above are useful in
Western blot methods.
[0139] Generally, samples are homogenized and cells are lysed using
detergent such as Triton-X. The material is then separated by the
standard techniques in Sambrook, J. et al., (1989) Molecular
Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, N.Y.
[0140] Kits which are useful for the detection of SI in a test
sample by Western Blot comprise a container comprising anti-SI
antibodies and a container or containers comprising controls.
Controls include one control sample which does not contain SI
and/or another control sample which contains SI. The anti-SI
antibodies used in the kit are detectable such as being detectably
labeled. If the detectable anti-SI antibody is not labeled, it may
be detected by second antibodies or protein A for example which may
also be provided in some kits in separate containers. Additional
components in some kits include instructions for carrying out the
assay. Additionally the kit may optionally comprise depictions or
photographs that represent the appearance of positive and negative
results.
[0141] Western blots are useful for detecting SI in homogenized
tissue samples and body fluid samples including the plasma portion
or cells in the fluid sample.
[0142] In vivo Imaging and Therapeutics
[0143] According to some embodiments of the invention, compositions
and in vivo methods are provided for detecting, imaging, or
treating metastatic colorectal cancer and primary and/or metastatic
stomach or esophageal tumors in an individual.
[0144] When the conjugated compositions of the present invention
are administered outside the intestinal tract such as when
administered in the circulatory system, they remain segregated from
the cells that line the intestinal tract and will bind only to
cells outside the intestinal tract which express SI. The conjugated
compositions will not bind to the normal cells but will bind to
metastatic colorectal cancer cells and primary and/or metastatic
stomach or esophageal cells. Thus, the active moieties of
conjugated compositions administered outside the intestinal tract
are delivered to cells which express SI such as metastatic
colorectal cancer cells and primary and/or metastatic stomach or
esophageal cancer cells.
[0145] Therapeutic and diagnostic pharmaceutical compositions
useful in the present invention include conjugated compounds that
specifically target cells that express SI. These conjugated
compounds include moieties that bind to SI which do not bind to
cells of normal tissue in the body except cells of the intestinal
tract since the cells of other tissues do not express SI.
[0146] Unlike normal colorectal cells, cancer cells that express SI
are accessible to substances administered outside the intestinal
tract, for example administered in the circulatory system. The only
SI in normal tissue exist in the apical membranes of intestinal
mucosa cells and thus effectively isolated from the targeted cancer
chemotherapeutics and imaging agents administered outside the
intestinal tract by the intestinal mucosa barrier. Thus, metastatic
colorectal cancer and primary and/or metastatic stomach or
esophageal cancer cells may be targeted by conjugated compounds of
the present invention by introducing such compounds outside the
intestinal tract such as for example by administering
pharmaceutical compositions that comprise conjugated compounds into
the circulatory system.
[0147] One having ordinary skill in the art can identify
individuals suspected of suffering from metastatic colorectal
cancer and primary and/or metastatic stomach or esophageal cancer.
In those individuals diagnosed with colorectal, stomach or
esophageal cancer, it is not unusual and in some cases standard
therapy to suspect metastasis and aggressively attempt to eradicate
metastasized cells. The present invention provides pharmaceutical
compositions and methods for imaging and thereby will more
definitively diagnose primary and metastastic disease. Further, the
present invention provides pharmaceutical compositions comprising
therapeutic agents and methods for specifically targeting and
eliminating metastatic colorectal cancer and primary and/or
metastatic stomach or esophageal cancer cells. Further, the present
invention provides pharmaceutical compositions that comprise
therapeutics and methods for specifically eliminating metastatic
colorectal cancer and primary and/or metastatic stomach or
esophageal cancer cells.
[0148] The pharmaceutical compositions which comprise conjugated
compositions of the present invention may be used to diagnose or
treat individuals suffering from metastatic colorectal cancer and
primary and/or metastatic stomach or esophageal tumors.
[0149] The present invention relies upon the use of a SI binding
moiety in a conjugated composition. The SI binding moiety is
essentially a portion of the conjugated composition which acts as a
ligand to a SI and thus specifically binds to it. The conjugated
composition also includes an active moiety which is associated with
the SI binding moiety; the active moiety being an active agent
which is either useful to image, target, neutralize or kill the
cell.
[0150] According to the present invention, the SI binding moiety is
the SI ligand portion of a conjugated composition. In some
embodiments, the SI ligand is an antibody.
[0151] In some preferred embodiments, conjugated compounds comprise
SI binding moieties that comprise an anti-SI antibody.
[0152] It is preferred that the SI ligand used as the SI binding
moiety be as small as possible. Thus it is preferred that the SI
ligand be a non-peptide small molecule or small peptide, preferably
less than 25 amino acids, more preferably less than 20 amino acids.
In some embodiments, the SI ligand which constitute the SI binding
moiety of a conjugated composition is less than 15 amino acids. SI
binding peptide comprising less than 10 amino acids and SI binding
peptide less than 5 amino acids may be used as SI binding moieties
according to the present invention. It is within the scope of the
present invention to include larger molecules which serve as SI
binding moieties including, but not limited to molecules such as
antibodies which specifically bind to SI.
[0153] Additionally, SI ligands may include any of the well known
carbohydrate substrates normally processed by the enzyme including
those substrates engineered to be recognized by the enzyme cleavage
site but which are resistant to being processed. Horii, S et al. J.
Med. Chem. 29:1038-1046 (1986), which is incorporated herein by
reference, disclose examples of such compounds.
[0154] SI ligands useful as SI binding moieties may be identified
using various well known combinatorial library screening
technologies such as those set forth in Example 1 herein.
[0155] An assay may be used to test both peptide and non-peptide
compositions to determine whether or not they are SI ligands or, to
test conjugated compositions to determine if they possess
SI-binding activity. Such compositions that specifically bind to SI
can be identified by a competitive binding assay using antibodies
known to bind to the SI. The competitive binding assay is a
standard technique in pharmacology which can be readily performed
by those having ordinary skill in the art using readily available
starting materials.
[0156] SI may be produced synthetically, recombinantly or isolated
from natural sources.
[0157] Using a solid phase synthesis as an example, the protected
or derivatized amino acid is attached to an inert solid support
through its unprotected carboxyl or amino group. The protecting
group of the amino or carboxyl group is then selectively removed
and the next amino acid in the sequence having the complementary
(amino or carboxyl) group suitably protected is admixed and reacted
with the residue already attached to the solid support. The
protecting group of the amino or carboxyl group is then removed
from this newly added amino acid residue, and the next amino acid
(suitably protected) is then added, and so forth. After all the
desired amino acids have been linked in the proper sequence, any
remaining terminal and side group protecting groups (and solid
support) are removed sequentially or concurrently, to provide the
final peptide. The peptide of the invention are preferably devoid
of benzylated or methylbenzylated amino acids. Such protecting
group moieties may be used in the course of synthesis, but they are
removed before the peptides are used. Additional reactions may be
necessary, as described elsewhere, to form intramolecular linkages
to restrain conformation.
[0158] Antibodies against SI may be routinely produced and used in
competition assays to identify SI ligands or as starting materials
for conjugated compounds according to the invention.
[0159] According to the present invention, the active moiety may be
a therapeutic agent or an imaging agent. One having ordinary skill
in the art can readily recognize the advantages of being able to
specifically target cancer cells with an SI ligand and conjugate
such a ligand with many different active agents.
[0160] Chemotherapeutics useful as active moieties which when
conjugated to a SI binding moiety are specifically delivered to
cells that express SI such as stomach or esophageal cancer cells,
are typically small chemical entities produced by chemical
synthesis. Chemotherapeutics include cytotoxic and cytostatic
drugs. Chemotherapeutics may include those which have other effects
on cells such as reversal of the transformed state to a
differentiated state or those which inhibit cell replication.
Examples of chemotherapeutics include common cytotoxic or
cytostatic drugs such as for example: methotrexate (amethopterin),
doxorubicin (adrimycin), daunorubicin, cytosinarabinoside,
etoposide, 5-4 fluorouracil, melphalan, chlorambucil, and other
nitrogen mustards (e.g. cyclophosphamide), cis-platinum, vindesine
(and other vinca alkaloids), mitomycin and bleomycin. Other
chemotherapeutics include: purothionin (barley flour oligopeptide),
macromomycin. 1,4-benzoquinone derivatives and trenimon.
[0161] Toxins are useful as active moieties. When a toxin is
conjugated to a SI binding moiety, the conjugated composition is
specifically delivered to a cell that expresses SI such as stomach
or esophageal cancer cells by way of the SI binding moiety and the
toxin moiety kills the cell. Toxins are generally complex toxic
products of various organisms including bacteria, plants, etc.
Examples of toxins include but are not limited to: ricin, ricin A
chain (ricin toxin), Pseudomonas exotoxin (PE), diphtheria toxin
(DT), Clostridium perfringens phospholipase C (PLC), bovine
pancreatic ribonuclease (BPR), pokeweed antiviral protein (PAP),
abrin, abrin A chain (abrin toxin), cobra venom factor (CVF),
gelonin (GEL), saporin (SAP), modeccin, viscumin and volkensin. As
discussed above, when protein toxins are employed with SI binding
peptides, conjugated compositions may be produced using recombinant
DNA techniques. Briefly, a recombinant DNA molecule can be
constructed which encodes both the SI ligand and the toxin on a
chimeric gene. When the chimeric gene is expressed, a fusion
protein is produced which includes a SI binding moiety and an
active moiety. Protein toxins are also useful to form conjugated
compounds with SI binding peptides through non-peptidyl bonds.
[0162] In addition, there are other approaches for utilizing active
agents for the treatment of cancer. For example, conjugated
compositions may be produced which include a SI binding moiety and
an active moiety which is an active enzyme. The SI binding moiety
specifically localizes the conjugated composition to the tumor
cells. An inactive prodrug which can be converted by the enzyme
into an active drug is administered to the patient. The prodrug is
only converted to an active drug by the enzyme which is localized
to the tumor. An example of an enzyme/prodrug pair includes
alkaline phosphatase/etoposidephosphate. In such a case, the
alkaline phosphatase is conjugated to a SI binding ligand. The
conjugated compound is administered and localizes at the cancer
cell. Upon contact with etoposidephosphate (the prodrug), the
etoposidephosphate is converted to etoposide, a chemotherapeutic
drug which is taken up by the cancer cell.
[0163] Radiosensitizing agents are substances that increase the
sensitivity of cells to radiation. Examples of radiosensitizing
agents include nitroimidazoles, metronidazole and misonidazole
(see: DeVita, V. T. Jr. in Harrison's Principles of Internal
Medicine, p.68, McGraw-Hill Book Co., N.Y. 1983, which is
incorporated herein by reference). The conjugated compound that
comprises a radiosensitizing agent as the active moiety is
administered and localizes at the metastatic colorectal cancer cell
and primary and/or metastatic stomach or esophageal cancer cell.
Upon exposure of the individual to radiation, the radiosensitizing
agent is "excited" and causes the death of the cell.
[0164] Radionuclides may be used in pharmaceutical compositions
that are useful for radiotherapy or imaging procedures.
