U.S. patent application number 16/266649 was filed with the patent office on 2020-01-09 for methods of inhibiting cancer stem cells with hmga1 inhibitors.
The applicant listed for this patent is THE JOHNS HOPKINS UNIVERSITY. Invention is credited to Leslie Cope, David Huso, Linda M. Smith Resar.
Application Number | 20200009177 16/266649 |
Document ID | / |
Family ID | 54354815 |
Filed Date | 2020-01-09 |
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United States Patent
Application |
20200009177 |
Kind Code |
A1 |
Smith Resar; Linda M. ; et
al. |
January 9, 2020 |
METHODS OF INHIBITING CANCER STEM CELLS WITH HMGA1 INHIBITORS
Abstract
The presently disclosed subject matter relates to methods of
inhibiting cancer stem cells and growth of aggressive and/or poorly
differentiated metastatic tumors comprising the cancer stem cells
with HMGA1 inhibitors. The presently disclosed subject matter also
provides methods of selecting and treating a subject with
aggressive and/or poorly differentiated metastatic cancer using
HMGA1 inhibitors.
Inventors: |
Smith Resar; Linda M.;
(Stevenson, MD) ; Huso; David; (Parkton, MD)
; Cope; Leslie; (Baltimore, MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE JOHNS HOPKINS UNIVERSITY |
Baltimore |
MD |
US |
|
|
Family ID: |
54354815 |
Appl. No.: |
16/266649 |
Filed: |
February 4, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15398944 |
Jan 5, 2017 |
10213454 |
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16266649 |
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14701586 |
May 1, 2015 |
9545417 |
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15398944 |
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61987264 |
May 1, 2014 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2600/158 20130101;
C12N 2310/14 20130101; A61K 45/06 20130101; C12Q 2600/106 20130101;
A61K 31/7068 20130101; G01N 33/57484 20130101; A61K 31/713
20130101; G01N 33/5748 20130101; A61K 31/7105 20130101; G01N
33/57407 20130101; A61K 9/14 20130101; C12Q 1/6886 20130101; C12N
15/113 20130101; C12Q 2600/178 20130101; C12N 2310/531 20130101;
C12N 2320/30 20130101; C12Q 1/68 20130101; A61K 31/7105 20130101;
A61K 2300/00 20130101; A61K 31/7068 20130101; A61K 2300/00
20130101 |
International
Class: |
A61K 31/713 20060101
A61K031/713; G01N 33/574 20060101 G01N033/574; A61K 9/14 20060101
A61K009/14; A61K 31/7068 20060101 A61K031/7068; A61K 31/7105
20060101 A61K031/7105; A61K 45/06 20060101 A61K045/06; C12Q 1/6886
20060101 C12Q001/6886; C12N 15/113 20060101 C12N015/113; C12Q 1/68
20060101 C12Q001/68 |
Goverment Interests
FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
[0002] This invention was made with government support under grant
no. CA149550 awarded by the National Institutes of Health. The
government has certain rights in the invention.
Claims
1. A method of inhibiting at least one cancer stem cell, the method
comprising contacting the at least one cancer stem cell with an
effective amount of at least one HMGA1 inhibitor.
2. The method of claim 1, wherein inhibiting the at least one
cancer stem cell is selected from the group consisting of: i)
inhibiting proliferation of the at least one cancer stem cell; ii)
inhibiting self-renewal of the at least one cancer stem cell; iii)
inhibiting anchorage-independent growth of the at least one cancer
stem cell; iv) inhibiting migration of the at least one cancer stem
cell; v) inhibiting invasion of the at least one cancer stem cell;
vi) reprogramming the at least one cancer stem cell from a
stem-like state that is refractory to apoptosis to a non stem-like
state that is susceptible to apoptosis; and vii) combinations
thereof.
3. The method of claim 1, wherein the at least one cancer stem cell
is in an aggressive and/or poorly differentiated metastatic tumor,
and inhibiting the at least one cancer stem cell inhibits at least
one of: i) growth of the aggressive and/or poorly differentiated
metastatic tumor; ii) proliferation of the aggressive and/or poorly
differentiated metastatic tumor; iii) migration of the aggressive
and/or poorly differentiated metastatic tumor; iv) invasion of the
aggressive and/or poorly differentiated metastatic tumor; v)
initiation of new aggressive and/or poorly differentiated
metastatic tumors; and vi) combinations thereof.
4. The method of claim 1, wherein the at least one cancer stem cell
expresses greater levels of HMGA1 as compared to non-stem cancer
cells in the aggressive and/or poorly differentiated metastatic
tumor.
5. The method of claim 1, wherein the at least one cancer stem cell
is selected from the group consisting of a triple-negative breast
cancer cell, a pancreatic ductal adenocarcinoma cell, a colorectal
cancer cell, and a leukemia cell.
6. The method of claim 1, wherein the at least one HMGA1 inhibitor
reduces the expression level and/or activity of HMGA1.
7. The method of claim 1, wherein the at least one HMG1 inhibitor
is an RNA interfering agent.
8. The method of claim 7, wherein the at least one HMGA1 inhibitor
is an shRNA.
9. The method of claim 8, wherein the shRNA targets the nucleotide
sequence of SEQ ID NO:1.
10. The method of claim 1, further comprising contacting the at
least one cancer stem cell with a chemotherapeutic agent.
11. The method of claim 10, wherein the chemotherapeutic agent is
gemcitabine.
12. The method of claim 1, wherein the at least one cancer stem
cell is contacted in a subject.
13. The method of claim 12, wherein the subject is a human
subject.