[0165] Examples of radionuclides useful as toxins in radiation
therapy include: .sup.47Sc, .sup.67Cu, .sup.90Y, .sup.109Pd,
.sup.123I, .sup.125I, 131I, .sup.186Re, .sup.188Re, .sup.199Au,
.sup.211At, .sup.212Pb and .sup.212B. Other radionuclides which
have been used by those having ordinary skill in the art include:
.sup.32P and .sup.33P, .sup.71Ge, .sup.77As, .sup.103Pb,
.sup.105Rh, .sup.111Ag, .sup.119Sb, .sup.121Sn, .sup.131Cs,
.sup.143Pr, .sup.161Tb, .sup.177Lu, .sup.191Os, .sup.193MPt,
.sup.197Hg, all beta negative and/or auger emitters. Some preferred
radionuclides include: .sup.90Y, .sup.131I .sup.211At and
.sup.212Pb/.sup.212Bi.
[0166] According to the present invention, the active moieties may
be an imaging agent. Imaging agents are useful diagnostic
procedures as well as the procedures used to identify the location
of cancer cells. Imaging can be performed by many procedures
well-known to those having ordinary skill in the art and the
appropriate imaging agent useful in such procedures may be
conjugated to a SI ligand by well-known means. Imaging can be
performed, for example, by radioscintigraphy, nuclear magnetic
resonance imaging (MRI) or computed tomography (CT scan). The most
commonly employed radionuclide imaging agents include radioactive
iodine and indium. Imaging by CT scan may employ a heavy metal such
as iron chelates. MRI scanning may employ chelates of gadolinium or
manganese. Additionally, positron emission tomography (PET) may be
possible using positron emitters of oxygen, nitrogen, iron, carbon,
or gallium. Example of radionuclides useful in imaging procedures
include: .sup.43K, .sup.52Fe, .sup.57Co, .sup.67Cu, .sup.67Ga,
.sup.68Ga, .sup.77Br, .sup.81Rb/.sup.81MKr, .sup.87MSr, .sup.99MTc,
.sup.111In, .sup.113MIn, .sup.123I, .sup.125I, .sup.127Cs,
.sup.129Cs, .sup.131I, .sup.132I, .sup.197Hg, .sup.203Pb and
.sup.206Bi.
[0167] It is preferred that the conjugated compositions be
non-immunogenic or immunogenic at a very low level. Accordingly, it
is preferred that the SI binding moiety be a small, poorly
immunogenic or non-immunogenic peptide or a non-peptide. The SI
binding moiety may be a humanized or primatized antibody or a human
antibody.
[0168] SI ligands are conjugated to active agents by a variety of
well-known techniques readily performed without undue
experimentation by those having ordinary skill in the art. The
technique used to conjugate the SI ligand to the active agent is
dependent upon the molecular nature of the SI ligand and the active
agent. After the SI ligand and the active agent are conjugated to
form a single molecule, assays may be performed to ensure that the
conjugated molecule retains the activities of the moieties. The
competitive binding assay described above may be used to confirm
that the SI binding moiety retains its binding activity as a
conjugated compound. Similarly, the activity of the active moiety
may be tested using various assays for each respective type of
active agent. Radionuclides retain there activity, i.e. their
radioactivity, irrespective of conjugation. With respect to active
agents which are toxins, drugs and targeting agents, standard
assays to demonstrate the activity of unconjugated forms of these
compounds may be used to confirm that the activity has been
retained.
[0169] Conjugation may be accomplished directly between the SI
ligand and the active agent or linking, intermediate molecular
groups may be provided between the SI ligand and the active agent.
Crosslinkers are particularly useful to facilitate conjugation by
providing attachment sites for each moiety. Crosslinkers may
include additional molecular groups which serve as spacers to
separate the moieties from each other to prevent either from
interfering with the activity of the other.
[0170] One having ordinary skill in the art may conjugate a SI
ligand to a chemotherapeutic drug using well-known techniques. For
example, Magerstadt, M. Antibody Conjugates and Malignant Disease.
(1991) CRC Press, Boca Raton, USA, pp. 110-152) which is
incorporated herein by reference, teaches the conjugation of
various cytostatic drugs to amino acids of antibodies. Such
reactions may be applied to conjugate chemotherapeutic drugs to SI
ligands, including anti-SI antibodies, with an appropriate linker.
Most of the chemotherapeutic agents currently in use in treating
cancer possess functional groups that are amenable to chemical
crosslinking directly with proteins. For example, free amino groups
are available on methotrexate, doxorubicin, daunorubicin,
cytosinarabinoside, cis-platin, vindesine, mitomycin and bleomycin
while free carboxylic acid groups are available on methotrexate,
melphalan, and chlorambucil. These functional groups, that is free
amino and carboxylic acids, are targets for a variety of
homobifunctional and heterobifunctional chemical crosslinking
agents which can crosslink these drugs directly to the single free
amino group of an antibody. For example, one procedure for
crosslinking SI ligands which have a free amino group to active
agents which have a free amino group such as methotrexate,
doxorubicin, daunorubicin, cytosinarabinoside, cis-platin,
vindesine, mitomycin and bleomycin, or alkaline phosphatase, or
protein- or peptide-based toxin employs homobifunctional
succinimidyl esters, preferably with carbon chain spacers such as
disuccinimidyl suberate (Pierce Co, Rockford, Ill.). In the event
that a cleavable conjugated compound is required, the same protocol
would be employed utilizing 3,3'- dithiobis
(sulfosuccinimidylpropionate; Pierce Co.).
[0171] In order to conjugate a SI ligand that is a peptide or
protein to a peptide-based active agent such as a toxin, the SI
ligand and the toxin may be produced as a single, fusion protein
either by standard peptide synthesis or recombinant DNA technology,
both of which can be routinely performed by those having ordinary
skill in the art. Alternatively, two peptides, the SI ligand
peptide and the peptide-based toxin may be produced and/or isolated
as separate peptides and conjugated using crosslinkers. As with
conjugated compositions that contain chemotherapeutic drugs,
conjugation of SI binding peptides and toxins can exploit the
ability to modify the single free amino group of a SI binding
peptide while preserving the receptor-binding function of this
molecule.
[0172] One having ordinary skill in the art may conjugate a SI
ligand to a radionuclide using well-known techniques. For example,
Magerstadt, M. (1991) Antibody Conjugates And Malignant Disease,
CRC Press, Boca Raton, Fla.,; and Barchel, S. W. and Rhodes, B. H.,
(1983) Radioimaging and Radiotherapy, Elsevier, NY, N.Y., each of
which is incorporated herein by reference, teach the conjugation of
various therapeutic and diagnostic radionuclides to amino acids of
antibodies.
[0173] The present invention provides pharmaceutical compositions
that comprise the conjugated compounds of the invention and
pharmaceutically acceptable carriers or diluents. The
pharmaceutical composition of the present invention may be
formulated by one having ordinary skill in the art. Suitable
pharmaceutical carriers are described in Remington's Pharmaceutical
Sciences, A. Osol, a standard reference text in this field, which
is incorporated herein by reference. In carrying out methods of the
present invention, conjugated compounds of the present invention
can be used alone or in combination with other diagnostic,
therapeutic or additional agents. Such additional agents include
excipients such as coloring, stabilizing agents, osmotic agents and
antibacterial agents. Pharmaceutical compositions are preferably
sterile and pyrogen free.
[0174] The conjugated compositions of the invention can be, for
example, formulated as a solution, suspension or emulsion in
association with a pharmaceutically acceptable parenteral vehicle.
Examples of such vehicles are water, saline, Ringer's solution,
dextrose solution, and 5% human serum albumin. Liposomes may also
be used. The vehicle may contain additives that maintain
isotonicity (e.g., sodium chloride, mannitol) and chemical
stability (e.g., buffers and preservatives). The formulation is
sterilized by commonly used techniques. For example, a parenteral
composition suitable for administration by injection is prepared by
dissolving 1.5% by weight of active ingredient in 0.9% sodium
chloride solution.
[0175] The pharmaceutical compositions according to the present
invention may be administered as either a single dose or in
multiple doses. The pharmaceutical compositions of the present
invention may be administered either as individual therapeutic
agents or in combination with other therapeutic agents. The
treatments of the present invention may be combined with
conventional therapies, which may be administered sequentially or
simultaneously.
[0176] The pharmaceutical compositions of the present invention may
be administered by any means that enables the conjugated
composition to reach the targeted cells. In some embodiments,
routes of administration include those selected from the group
consisting of intravenous, intraarterial, intraperitoneal, local
administration into the blood supply of the organ in which the
tumor resides or directly into the tumor itself. In addition to an
intraoperative spray, conjuagated compounds may be delivered
intrathecally, intraventrically, stereotactically, intrahepatically
such as via the portal vein, by inhalation, and intrapleurally.
Intravenous administration is the preferred mode of administration.
It may be accomplished with the aid of an infusion pump.
[0177] The dosage administered varies depending upon factors such
as: the nature of the active moiety; the nature of the conjugated
composition; pharmacodynamic characteristics; its mode and route of
administration; age, health, and weight of the recipient; nature
and extent of symptoms; kind of concurrent treatment; and frequency
of treatment.
[0178] Because conjugated compounds are specifically targeted to
cells with one or more SI molecules, conjugated compounds which
comprise chemotherapeutics or toxins are administered in doses less
than those which are used when the chemotherapeutics or toxins are
administered as unconjugated active agents, preferably in doses
that contain up to 100 times less active agent. In some
embodiments, conjugated compounds which comprise chemotherapeutics
or toxins are administered in doses that contain 10-100 times less
active agent as an active moiety than the dosage of
chemotherapeutics or toxins administered as unconjugated active
agents. To determine the appropriate dose, the amount of compound
is preferably measured in moles instead of by weight. In that way,
the variable weight of different SI binding moieties does not
affect the calculation. Presuming a one to one ratio of SI binding
moiety to active moiety in conjugated compositions of the
invention, less moles of conjugated compounds may be administered
as compared to the moles of unconjugated compounds administered,
preferably up to 100 times less moles.
[0179] Typically, chemotherapeutic conjugates are administered
intravenously in multiple divided doses.
[0180] Up to 20 gm IV/dose of methotrexate is typically
administered in an unconjugated form. When methotrexate is
administered as the active moiety in a conjugated compound of the
invention, there is a 10-to 100-fold dose reduction. Thus,
presuming each conjugated compound includes one molecule of
methotrexate conjugated to one SI binding moiety, of the total
amount of conjugated compound administered, up to about 0.2-2.0 g
of methotrexate is present and therefore administered. In some
embodiments, of the total amount of conjugated compound
administered, up to about 200 mg-2 g of methotrexate is present and
therefore administered.
[0181] To dose conjugated compositions comprising SI binding
moieties linked to active moieties that are radioisotopes in
pharmaceutical compositions useful as imaging agents, it is
presumed that each SI binding moiety is linked to one radioactive
active moiety. The amount of radioisotope to be administered is
dependent upon the radioisotope. Those having ordinary skill in the
art can readily formulate the amount of conjugated compound to be
administered based upon the specific activity and energy of a given
radionuclide used as an active moiety. Typically 0.1-100
millicuries per dose of imaging agent, preferably 110 millicuries,
most often 2-5 millicuries are administered. Thus, pharmaceutical
compositions according to the present invention useful as imaging
agents which comprise conjugated compositions comprising a SI
binding moiety and a radioactive moiety comprise 0.1-100
millicuries, in some embodiments preferably 1-10 millicuries, in
some embodiments preferably 2-5 millicuries, in some embodiments
more preferably 1-5 millicuries. Examples of dosages include:
.sup.311I=between about 0.1-100 millicuries per dose, in some
embodiments preferably 1-10 millicuries, in some embodiments 2-5
millicuries, and in some embodiments about 4 millicuries;
.sup.111In=between about 0.1-100 millicuries per dose, in some
embodiments preferably 1-10 millicuries, in some embodiments 1-5
millicuries, and in some embodiments about 2 millicuries;
.sup.99mTc between about 0.1-100 millicuries per dose, in some
embodiments preferably 5-75 millicuries, in some embodiments 10-50
millicuries, and in some embodiments about 27 millicuries. Wessels
B. W. and R. D. Rogus (1984) Med. Phys. 11:638 and Kwok, C. S. et
al. (1985) Med. Phys. 12:405, both of which are incorporated herein
by reference, disclose detailed dose calculations for diagnostic
and therapeutic conjugates which may be used in the preparation of
pharmaceutical compositions of the present invention which include
radioactive conjugated compounds.
[0182] One aspect of the present invention relates to a method of
treating individuals suspected of suffering from metastatic
colorectal cancer and primary and/or metastatic stomach or
esophageal cancer. Such individuals may be treated by administering
to the individual a pharmaceutical composition that comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises a SI-binding moiety and an active moiety
wherein the active moiety is a radiostable therapeutic agent. In
some embodiments of the present invention, the pharmaceutical
composition comprises a pharmaceutically acceptable carrier or
diluent and a conjugated compound that comprises a SI binding
moiety and an active moiety wherein the active moiety is a
radiostable active agent and the SI binding moiety is an antibody.
In some embodiments of the present invention, the pharmaceutical
composition comprises a pharmaceutically acceptable carrier or
diluent and a conjugated compound that comprises a SI binding
moiety and an active moiety wherein the active moiety is a
radiostable therapeutic agent. In some embodiments of the present
invention, the pharmaceutical composition comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises a SI binding moiety and an active moiety
wherein the active moiety is a radiostable active agent selected
from the group consisting of: methotrexate, doxorubicin,
daunorubicin, cytosinarabinoside, etoposide, 5-4 fluorouracil,
melphalan, chlorambucil, cis-platinum, vindesine, mitomycin,
bleomycin, purothionin, macromomycin, 1,4-benzoquinone derivatives,
trenimon, ricin, ricin A chain, Pseudomonas exotoxin, diphtheria
toxin, Clostridium perfringens phospholipase C, bovine pancreatic
ribonuclease, pokeweed antiviral protein, abrin, abrin A chain,
cobra venom factor, gelonin, saporin, modeccin, viscumin,
volkensin, alkaline phosphatase, nitroimidazole, metronidazole and
misonidazole. The individual being treated may be diagnosed as
having metastasized colorectal, stomach or esophageal cancer or may
be diagnosed as having primary colorectal, stomach or esophageal
cancer and may undergo the treatment proactively in the event that
there is some metastasis as yet undetected. The pharmaceutical
composition contains a therapeutically effective amount of the
conjugated composition. A therapeutically effective amount is an
amount which is effective to cause a cytotoxic or cytostatic effect
on cancer cells without causing lethal side effects on the
individual.
[0183] One aspect of the present invention relates to a method of
treating individuals suspected of suffering from metastatic
colorectal cancer and primary and/or metastatic stomach or
esophageal cancer. Such individuals may be treated by administering
to the individual a pharmaceutical composition that comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises a SI binding moiety and an active moiety
wherein the active moiety is a radioactive. In some embodiments of
the present invention, the pharmaceutical composition comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises a SI binding moiety and an active moiety
wherein the active moiety is a radioactive and the SI binding
moiety is an antibody. In some embodiments of the present
invention, the pharmaceutical composition comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises a SI binding moiety and an active moiety
wherein the active moiety is a radioactive agent selected from the
group consisting of: .sup.47Sc, .sup.67Cu, .sup.90Y, .sup.109Pd,
.sup.123I, .sup.125I, .sup.131I, .sup.186Re, .sup.188Re,
.sup.199Au, .sup.211At, .sup.212Pb, .sup.212B, .sup.32P and
.sup.33P, .sup.71Ge, .sup.77As, .sup.103Pb, .sup.105Rh, .sup.111Ag,
.sup.119Sb, .sup.121Sn, .sup.131Cs, .sup.143Pr, .sup.161Tb,
.sup.177Lu, .sup.191OS, .sup.193MPt, .sup.197Hg, .sup.32P and
.sup.33P, .sup.71Ge, .sup.77As, .sup.103Pb, .sup.105Rh, .sup.111Ag,
.sup.119Sb, .sup.121Sn, .sup.131Cs, .sup.143Pr, .sup.161Tb,
.sup.177Lu, .sup.191Os, .sup.193MPt, .sup.197Hg, all beta negative
and/or auger emitters. The individual being treated may be
diagnosed as having metastasized cancer or may be diagnosed as
having localized cancer and may undergo the treatment proactively
in the event that there is some metastasis as yet undetected. The
pharmaceutical composition contains a therapeutically effective
amount of the conjugated composition. A therapeutically effective
amount is an amount which is effective to cause a cytotoxic or
cytostatic effect on metastatic colorectal cancer and primary
and/or metastatic stomach or esophageal cancer cells without
causing lethal side effects on the individual. The composition may
be injected intratumorally into primary tumors.
[0184] One aspect of the present invention relates to a method of
detecting metastatic colorectal cancer and primary and/or
metastatic stomach or esophageal cancer cells in an individual
suspected of suffering from primary or metastasized colorectal,
stomach or esophageal cancer by radioimaging. Individuals may be
suspected of having primary stomach or esophageal tumors which
diagnosis can be confirmed by administering to the individual, an
imaging agent which binds to SI. Tumors can be imaged by detecting
localization at the stomach or esophagus. Individuals may be
diagnosed as suffering from metastasized colorectal, stomach or
esophageal cancer and the metastasized colorectal, stomach or
esophageal cancer cells may be detected by administering to the
individual, preferably by intravenous administration, a
pharmaceutical composition that comprises a pharmaceutically
acceptable carrier or diluent and a conjugated compound that
comprises a SI binding moiety and an active moiety wherein the
active moiety is a radioactive and detecting the presence of a
localized accumulation or aggregation of radioactivity, indicating
the presence of cells with SI. In some embodiments of the present
invention, the pharmaceutical composition comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises a SI binding moiety and an active moiety
wherein the active moiety is a radioactive and the SI binding
moiety is an antibody. In some embodiments of the present
invention, the pharmaceutical composition comprises a
pharmaceutically acceptable carrier or diluent and a conjugated
compound that comprises an SI binding moiety and an active moiety
wherein the active moiety is a radioactive agent selected from the
group consisting of: radioactive heavy metals such as iron
chelates, radioactive chelates of gadolinium or manganese, positron
emitters of oxygen, nitrogen, iron, carbon, or gallium, .sup.43K,
.sup.52Fe, .sup.57Co, .sup.67Cu, .sup.67Ga, .sup.68Ga, .sup.77Br,
.sup.81Rb/.sup.81MKr, .sup.87MSr, .sup.99MTc, .sup.111In,
.sup.113MIn, .sup.123I, .sup.125I, .sup.127Cs, .sup.129Cs,
.sup.131I, .sup.132I, .sup.197Hg, .sup.203Pb and .sup.206Bi. The
individual being treated may be diagnosed as having metastasizing
colorectal, stomach or esophageal cancer or may be diagnosed as
having localized colorectal, stomach or esophageal cancer and may
undergo the treatment proactively in the event that there is some
metastasis as yet undetected. The pharmaceutical composition
contains a diagnostically effective amount of the conjugated
composition. A diagnostically effective amount is an amount which
can be detected at a site in the body where cells with SI are
located without causing lethal side effects on the individual.
[0185] Photodynamic imaging and Therapy
[0186] According to some embodiments of the invention, SI binding
moieties are conjugates to photoactivated imaging agents or
therapeutics. Maier A. et al. Lasers in Surgery and Medicine
26:461-466 (2000) which is incorporated herein by reference
disclose an example of photodynamic therapy. QLT, Inc (Vancouver,
BC) commercially distribute photosensitive active agents which can
be linked to SI ligands. Such conjugated compounds can be used in
photodynamic therapeutic and imaging protocols to activate the
SI-bound conjugated agents which are thus targeted to tumor cells.
In some embodiments, the conjugated compounds are applied as an
intraoperative spray which is subsequently exposed to light to
activate compounds bound to cells that express SI.
[0187] In some embodiments, the photodynamic agent is fluorophore
or porphyrins. Examples of porphyrin include: hematoporphyrin
derivative (HPD) and porfimer sodium (Photofrin.RTM.). A second
generation photosensitizers is BPD verteporfin. In some
embiodiments the fluorophore is tetramethylrotamine. Lasers are
generally the primary light source used to activate porphyrins.
Light Emitting Diodes (LEDs) and florescent light sources may also
be used in some applications.
[0188] In addition to an intraoperative spray, conjuagated
compounds may be delivered intrathecally, intraventrically,
stereotactically, intrahepatically such as via the portal vein, by
inhalation, and intrapleurally.
[0189] Drug Delivery Targeted To Stomach or Esophageal Cancer Cells
Generally
[0190] Another aspect of the invention relates to unconjugated and
conjugated compositions which comprise a SI ligand used to deliver
therapeutic agents to cells that comprise a SI such as metastatic
colorectal cancer and primary and/or metastatic stomach or
esophageal cancer cells. In some embodiments, the agent is a drug
or toxin such as: methotrexate, doxorubicin, daunorubicin,
cytosinarabinoside, etoposide, 5-4 fluorouracil, melphalan,
chlorambucil, cis-platinum, vindesine, mitomycin, bleomycin,
purothionin, macromomycin, 1,4-benzoquinone derivatives, trenimon,
ricin, ricin A chain, Pseudomonas exotoxin, diphtheria toxin,
Clostridium perfringens phospholipase C, bovine pancreatic
ribonuclease, pokeweed antiviral protein, abrin, abrin A chain,
cobra venom factor, gelonin, saporin, modeccin, viscumin,
volkensin, alkaline phosphatase, nitroimidazole, metronidazole and
misonidazole. Genetic material is delivered to cancer cells to
produce an antigen that can be targeted by the immune system or to
produce a protein which kills the cell or inhibits its
proliferation. In some embodiments, the SI ligand is used to
deliver nucleic acids that encode nucleic acid molecules which
replace defective endogenous genes or which encode therapeutic
proteins. In some embodiments, the compositions are used in gene
therapy protocols to deliver to individuals, genetic material
needed and/or desired to make up for a genetic deficiency.
[0191] In some embodiments, the SI ligand is combined with or
incorporated into a delivery vehicle thereby converting the
delivery vehicle into a specifically targeted delivery vehicle. For
example, a SI binding peptide may be integrated into the outer
portion of a viral particle making such a virus a SI-bearing cell
specific virus. Similarly, the coat protein of a virus may be
engineered such that it is produced as a fusion protein which
includes an active SI binding peptide that is exposed or otherwise
accessible on the outside of the viral particle making such a virus
a SI-bearing cell-specific virus. In some embodiments, a SI ligand
may be integrated or otherwise incorporated into the liposomes
wherein the SI ligand is exposed or otherwise accessible on the
outside of the liposome making such liposomes specifically targeted
to SI-bearing cells.
[0192] The active agent in the conjugated or unconjugated
compositions according to this aspect of the invention is a drug,
toxin or nucleic acid molecule. The nucleic acid may be RNA or
preferably DNA. In some embodiments, the nucleic acid molecule is
an antisense molecule or encodes an antisense sequence whose
presence in the cell inhibits production of an undesirable protein.
In some embodiments, the nucleic acid molecule encodes a ribozyme
whose presence in the cell inhibits production of an undesirable
protein. In some embodiments, the nucleic acid molecule encodes a
protein or peptide that is desirably produced in the cell. In some
embodiments, the nucleic acid molecule encodes a functional copy of
a gene that is defective in the targeted cell. The nucleic acid
molecule is preferably operably linked to regulatory elements
needed to express the coding sequence in the cell.
[0193] Liposomes are small vesicles composed of lipids. Genetic
constructs which encode proteins that are desired to be expressed
in SI-bearing cells are introduced into the center of these
vesicles. The outer shell of these vesicles comprise an a SI
ligand. Liposomes Volumes 1, 2 and 3 CRC Press Inc. Boca Raton
Fla., which is incorporated herein by reference, disclose
preparation of liposome-encapsulated active agents which include
antibodies in the outer shell. In the present invention, a SI
ligand such as for example an anti-SI antibodies is associated with
the in the outer shell. Unconjugated compositions which comprise a
SI ligand in the matrix of a liposome with an active agent inside
include such compositions in which the SI ligand is preferably an
antibody.
[0194] In one embodiment, the delivery of normal copies of the p53
tumor suppressor gene to the cancer cells is accomplished using SI
ligand to target the gene therapeutic. Mutations of the p53 tumor
suppressor gene appears to play a prominent role in the development
of many cancers. One approach to combating this disease is the
delivery of normal copies of this gene to the cancer cells
expressing mutant forms of this gene. Genetic constructs that
comprise normal p53 tumor suppressor genes are incorporated into
liposomes that comprise a SI ligand. The composition is delivered
to the tumor. SI ligands specifically target and direct the
liposomes containing the normal gene to correct the lesion created
by mutation of p53 suppressor gene. Preparation of genetic
constructs is with the skill of those having ordinary skill in the
art. The present invention allows such construct to be specifically
targeted by using the SI ligands of the present invention. The
compositions of the invention include a SI ligand such as an
anti-SI antibody associated with a delivery vehicle and a gene
construct which comprises a coding sequence for a protein whose
production is desired in the cells of the intestinal tract linked
to necessary regulatory sequences for expression in the cells. For
uptake by cells of the intestinal tract, the compositions are
administered orally or by enema whereby they enter the intestinal
tract and contact cells which comprise SI. The delivery vehicles
associate with the SI by virtue of the SI ligand and the vehicle is
internalized into the cell or the active agent/genetic construct is
otherwise taken up by the cell. Once internalized, the construct
can provide a therapeutic effect on the individual.
[0195] Antisense
[0196] The present invention provides compositions, kits and
methods which are useful to prevent and treat colorectal, stomach
or esophageal cancer cells by providing the means to specifically
deliver antisense compounds to colorectal, stomach or esophageal
cancer cells and thereby stop expression of genes in such cells in
which undesirable gene expression is taking place without
negatively effecting cells in which no such expression occurs.
[0197] The conjugated compositions of the present invention are
useful for targeting cells that express SI including colorectal,
stomach or esophageal cancer cells. The conjugated compositions
will not bind to non-colorectal derived cells. Non-colorectal
cells, lacking SI, do not take up the conjugated compositions.
Normal colorectal cells do have SI and will take up the
compositions. The present invention provides compositions and
methods of delivering antisense compositions to normal and
cancerous colorectal cells and stomach or esophageal cancer
cells.
[0198] The present invention provides a cell specific approach in
which only normal and cancerous colorectal cells and primary and/or
metastatic stomach or esophageal cancer cells are exposed to the
active portion of the compound and only those cells are effected by
the conjugated compound. The SI binding moiety binds to normal and
cancerous colorectal cells and primary and/or metastatic stomach or
esophageal cancer cells. Upon binding to these cells, the
conjugated compound is internalized and the delivery of the
conjugated compound including the antisense portion of the molecule
is effected. The presence of the conjugated compound in normal
colorectal cells has no effect on such cells because the
cancer-associated gene for which the antisense molecule that makes
up the active moiety of the conjugated compound is complementary is
not being expressed. However, in colorectal cancer cells, the
cancer gene for which the antisense molecule that makes up the
active moiety of the conjugated compound is complementary is being
expressed. The presence of the conjugated compound in colorectal
cancer cells serves to inhibit or prevent transcription or
translation of the cancer gene and thereby reduce or eliminate the
transformed phenotype.
[0199] The invention can be used to combat primary and/or
metastasized colorectal, stomach or esophageal cancer as well as to
prevent the emergence of the transformed phenotype in normal colon
cells. Thus the invention can be used therapeutically as well as
prophylactically.
[0200] One having ordinary skill in the art can readily identify
individuals suspected of suffering from stomach or esophageal
cancer. In those individuals diagnosed with stomach or esophageal
cancer, it is standard therapy to suspect metastasis and
aggressively attempt to eradicate metastasized cells. The present
invention provides pharmaceutical compositions and methods for
specifically targeting and eliminating metastasized colorectal
cancer cells and primary and/or metastatic stomach or esophageal
cancer cells. Further, the present invention provides
pharmaceutical compositions that comprise therapeutics and methods
for specifically eliminating metastasized colorectal cancer cells
and primary and/or metastatic stomach or esophageal cancer
cells.
[0201] The present invention relies upon the use of a SI binding
moiety in a conjugated composition. The SI product binding moiety
is essentially a portion of the conjugated composition which acts
as a ligand to the SI and thus specifically binds to these
receptors. The conjugated composition also includes an active
moiety which is associated with the SI binding moiety; the active
moiety being an antisense composition useful to inhibit or prevent
transcription or translation of expression of genes whose
expression is associated with cancer.
[0202] According to the present invention, the active moiety is an
antisense composition. In particular, the antisense molecule that
makes up the active moiety of a conjugated compound hybridizes to
DNA or RNA in a colorectal, stomach or esophageal cancer cell and
inhibits and/or prevents transcription or translation of the DNA or
RNA from taking place. The antisense compositions may be a nucleic
acid molecule, a derivative or an analogs thereof. The chemical
nature of the antisense composition may be that of a nucleic acid
molecule or a modified nucleic acid molecule or a non-nucleic acid
molecule which possess functional groups that mimic a DNA or RNA
molecule that is complementary to the DNA or RNA molecule whose
expression is to be inhibited or otherwise prevented. Antisense
compositions inhibit or prevent transcription or translation of
genes whose expression is linked to colorectal, stomach or
esophageal cancer, i.e. cancer associated genes.
[0203] Point mutations insertions, and deletions in K-ras and H-ras
have been identified in many tumors. Complex characteristics of the
alterations of oncogenes HER-2/ERBB-2, HER-1/ERBB-1, HRAS-1, C-MYC
and anti-oncogenes p53, RB1.
[0204] Chemical carcinogenesis in a rat model demonstrated point
mutations in fos, an oncogene which mediates transcriptional
regulation and proliferation. See: Alexander, R J, et al. Oncogene
alterations in rat colon tumors induced by N-methyl-N-nitrosourea.
American Journal of the Medical Sciences. 303(1):16-24, 1992,
January. which is hereby incorporated herein by reference including
all references cited therein which are also hereby incorporated
herein by reference.
[0205] Chemical carcinogenesis in a rat model demonstrated point
mutations in the oncogene abl. See: Alexander, R J, et al. Oncogene
alterations in rat colon tumors induced by N-methyl-N-nitrosourea.
American Journal of the Medical Sciences. 303(1):16-24, 1992,
January.
[0206] MYC is an oncogene that plays a role in regulating
transcription and proliferation. A 15-base antisense
oligonucleotide to myc complementary to the translation initiation
region of exon II was incubated with colorectal cancer cells. This
antisense molecule inhibited proliferation of colorectal cancer
cells in a dos-dependent fashion. Interestingly, the uptake of this
oligonucleotide was low (0.7%). Also, transfer of a normal
chromosome 5 to colorectal cancer cells resulted in the regulation
of myc expression and loss of proliferation. These data suggest
that a tumor suppressor gene important in the regulation of myc is
contained on this chromosome.
[0207] A novel protein tyrosine phosphatase, G1, has been
identified. Examination of the mRNA encoding this protein in
colorectal tumor cells revealed that it undergoes point mutations
and deletions in these cells and may play a role in proliferation
characteristic of these cells. Takekawa, M. et al. Chromosomal
localization of the protein tyrosine phosphatase G1 gene and
characterization of the aberrant transcripts in human colon cancer
cells. FEBS Letters. 339(3):222-8, 1994 February. 21, which is
hereby incorporated herein by reference including all references
cited therein which are also hereby incorporated herein by
reference.
[0208] Gastrin regulates colon cancer cell growth through a cyclic
AMP-dependent mechanism mediated by PKA. Antisense
oligodeoxynucleotides to the regulatory subunit of a specific class
of PKA inhibited the growth-promoting effects of cyclic AMP in
colon carcinoma cells. See: Bold, R J, et al. Experimental gene
therapy of human colon cancer. Surgery. 116(2):189-95; discussion
195-6,1994 August. and Yokozaki, H., et al. An antisense
oligodeoxynucleotide that depletes RI alpha subunit of cyclic
AMP-dependent protein kinase induces growth inhibition in human
cancer cells. Cancer Research. 53(4):868-72, 1993 February 15,
which are both hereby incorporated herein by reference including
all references cited therein which are also hereby incorporated
herein by reference.
[0209] CRIPTO is an epidermal growth factor-related gene expressed
in a majority of colorectal cancer tumors. Antisense
phosphorothioate oligodeoxynucleotides to the 5'-end of CRIPTO mRNA
significantly reduced CRIPTO expression and inhibited colorectal
tumor cell growth in vitro and in vivo. Ciardiello, F. et al.
Inhibition of CRIPTO expression and tumorigenicity in human colon
cancer cells by antisense RNA and oligodeoxynucleotides. Oncogene.
9(1):291-8, 1994 January. which are both hereby incorporated herein
by reference including all references cited therein which are also
hereby incorporated herein by reference.
[0210] Many carcinoma cells secrete transforming growth factor
alpha. A 23 nucleotide antisense oligonucleotide to TGF alpha mRNA
inhibited both DNA synthesis an proliferation of colorectal cancer
cells. Sizeland, A M, Burgess, A W. Antisense transforming growth
factor alpha oligonucleotides inhibit autocrine stimulated
proliferation of a colon carcinoma cell line. Molecular Biology of
the Cell. 3(11): 1235-43, 1992 November. which is hereby
incorporated herein by reference including all references cited
therein which are also hereby incorporated herein by reference.
[0211] Antisense compositions including oligonucleotides,
derivatives and analogs thereof, conjugation protocols, and
antisense strategies for inhibition of transcription and
translation are generally described in: Antisense Research and
Applications, Crooke, S. and B. Lebleu, eds. CRC Press, Inc. Boca
Raton Fla. 1993; Nucleic Acids in Chemistry and Biology Blackburn,
G. and M. J. Gait, eds. IRL Press at Oxford University Press, Inc.
New York 1990; and Oligonucleotides and Analogues: A Practical
Approach Eckstein, F. ed., IRL Press at Oxford University Press,
Inc. New York 1991; which are each hereby incorporated herein by
reference including all references cited therein which are hereby
incorporated herein by reference.
[0212] The antisense molecules of the present invention comprise a
sequence complementary to a fragment of a colorectal cancer gene.
See Ullrich et al., EMBO J., 1986, 5:2503, which is hereby
incorporated herein by reference.
[0213] Antisense compositions which can make up an active moiety in
conjugated compounds of the invention include oligonucleotides
formed of homopyrimidines can recognize local stretches of
homopurines in the DNA double helix and bind to them in the major
groove to form a triple helix. See: Helen, C and Toulme, J J.
Specific regulation of gene expression by antisense, sense, and
antigene nucleic acids. Biochem. Biophys Acta, 1049:99-125, 1990
which is hereby incorporated herein by reference including all
references cited therein which are hereby incorporated herein by
reference. Formation of the triple helix would interrupt the
ability of the specific gene to undergo transcription by RNA
polymerase. Triple helix formation using myc-specific
oligonucleotides has been observed. See: Cooney, M, et al. Science
241:456-459 which is hereby incorporated herein by reference
including all references cited therein which are hereby
incorporated herein by reference.
[0214] Antisense oligonucleotides of DNA or RNA complementary to
sequences at the boundary between introns and exons can be employed
to prevent the maturation of newly-generated nuclear RNA
transcripts of specific genes into MRNA for transcription.
Antisense RNA complimentary to specific genes can hybridize with
the mRNA for tat gene and prevent its translation. Antisense RNA
can be provided to the cell as "ready-to-use" RNA synthesized in
vitro or as an antisense gene stably transfected into cells which
will yield antisense RNA upon transcription. Hybridization with
mRNA results in degradation of the hybridized molecule by RNAse H
and/or inhibition of the formation of translation complexes. Both
result in a failure to produce the product of the original
gene.
[0215] Antisense sequences of DNA or RNA can be delivered to cells.
Several chemical modifications have been developed to prolong the
stability and improve the function of these molecules without
interfering in their ability to recognize specific sequences. These
include increasing their resistance to degradation by DNases,
including phosphotriesters, methylphosphonates, phosphorothioates,
alpha-anomers, increasing their affinity for their target by
covalent linkage to various intercalating agents such as psoralens,
and increasing uptake by cells by conjugation to various groups
including polylysine. These molecules recognize specific sequences
encoded in mRNA and their hybridization prevents translation of and
increases the degradation of these messages.
[0216] Conjugated compositions of the invention provide a specific
and effective means for terminating the expression of genes which
cause neoplastic transformation. SI undergo ligand-induced
endocytosis and can deliver conjugated compounds to the cytoplasm
of cells.
[0217] SI-binding moieties are conjugated directly to antisense
compositions such as nucleic acids which are active in inducing a
response. For example, antisense oligonucleotides to MYC are
conjugated directly to an anti-SI antibody. This has been performed
employing peptides that bind to the CD4 receptor. See: Cohen, J S,
ed. Oligodeoxynucleotides: Antisense Inhibitors of Gene Expression.
Topics in Molecular and Structural Biology. CRC Press, Inc., Boca
Raton, 1989. which is hereby incorporated herein by reference
including all references cited therein which are hereby
incorporated herein by reference. The precise backbone and its
synthesis is not specified and can be selected from
well-established techniques. Synthesis would involve either
chemical conjugation or direct synthesis of the chimeric molecule
by solid phase synthesis employing FMOC chemistry. See:
Haralambidis, J, et al. (1987) Tetrahedron Lett. 28:5199-5202,
which is hereby incorporated herein by reference including all
references cited therein which are hereby incorporated herein by
reference. Alternatively, the peptide-nucleic acid conjugate may be
synthesized directly by solid phase synthesis as a peptide-peptide
nucleic acid chimera by solid phase synthesis. Nielsen, P E, et al.
(1994) Sequence-specific transcription arrest by peptide nucleic
acid bound to the DNA template strand. Gene 149:139-145, which is
hereby incorporated herein by reference including all references
cited therein which are hereby incorporated herein by
reference.
[0218] In some embodiments, polylysine can be complexed to
conjugated compositions of the invention in a non-covalent fashion
to nucleic acids and used to enhance delivery of these molecules to
the cytoplasm of cells. In addition, peptides and proteins can be
conjugated to polylysine in a covalent fashion and this conjugate
complexed with nucleic acids in a non-covalent fashion to further
enhance the specificity and efficiency of uptake of the nucleic
acids into cells. Thus, SI ligand is conjugated chemically to
polylysine by established techniques. The polylysine-SI translation
product ligand conjugate may be complexed with nucleic acids of
choice. Thus, polylysine-orosomucoid conjugates were employed to
specifically plasmids containing genes to be expressed to hepatoma
cells expressing the orosomucoid receptor. This approach can be
used to delivery whole genes, or oligonucleotides. Thus, it has the
potential to terminate the expression of an undesired gene (eg.
MYC, ras) or replace the function of a lost or deleted gene (eg.
hMSH2, HMLH1, hPMS1, and hPMS2).
[0219] According to a preferred embodiment, Myc serves as a gene
whose expression is inhibited by an antisense molecule within a
conjugated composition. SI binding moieties are used to deliver a
15-based antisense oligonucleotide to myc complementary to the
translation initiation region of exon II. The 15-base antisense
oligonucleotide to MYC is synthesized as reported in Collins, J F,
Herman, P, Schuch, C, Bagby G C, Jr. Journal of Clinical
Investigation. 89(5):1523-7, 1992 May. In some embodiments, the
conjugated composition is conjugated to polylysine as reported
previously. Wu, G Y, and Wu, C H. (1988) Evidence for ed gene
delivery to Hep G2 hepatoma cells in vitro. Biochem. 27:887-892
which is incorporated herein by reference.
[0220] Conjugated compositions may be synthesized as a chimeric
molecule directly by solid phase synthesis. pmolar to nanomolar
concentrations for this conjugate suppress MYC synthesis in
colorectal cancer cells in vitro.
[0221] Antisense molecules are preferably hybridize to, i.e. are
complementary to, a nucleotide sequence that is 5-50 nucleotides in
length, more preferably 5-25 nucleotides and in some embodiments
10-15 nucleotides.
[0222] In addition, mismatches within the sequences identified
above, which achieve the methods of the invention, such that the
mismatched sequences are substantially complementary to the cancer
gene sequences are also considered within the scope of the
disclosure. Mismatches which permit substantial complementarity to
the cancer gene sequences will be known to those of skill in the
art once armed with the present disclosure. The oligos may also be
unmodified or modified.
[0223] Therapeutic compositions and methods may be used to combat
colorectal, stomach or esophageal cancer in cases where the cancer
is localized and/or metastasized. Individuals are administered a
therapeutically effective amount of conjugated compound. A
therapeutically effective amount is an amount which is effective to
cause a cytotoxic or cytostatic effect on cancer cells without
causing lethal side effects on the individual. An individual who
has been administered a therapeutically effective amount of a
conjugated composition has a increased chance of eliminating
colorectal, stomach or esophageal cancer as compared to the risk
had the individual not received the therapeutically effective
amount.
[0224] To treat localized colorectal, stomach or esophageal cancer,
a therapeutically effective amount of a conjugated compound is
administered such that it will come into contact with the localized
tumor. Thus, the conjugated compound may be administered orally or
intratumorally. Oral and rectal formulation are taught in
Remington's Pharmaceutical Sciences, 18th Edition, 1990, Mack
Publishing Co., Easton Pa. which is incorporated herein by
reference.
[0225] The pharmaceutical compositions according to the present
invention may be administered as either a single dose or in
multiple doses. The pharmaceutical compositions of the present
invention may be administered either as individual therapeutic
agents or in combination with other therapeutic agents. The
treatments of the present invention may be combined with
conventional therapies, which may be administered sequentially or
simultaneously.
[0226] The present invention is directed to a method of delivering
antisense compounds to normal and cancerous colorectal cells and to
stomach or esophageal cancer cells and inhibiting expression of
cancer genes in mammals. The methods comprise administering to a
mammal an effective amount of a conjugated composition which
comprises a SI binding moiety conjugated to an antisense
oligonucleotide having a sequence which is complementary to a
region of DNA or MRNA of a cancer gene.
[0227] The conjugated compounds may be administering to mammals in
a mixture with a pharmaceutically-acceptable carrier, selected with
regard to the intended route of administration and the standard
pharmaceutical practice. Dosages will be set with regard to weight,
and clinical condition of the patient. The conjugated compositions
of the present invention will be administered for a time sufficient
for the mammals to be free of undifferentiated cells and/or cells
having an abnormal phenotype. In therapeutic methods treatment
extends for a time sufficient to inhibit transformed cells from
proliferating and conjugated compositions may be administered in
conjunction with other chemotherapeutic agents to manage and combat
the patient's cancer.
[0228] The conjugated compounds of the invention may be employed in
the method of the invention singly or in combination with other
compounds. The amount to be administered will also depend on such
factors as the age, weight, and clinical condition of the patient.
See Gennaro, Alfonso, ed., Remington's Pharmaceutical Sciences,
18th Edition, 1990, Mack Publishing Co., Easton, Pa.
[0229] Therapeutic and Prophylactic Vaccines
[0230] The invention relates to prophylactic and therapeutic
vaccines for protecting individuals against metastasized colorectal
cancer cells and primary and/or metastatic stomach or esophageal
cancer cells and for treating individuals who are suffering from
metastasized colorectal cancer cells and primary and/or metastatic
stomach or esophageal cancer cells.
[0231] According to the present invention, SI serves as targets
against which a protective and therapeutic immune response can be
induced. Specifically, vaccines are provided which induce an immune
response against SI. The vaccines of the invention include, but are
not limited to, the following vaccine technologies:
[0232] 1) DNA vaccines, i.e. vaccines in which DNA that encodes at
least an epitope from an SI is administered to an individual's
cells where the epitope is expressed and serves as a target for an
immune response;
[0233] 2) infectious vector mediated vaccines such as recombinant
adenovirus, vaccinia, Salmonella, and BCG wherein the vector
carries genetic information that encodes at least an epitope from
an SI protein such that when the infectious vector is administered
to an individual, the epitope is expressed and serves as a target
for an immune response;
[0234] 3) killed or inactivated vaccines which a) comprise either
killed cells or inactivated viral particles that display at least
an epitope from an SI protein and b) when administered to an
individual serves as a target for an immune response;
[0235] 4) haptenized killed or inactivated vaccines which a)
comprise either killed cells or inactivated viral particles that
display at least an epitope from an SI protein, b) are haptenized
to be more immunogenic and c) when administered to an individual
serves as a target for an immune response;
[0236] 5) subunit vaccines which are vaccines that include protein
molecules that include at least an epitope from an SI protein;
and
[0237] 6) haptenized subunit vaccines which are vaccines that a)
include protein molecules that include at least an epitope from an
SI protein and b) are haptenized to be more immunogenic.
[0238] The present invention relates to administering to an
individual a protein or nucleic acid molecule that comprises or
encodes, respectively, an immunogenic epitope against which an
therapeutic and prophylactic immune response can be induced. Such
epitopes are generally at least 6-8 amino acids in length. The
vaccines of the invention therefore comprise proteins which are at
least, or nucleic acids which encode at least, 6-8 amino acids in
length from SI protein. The vaccines of the invention may comprise
proteins which are at least, or nucleic acids which encode at least
10 to about 1000 amino acids in length. The vaccines of the
invention may comprise proteins which are at least, or nucleic
acids which encode at least, about 25 to about 500 amino acids in
length. The vaccines of the invention may comprise proteins which
are at least, or nucleic acids which encode at least, about 50 to
about 400 amino acids in length. The vaccines of the invention may
comprise proteins which are at least, or nucleic acids which encode
at least, about 100 to about 300 amino acids in length.
[0239] The present invention relates to compositions for and
methods of treating individuals who are known to have metastasized
colorectal cancer cells and primary and/or metastatic stomach or
esophageal cancer cells. Metastasized colorectal cancer and primary
and/or metastatic stomach or esophageal cancer may be diagnosed by
those having ordinary skill in the art using the methods described
herein or art accepted clinical and laboratory pathology protocols.
The present invention provides an immunotherapeutic vaccine useful
to treat individuals who have been diagnosed as suffering from
metastatic colorectal cancer and primary and/or metastatic stomach
or esophageal cancer. The immunotherapeutic vaccines of the present
invention may be administered in combination with other
therapies.
[0240] The present invention relates to compositions for and
methods of preventing metastatic colorectal cancer and primary
and/or metastatic stomach or esophageal cancer in individual is
suspected of being susceptible to colorectal, stomach or esophageal
cancer. Such individuals include those whose family medical history
indicates above average incidence of colorectal, stomach or
esophageal cancer among family members and/or those who have
already developed colorectal, stomach or esophageal cancer and have
been effectively treated who therefore face a risk of relapse and
recurrence. Such individuals include those which have been
diagnosed as having colorectal, stomach or esophageal cancer
including localized only or localized and metastasized colorectal,
stomach or esophageal cancer which has been resected or otherwise
treated. The vaccines of the present invention may be to
susceptible individuals prophylactically to prevent and combat
metastatic colorectal cancer and primary and metastatic stomach or
esophageal cancer.
[0241] The invention relates to compositions which are the active
components of such vaccines or required to make the active
components, to methods of making such compositions including the
active components, and to methods of making and using vaccines.
[0242] The amino acid and nucleotide sequences of the SI is set
forth as SEQ ID NO:1.
[0243] The present invention relates to recombinant vectors,
including expression vectors, that comprise the SI gene transcript
or a fragment thereof. The present invention relates to recombinant
vectors, including expression vectors that comprise nucleotide
sequences that encode a SI protein or a functional fragment
thereof.
[0244] The present invention relates to host cells which comprise
such vectors and to methods of making SI protein using such
recombinant cells.
[0245] The present invention relates to the isolated SI gene
transcript and to the isolated SI proteins and to isolated
antibodies specific for such protein and to hybridomas which
produce such antibodies.
[0246] The present invention relates to the isolated SI and
functional fragments thereof. Accordingly, some aspects of the
invention relate to isolated proteins that comprise at least one
epitope of an SI.
[0247] Some aspects of the invention relate to the above described
isolated proteins which are haptenized to render them more
immunogenic. That is, some aspects of the invention relate to
haptenized proteins that comprise at least one SI epitope.
[0248] Accordingly, some aspects of the invention relate to
isolated nucleic acid molecules that encode proteins that comprise
at least one SI epitope.
[0249] Naked DNA vaccines are described in PCT/US90/01515, which is
incorporated herein by reference. Others teach the use of liposome
mediated DNA transfer, DNA delivery using microprojectiles (U.S.
Pat. No. 4,945,050 issued Jul. 31, 1990 to Sanford et al., which is
incorporated herein by reference), and DNA delivery using
electroporation. In each case, the DNA may be plasmid DNA that is
produced in bacteria, isolated and administered to the animal to be
treated. The plasmid DNA molecules are taken up by the cells of the
animal where the sequences that encode the protein of interest are
expressed. The protein thus produced provides a therapeutic or
prophylactic effect on the animal.
[0250] The use of vectors including viral vectors and other means
of delivering nucleic acid molecules to cells of an individual in
order to produce a therapeutic and/or prophylactic immunological
effect on the individual are similarly well known. Recombinant
vaccines that employ vaccinia vectors are, for example, disclosed
in U.S. Pat. No. 5,017,487 issued May 21, 1991 to Stunnenberg et
al. which is incorporated herein by reference.
[0251] In some cases, tumor cells from the patient are killed or
inactivated and administered as a vaccine product. Berd et al. May
1986 Cancer Research 46:2572-2577 and Berd et al. May 1991 Cancer
Research 51:2731-2734, which are incorporated herein by reference,
describes the preparation and use of tumor cell based vaccine
products. According to some aspects of the present invention, the
methods and techniques described in Berd et al are adapted by using
colorectal, stomach or esophageal cancer cells instead of melanoma
cells.
[0252] The manufacture and use of isolated translation products and
fragments thereof useful for example as laboratory reagents or
components of subunit vaccines are well known. One having ordinary
skill in the art can isolate the SI gene transcript or the specific
portion thereof that encodes SI or a fragment thereof. Once
isolated, the nucleic acid molecule can be inserted it into an
expression vector using standard techniques and readily available
starting materials.
[0253] The recombinant expression vector that comprises a
nucleotide sequence that encodes the nucleic acid molecule that
encodes SI or a fragment thereof or a protein that comprises the SI
or a fragment thereof. The recombinant expression vectors of the
invention are useful for transforming hosts to prepare recombinant
expression systems for preparing the isolated proteins of the
invention.
[0254] The present invention relates to a host cell that comprises
the recombinant expression vector that includes a nucleotide
sequence that encodes SI protein or a fragment thereof or an SI or
a fragment thereof. Host cells for use in well known recombinant
expression systems for production of proteins are well known and
readily available. Examples of host cells include bacteria cells
such as E. coli, yeast cells such as S. cerevisiae, insect cells
such as S. frugiperda, non-human mammalian tissue culture cells
chinese hamster ovary (CHO) cells and human tissue culture cells
such as HeLa cells.
[0255] The present invention relates to a transgenic non-human
mammal that comprises the recombinant expression vector that
comprises a nucleic acid sequence that encodes the proteins of the
invention. Transgenic non-human mammals useful to produce
recombinant proteins are well known as are the expression vectors
necessary and the techniques for generating transgenic animals.
Generally, the transgenic animal comprises a recombinant expression
vector in which the nucleotide sequence that encodes SI or a
fragment thereof or a protein that comprises SI or a fragment
thereof operably linked to a mammary cell specific promoter whereby
the coding sequence is only expressed in mammary cells and the
recombinant protein so expressed is recovered from the animal's
milk.
[0256] In some embodiments, for example, one having ordinary skill
in the art can, using well known techniques, insert such DNA
molecules into a commercially available expression vector for use
in well known expression systems such as those described
herein.
[0257] The expression vector including the DNA that encodes a SI or
a functional fragment thereof or a protein that comprises a SI or a
functional fragment thereof is used to transform the compatible
host which is then cultured and maintained under conditions wherein
expression of the foreign DNA takes place. The protein of the
present invention thus produced is recovered from the culture,
either by lysing the cells or from the culture medium as
appropriate and known to those in the art. The methods of purifying
the SI or a fragment thereof or a protein that comprises the same
using antibodies which specifically bind to the protein are well
known. Antibodies which specifically bind to a particular protein
may be used to purify the protein from natural sources using well
known techniques and readily available starting materials. Such
antibodies may also be used to purify the protein from material
present when producing the protein by recombinant DNA methodology.
The present invention relates to antibodies that bind to an epitope
which is present on one or more SI translation products or a
fragment thereof or a protein that comprises the same. Antibodies
that bind to an epitope which is present on the SI are useful to
isolate and purify the protein from both natural sources or
recombinant expression systems using well known techniques such as
affinity chromatography. Immunoaffinity techniques generally are
described in Waldman et al 1991 Methods of Enzymol. 195:391-396,
which is incorporated herein by reference. Antibodies are useful to
detect the presence of such protein in a sample and to determine if
cells are expressing the protein. The production of antibodies and
the protein structures of complete, intact antibodies, Fab
fragments and F(ab).sub.2 fragments and the organization of the
genetic sequences that encode such molecules are well known and are
described, for example, in Harlow, E. and D. Lane (1988)
ANTIBODIES: A Laboratory Manual, Cold Spring Harbor Laboratory,
Cold Spring Harbor, N.Y. which is incorporated herein by
reference.
[0258] In some embodiments of the invention, transgenic non-human
animals are generated. The transgenic animals according to the
invention contain nucleotides that encode SI or a fragment thereof
or a protein that comprises the same under the regulatory control
of a mammary specific promoter. One having ordinary skill in the
art using standard techniques, such as those taught in U.S. Pat.
No. 4,873,191 issued Oct. 10, 1989 to Wagner and U.S. Pat. No.
4,736,866 issued Apr. 12, 1988 to Leder, both of which are
incorporated herein by reference, can produce transgenic animals
which produce SI or a fragment thereof or a protein that comprises
the same. Preferred animals are goats and rodents, particularly
rats and mice.
[0259] In addition to producing these proteins by recombinant
techniques, automated peptide synthesizers may also be employed to
produce SI or a fragment thereof or a fragment thereof or a protein
that comprises the same. Such techniques are well known to those
having ordinary skill in the art and are useful if derivatives
which have substitutions not provided for in DNA-encoded protein
production.
[0260] In some embodiments, the protein that makes up a subunit
vaccine or the cells or particles of a killed or inactivated
vaccine may be haptenized to increase immunogenicity. In some
cases, the haptenization is the conjugation of a larger molecular
structure to SI or a fragment thereof or a protein that comprises
the same. In some cases, tumor cells from the patient are killed
and haptenized as a means to make an effective vaccine product. In
cases in which other cells, such as bacteria or eukaryotic cells
which are provided with the genetic information to make and display
a SI or a fragment thereof or a protein that comprises the same,
are killed and used as the active vaccine component, such cells are
haptenized to increase immunogenicity. Haptenization is well known
and can be readily performed.
[0261] Methods of haptenizing cells generally and tumor cells in
particular are described in Berd et al. May 1986 Cancer Research
46:2572-2577 and Berd et al. May 1991 Cancer Research 51:2731-2734,
which are incorporated herein by reference. Additional
haptenization protocols are disclosed in Miller et al. 1976 J.
Immunol. 117(5:1):1591-1526.
[0262] Haptenization compositions and methods which may be adapted
to be used to prepare haptenized SI immunogens according to the
present invention include those described in the following U.S.
Patents which are each incorporated herein by reference: U.S. Pat.
No. 5,037,645 issued Aug. 6, 1991 to Strahilevitz; U.S. Pat. No.
5,112,606 issued May 12, 1992 to Shiosaka et al.; U.S. Pat. No.
4,526,716 issued Jul. 2, 1985 to Stevens; U.S. Pat. No. 4,329,281
issued May 11, 1982 to Christenson et al.; and U.S. Pat. No.
4,022,878 issued May 10, 1977 to Gross. Peptide vaccines and
methods of enhancing immunogenicity of peptides which may be
adapted to modify SI immunogens of the invention are also described
in Francis et al. 1989 Methods of Enzymol. 178:659-676, which is
incorporated herein by reference. Sad et al. 1992 Immunolology
76:599-603, which is incorporated herein by reference, teaches
methods of making immunotherapeutic vaccines by conjugating
gonadotropin releasing hormone to diphtheria toxoid. SI immunogens
may be similarly conjugated to produce an immunotherapeutic vaccine
of the present invention. MacLean et al. 1993 Cancer Immunol.
Immunother. 36:215-222, which is incorporated herein by reference,
describes conjugation methodologies for producing immunotherapeutic
vaccines which may be adaptable to produce an immunotherapeutic
vaccine of the present invention. The hapten is keyhole limpet
hemocyanin which may be conjugated to a SI immunogen.
[0263] Vaccines according to some aspects of the invention comprise
a pharmaceutically acceptable carrier in combination with a SI
immunogen. Pharmaceutical formulations are well known and
pharmaceutical compositions comprising such proteins may be
routinely formulated by one having ordinary skill in the art.
Suitable pharmaceutical carriers are described in Remington's
Pharmaceutical Sciences, A. Osol, a standard reference text in this
field, which is incorporated herein by reference. The present
invention relates to an injectable pharmaceutical composition that
comprises a pharmaceutically acceptable carrier and a SI immunogen.
The SI immunogen is preferably sterile and combined with a sterile
pharmaceutical carrier.
[0264] In some embodiments, for example, SI or a fragment thereof
or a fragment thereof or a protein that comprises the same can be
formulated as a solution, suspension, emulsion or lyophilized
powder in association with a pharmaceutically acceptable vehicle.
Examples of such vehicles are water, saline, Ringer's solution,
dextrose solution, and 5% human serum albumin. Liposomes and
nonaqueous vehicles such as fixed oils may also be used. The
vehicle or lyophilized powder may contain additives that maintain
isotonicity (e.g., sodium chloride, mannitol) and chemical
stability (e.g., buffers and preservatives). The formulation is
sterilized by commonly used techniques.
[0265] An injectable composition may comprise the SI immunogen in a
diluting agent such as, for example, sterile water,
electrolytes/dextrose, fatty oils of vegetable origin, fatty
esters, or polyols, such as propylene glycol and polyethylene
glycol. The injectable must be sterile and free of pyrogens.
[0266] The vaccines of the present invention may be administered by
any means that enables the immunogenic agent to be presented to the
body's immune system for recognition and induction of an
immunogenic response. Pharmaceutical compositions may be
administered parenterally, i.e., intravenous, subcutaneous,
intramuscular.
[0267] Dosage varies depending upon known factors such as the
pharmacodynamic characteristics of the particular agent, and its
mode and route of administration; age, health, and weight of the
recipient; nature and extent of symptoms, kind of concurrent
treatment, frequency of treatment, and the effect desired. An
amount of immunogen is delivered to induce a protective or
therapeutically effective immune response. Those having ordinary
skill in the art can readily determine the range and optimal dosage
by routine methods.
[0268] The following examples are illustrative but are not meant to
be limiting of the present invention.
EXAMPLES
[0269] As stated above, a SI binding moiety is a SI ligand that may
be an antibody, a protein, a polypeptide, a peptide or a
non-peptide. Peptides and non-peptide SI ligands may be identified
using well known technology.
[0270] Over the past 10 years, it has become recognized that the
specific high-affinity interaction of a receptor and a ligand, for
example a SI and an anti-SI antibody, has its basis in the
3-dimensional conformational space of the ligand and the
complimentary 3-dimensional configuration of the region of the
molecule involved in ligand binding. In addition, it has become
recognized that various arrays of naturally-occurring amino acids,
non-natural amino acids, and organic molecules can be organized in
configurations that are unrelated to the natural ligands in their
linear structure, but resemble the 3-dimensional structure of the
natural ligands in conformational space and, thus, are recognized
by receptors with high affinity and specificity. Furthermore,
techniques have been described in the literature that permit one of
ordinary skill in the art to generate large libraries of these
arrays of natural amino acids, non-natural amino acids and organic
compounds to prospectively identify individual compounds that
interact with receptors with high affinity and specificity which
are unrelated to the native ligand of that receptor. Thus, it is a
relatively straightforward task for one of ordinary skill in the
art to identify arrays of naturally occurring amino acids,
non-natural amino acids, or organic compounds which can bind
specifically and tightly to the SI, which bear no structural
relationship to an anti-SI antibody.
[0271] To identify SI ligands that are peptides, those having
ordinary skill in the art can use any of the well known
methodologies for screening random peptide libraries in order to
identify peptides which bind to the SI. In the most basic of
methodologies, the peptides which bind to the target are isolated
and sequenced. In some methodologies, each random peptide is linked
to a nucleic acid molecule which includes the coding sequence for
that particular random peptide. The random peptides, each with an
attached coding sequence, are contacted with a SI and the peptides
which are unbound to the SI are removed. The nucleic acid molecule
which includes the coding sequence of the peptide that binds to the
SI can then be used to determine the amino acid sequence of the
peptide as well as produce large quantities of the peptide. It is
also possible to produce peptide libraries on solid supports where
the spatial location on the support corresponds to a specific
synthesis and therefore specific peptide. Such methods often use
photolithography-like steps to create diverse peptide libraries on
solid supports in which the spatial address on the support allows
for the determination of the sequence.
[0272] The production of organic compound libraries on solid
supports may also be used to produce combinatorial libraries of
non-peptide compounds such as oligonucleotides and sugars, for
example. As in the case of peptide libraries on solid supports, the
spatial location on the support corresponds to a specific synthesis
and therefore specific compound. Such methods often use
photolithography-like steps to create diverse compound libraries on
solid supports in which the spatial address on the support allows
for the determination of the synthesis scheme which produced the
compound. Once the synthesis scheme is identified, the structure of
the compound can become known.
[0273] Gallop et al. 1994 J. Medicinal Chemistry 37:1233, which is
incorporated herein by reference, provides a review of several of
the various methodologies of screening random peptide libraries and
identifying peptides from such libraries which bind to target
proteins. Following these teachings, SI specific ligands that are
peptides and that are useful as SI specific binding moieties may be
identified by those having ordinary skill in the art.
[0274] Peptides and proteins displayed on phage particles are
described in Gallop et al. Supra. Random arrays of nucleic acids
can be inserted into genes encoding surface proteins of
bacteriophage which are employed to infect bacteria, yielding phage
expressing the peptides encoded by the random array of nucleotides
on their surface. These phage displaying the peptide can be
employed to determine whether those peptides can bind to specific
proteins, receptors, antibodies, etc. The identity of the peptide
can be determined by sequencing the recombinant DNA from the phage
expressing the peptide. This approach has the potential to yield
vast arrays of peptides in a library (up to 10.sup.9 unique
peptides). This technique has been employed to identify novel
binding peptides to the fibrinogen receptor on platelets, which
bear no sequence homology to the natural occurring ligands of this
receptor (Smith et al., 1993 Gene 128:37, which is incorporated
herein by reference). Similarly, this technique has been applied to
identify peptides which bind to the MHC class II receptor (Hammer
et al., 1993 Cell 74:197, which is incorporated herein by
reference) and the chaperonin receptor (Blond-Elguindi et al., 1993
Cell 75:717, which is incorporated herein by reference).
[0275] Peptides displayed on plasmids are described in Gallop et
al. Supra. In this approach, the random oligonucleotides which
encode the library of peptides can be expressed on a specific
plasmid whose expression is under the control of a specific
promoter, such as the lac operon. The peptides are expressed as
fusion proteins coupled to the Lac I protein, under the control of
the lac operon. The fusion protein specifically binds to the lac
operator on the plasmid and so the random peptide is associated
with the specific DNA element that encodes it. In this way, the
sequence of the peptide can be deduced, by PCR of the DNA
associated with the fusion protein. These proteins can be screened
in solution phase to determine whether they bind to specific
receptors. Employing this approach, novel substrates have been
identified for specific enzymes (Schatz 1993).
[0276] A variation of the above technique, also described in Gallop
et al. Supra, can be employed in which random oligonucleotides
encoding peptide libraries on plasmids can be expressed in
cell-free systems. In this approach, a molecular DNA library can be
constructed containing the random array of oligonucleotides, which
are then expressed in a bacterial in vitro
transcription/translation system. The identity of the ligand is
determined by purifying the complex of nascent chain
peptide/polysome containing the mRNA of interest on affinity resins
composed of the receptor and then sequencing following
amplification with RT-PCR. Employing this technique permits
generation of large libraries (up to 10.sup.11 recombinants).
Peptides which recognize antibodies specifically directed to
dynorphin have been identified employing this technique (Cull et
al, 1992 Proc. Natl. Acad. Sci. USA 89:1865, which is incorporated
herein by reference).
[0277] Libraries of peptides can be generated for screening against
a receptor by chemical synthesis. For example, simultaneous
preparation of large numbers of diverse peptides have been
generated employing the approach of multiple peptide synthesis as
described in Gallop et al. Supra. In one application, random
peptides are generated by standard solid-phase Merrifield synthesis
on polyacrylamide microtiter plates (multipin synthesis) which are
subsequently screened for their ability to compete with receptor
binding in a standard competitive binding assay (Wang et al., 1993
Bioorg. Med. Chem. Lett. 3:447, which is incorporated herein by
reference). Indeed, this approach has been employed to identify
novel binding peptides to the substance P receptor (Wang et al.
Supra). Similarly, peptide libraries can be constructed by multiple
peptide synthesis employing the "tea bag" method in which bags of
solid support resin are sequentially incubated with various amino
acids to generate arrays of different peptides (Gallop et al.
Supra). Employing this approach, peptides which bind to the
integrin receptor (Ruggeri et al., 1986 Proc. Natl. Acad. Sci. USA
83:5708, which is incorporated herein by reference) and the
neuropeptide Y receptor (Beck-Sickinger et al, 1990 Int. J. Peptide
Protein Res. 36:522, which is incorporated herein by reference)
have been identified.
[0278] In general, the generation and utility of combinatorial
libraries depend on (1) a method to generate diverse arrays of
building blocks, (2) a method for identifying members of the array
that yield the desired function, and (3) a method for deconvoluting
the structure of that member. Several approaches to these
constraints have been defined.
[0279] The following is a description of methods of library
generation which can be used in procedures for identifying SI
ligands according to the invention.
[0280] Modifications of the above approaches can be employed to
generate libraries of vast molecular diversity by connecting
together members of a set of chemical building blocks, such as
amino acids, in all possible combinations (Gallop et al. Supra) In
one approach, mixtures of activated monomers are coupled to a
growing chain of amino acids on a solid support at each cycle. This
is a multivalent synthetic system.
[0281] Also, split synthesis involves incubating the growing chain
in individual reactions containing only a single building block
(Gallop et al. Supra). Following attachment, resin from all the
reactions are mixed and apportioned into individual reactions for
the next step of coupling. These approaches yield a stochastic
collection of nx different peptides for screening, where n is the
number of building blocks and x is the number of cycles of
reaction.
[0282] Alternatively, arrays of molecules can be generated in which
one or more positions contain known amino acids, while the
remainder are random (Gallop et al. Supra). These yield a limited
library which is screened for members with the desired activity.
These members are identified, their structure determined, and the
structure regenerated with another position containing defined
amino acids and screened. This iterative approach ultimately yields
peptides which are optimal for recognizing the conformational
binding pocket of a receptor.
[0283] In addition, arrays are not limited to amino acids forming
peptides, but can be extended to linear and nonlinear arrays of
organic molecules (Gordon et al., 1994 J. Medicinal Chemistry
37:1385, which is incorporated herein by reference). Indeed,
employing this approach of generating libraries of randomly arrayed
inorganic building blocks, ligands which bound to 7-transmembrane
receptors were identified (Zuckermann et al., 1994 J. Med. Chem.
37:2678, which is incorporated herein by reference).
[0284] Libraries are currently being constructed which can be
modified after synthesis to alter the chemical side groups and
bonds, to give "designer" arrays to test for their interaction with
receptors (Osteresh et al., 1994 Proc. NatL. Acad. Sci. USA
91:11138, which is incorporated herein by reference). This
technique, generating "libraries from libraries", was applied to
the permethylation of a peptide library which yielded compounds
with selective antimicrobial activity against gram positive
bacteria.
[0285] Libraries are also being constructed to express arrays of
pharmacological motifs, rather than specific structural arrays of
amino acids (Sepetov et al., 1995 Proc. Natl. Acad. Sci. USA
92:5426, which is incorporated herein by reference). This technique
seeks to identify structural motifs that have specific affinities
for receptors, which can be modified in further refinements
employing libraries to define structure-activity relationships.
Employing this approach of searching motif libraries, generating
"libraries of libraries", reduces the number of component members
required for screening in the early phase of library
examination.
[0286] The following is a description of methods of identifying SI
ligands according to the invention from libraries of randomly
generated molecules.
[0287] Components in the library which interact with receptors may
be identified by their binding to receptors immobilized on solid
support (Gordon et al. Supra).
[0288] They may also be identified by their ability to compete with
native ligand for binding to cognate receptors in solution phase
(Gordon et al. Supra).
[0289] Components may be identified by their binding to soluble
receptors when those components are immobilized on solid supports
(Gordon et al. Supra).
[0290] Once a member of a library which binds receptors has been
identified, the structure of that member must be deconvoluted
(deduced) in order to identify the structure and generate large
quantities to work with, or develop further analogs to study
structure-activity relationships. The following is a description of
methods of deconvolution for deducing the structure of molecules
identified as potential SI ligands according to the invention.
[0291] Peptide libraries may be expressed on the surface of
bacteriophage particles (Gallop et al. Supra). Once the peptide
interacting with the receptor has been identified, its structure
can be deduced by isolating the DNA from the phage and determining
its sequence by PCR.
[0292] Libraries expressed on plasmids, under the control of the
Lac operon can be deconvoluted since these peptides are fused with
the lac I protein which specifically interacts with the lac operon
on the plasmid encoding the peptide (Gallop et al. Supra) The
structure can be deduced by isolating that plasmid attached to the
lac I protein and deducing the nucleotide and peptide sequence by
PCR.
[0293] Libraries expressed on plasmids can also be expressed in
cell-free systems employing transcription/translation systems
(Gallop et al. Supra). In this paradigm, the protein interacting
with receptors is isolated with its attached ribosome and mRNA. The
sequence of the peptide is deduced by RT-PCR of the associated
mRNA.
[0294] Library construction can be coupled with photolithography,
so that the structure of any member of the library can be deduced
by determining its position within the substrate array (Gallop et
al. Supra). This technique is termed positional addressability,
since the structural information can be deduced by the precise
position of the member.
[0295] Members of a library can also be identified by tagging the
library with identifiable arrays of other molecules (Ohlmeyer et
al, 1993 Proc. Natl. Acad. Sci. USA 90:10922, which is incorporated
herein by reference, and Gallop et al. Supra). This technique is a
modification of associating the peptide with the plasmid of phage
encoding the sequence, described above. Some methods employ arrays
of nucleotides to encode the sequential synthetic history of the
peptide. Thus, nucleotides are attached to the growing peptide
sequentially, and can be decoded by PCR to yield the structure of
the associated peptide. Alternatively, arrays of small organic
molecules can be employed as sequencable tags which encode the
sequential synthetic history of the peptide. Thus, nucleotides are
attached to the growing peptide sequentially, and can be decoded by
PCR to yield the structure of the associated peptide.
Alternatively, arrays of small organic molecules can be employed as
sequencable tags which encode the sequential synthetic history of
the library member.
[0296] Finally, the structure of a member of the library can be
directly determined by amino acid sequence analysis.
[0297] The following patents, which are each incorporated herein by
reference, describe methods of making random peptide or non-peptide
libraries and screening such libraries to identify compounds that
bind to target proteins. As used in the present invention, SI can
be the targets used to identify the peptide and non-peptide ligands
generated and screened as disclosed in the patents.
[0298] U.S. Pat. No. 5,270,170 issued to Schatz et al. on Dec. 14,
1993, and U.S. Pat. No. 5,338,665 issued to Schatz et al. on Aug.
16, 1994, which are both incorporated herein by reference, refer to
peptide libraries and screening methods which can be used to
identify SI ligands.
[0299] U.S. Pat. No. 5,395,750 issued to Dillon et al. on Mar. 7,
1995, which is incorporated herein by reference, refers to methods
of producing proteins which bind to predetermined antigens. Such
methods can be used to produce SI ligands.
[0300] U.S. Pat. No. 5,223,409 issued to Ladner et al. on Jun. 29,
1993, which is incorporated herein by reference, refers to the
directed evolution to novel binding proteins. Such proteins may be
produced and screened as disclosed therein to identify SI
ligands.
[0301] U.S. Pat. No. 5,366,862 issued to Venton et al. on Nov. 22,
1994, which is incorporated herein by reference, refers to methods
for generating and screening useful peptides. The methods herein
described can be used to identify SI ligands.
[0302] U.S. Pat. No. 5,340,474 issued to Kauvar on Aug. 23, 1994 as
well as U.S. Pat. No. 5,133,866, U.S. Pat. No. 4,963,263 and U.S.
Pat. No. 5,217,869, which are each incorporated herein by
reference, can be used to identify SI ligands.
[0303] U.S. Pat. No. 5,405,783 issued to Pirrung et al. on Apr. 11,
1995, which is incorporated herein by reference, refers to large
scale photolithographic solid phase synthesis of an array of
polymers. The teachings therein can be used to identify SI
ligands.
[0304] U.S. Pat. No. 5,143,854 issued to Pirrung et al. on Sep. 1,
1992, which is incorporated herein by reference, refers to a large
scale photolithographic solid phase synthesis of polypeptides and
receptor binding screening thereof.
[0305] U.S. Pat. No. 5,384,261 issued to Winkler et al. on Jan. 24,
1995, which is incorporated herein by reference, refers to very
large scale immobilized polymer synthesis using mechanically
directed flow patterns. Such methods are useful to identify SI
ligands.
[0306] U.S. Pat. No. 5,221,736 issued to Coolidge et al. on Jun.
22, 1993, which is incorporated herein by reference, refers to
sequential peptide and oligonucleotide synthesis using
immunoaffinity techniques. Such techniques may be used to identify
SI ligands.
[0307] U.S. Pat. No. 5,412,087 issued to McGall et al. on May 2,
1995, which is incorporated herein by reference, refers to
spatially addressable immobilization of oligonucleotides and other
biological polymers on surfaces. Such methods may be used to
identify SI ligands.
[0308] U.S. Pat. No. 5,324,483 issued to Cody et al. on Jun. 28,
1994, which is incorporated herein by reference, refers to
apparatus for multiple simultaneous synthesis. The apparatus and
method disclosed therein may be used to produce multiple compounds
which can be screened to identify SI ligands.
[0309] U.S. Pat. No. 5,252,743 issued to Barrett et al. on Oct. 12,
1993, which is incorporated herein by reference, refers to
spatially addressable immobilization of anti-ligands on surfaces.
The methods and compositions described therein may be used to
identify SI ligands.
[0310] U.S. Pat. No. 5,424,186 issued to Foder et al. on Jun. 13,
1995, which is incorporated herein by reference, refers to a very
large scale immobilized polymer synthesis. The method of
synthesizing oligonucleotides described therein may be used to
identify SI ligands.
[0311] U.S. Pat. No. 5,420,328 issued to Campbell on May 30, 1995,
which is incorporated herein by reference, refers to methods of
synthesis of phosphonate esters. The phosphonate esters so produced
may be screened to identify compounds which are SI ligands.
[0312] U.S. Pat. No. 5,288,514 issued to Ellman on Feb. 22, 1994,
which is incorporated herein by reference, refers to solid phase
and combinatorial synthesis of benzodiazepine compounds on a solid
support. Such methods and compounds may be used to identify ST
ligands.
[0313] As noted above, SI ligands may also be antibodies and
fragments thereof. Indeed, antibodies raised to unique determinants
of these receptors will recognize that protein, and only that
protein and, consequently, can serve as a specific targeting
molecule which can be used to direct novel diagnostics and
therapeutics to this unique marker. In addition, these antibodies
can be used to identify the presence of SI or fragments there of in
biological samples.
* * * * *