14. A method of treating an aggressive and/or poorly differentiated
metastatic cancer in a subject in need thereof comprising
administering a therapeutically effective amount of at least one
HMGA1 inhibitor to the subject.
15. The method of claim 14, wherein the aggressive and/or poorly
differentiated metastatic cancer is selected from the group
consisting of triple-negative breast cancer, pancreatic ductal
adenocarcinoma cell, colorectal cancer cell, and leukemia.
16. The method of claim 14, wherein the aggressive and/or poorly
differentiated metastatic cancer comprises at least one cancer stem
cell that overexpresses HMGA1 protein.
17. The method of claim 14, further comprising selecting the
subject for treatment of the aggressive and/or poorly
differentiated metastatic cancer with the at least one HMGA1
inhibitor.
18. The method of claim 17, wherein selecting the subject for
treatment of the aggressive and/or poorly differentiated metastatic
cancer comprises: (i) obtaining a biological sample comprising
cells from the aggressive and/or poorly differentiated metastatic
cancer; (ii) assaying the level of HMGA1 expression in the cells
from the aggressive and/or poorly differentiated metastatic cancer;
(iii) comparing the level of HMGA1 expression in the cells to the
level of HMGA1 expression in a normal control cell; and (iv)
selecting the subject for treatment of the aggressive and/or poorly
differentiated metastatic cancer with the at least one HMGA1
inhibitor if the level of HMGA1 expression in the cells is greater
than the level of HMGA1 expression in the normal control cell.
19. The method of claim 18, wherein the biological sample is
selected from the group consisting of a breast tissue sample, a
pancreatic tissue sample, a colon tissue sample, and a bone marrow
tissue sample.
20. The method of claim 18, wherein at least some of the cells from
the aggressive and/or poorly differentiated metastatic cancer
comprise cancer stem cells.
21. The method of claim 14, wherein the at least one HMGA1
inhibitor reduces the expression level and/or activity of
HMGA1.
22. The method of claim 14, wherein the at least one HMGA1
inhibitor is formulated for delivery in a nanoparticle.
23. The method of claim 14, wherein the at least one HMG1 inhibitor
is an RNA interfering agent.
24. The method of claim 23, wherein the at least one HMGA1
inhibitor is an shRNA.
25. The method of claim 24, wherein the shRNA targets the
nucleotide sequence of SEQ ID NO:1.
26. The method of claim 24, wherein the shRNA is formulated for
delivery in a nanoparticle.
27. The method of claim 14, wherein the subject is a human
subject.
28. The method of claim 14, further comprising administering an
effective amount of a chemotherapeutic agent to the subject.
29. The method of claim 28, wherein the chemotherapeutic agent is
gemcitabine.
30. A method of selecting a subject with an aggressive and/or
poorly differentiated metastatic cancer for treatment with at least
one HMGA1 inhibitor, the method comprising: (a) obtaining a
biological sample from the subject, wherein the biological sample
comprises cells from the aggressive and/or poorly differentiated
metastatic cancer; (b) determining the level of expression of HMGA1
in the biological sample; (c) comparing the level of expression of
HMGA1 in the biological sample with the level of expression of
HMGA1 in a control sample; and (d) selecting the subject with
aggressive and/or poorly differentiated metastatic cancer for
treatment with at least one HMGA1 inhibitor when the level of HMGA1
expression in the biological sample is greater than the level of
HMGA1 expression in the control sample.
31. The method of claim 30, wherein the biological sample is
selected from the group consisting of a breast tissue sample, a
pancreatic tissue sample, a colon tissue sample, and a bone marrow
tissue sample.
32. The method of claim 30, wherein the aggressive and/or poorly
differentiated metastatic cancer is selected from the group
consisting of triple-negative breast cancer, pancreatic ductal
adenocarcinoma cell, colorectal cancer cell, and leukemia.
33. The method of claim 30, wherein the subject is a human
subject.
34. The method of claim 30, further comprising treating the subject
with aggressive and/or poorly differentiated metastatic cancer by
administering an effective amount of at least one HMGA1 inhibitor
to the subject.
35. The method of claim 34, further comprising administering an
effective amount of at least one chemotherapeutic agent to the
subject.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a Continuation of U.S. patent
application Ser. No. 15/398,944, filed Jan. 5, 2017, which is a
U.S. Divisional application Ser. No. 14/701,586, filed May 1, 2015,
now U.S. Pat. No. 9,545,417, granted Jan. 17, 2017, which claims
the benefit of U.S. Provisional Application No. 61/987,264, filed
May 1, 2014, the content of each of the aforementioned applications
is herein incorporated by reference in their entirety.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY
[0003] This application contains a sequence listing. It has been
submitted electronically via EFS-Web as an ASCII text file entitled
"111232-00396_ST25.txt". The sequence listing is 390 bytes in size,
and was created on Apr. 29, 2015. It is hereby incorporated by
reference in its entirety.
FIELD OF INVENTION
[0004] The presently disclosed subject matter relates to the field
of molecular biology, and particularly to methods of inhibiting
cancer stem cells and growth of aggressive and/or poorly
differentiated metastatic tumors with HGMA1 inhibitors.
BACKGROUND
[0005] Despite advances in the ability to detect and treat breast
cancer, it remains a leading cause of death in women with cancer,
and the incidence is rising (Siegel et al. (2013) CA Cancer J.
Clin. 63:11-30). Approximately 15-20% of all cases are classified
as triple-negative breast cancer, a subtype that is frequently
associated with rapid progression and poor outcomes (Siegel et al.
(2013) CA Cancer J. Clin. 63:11-30; Lee et al. (2010) Cancer Biol.
Ther. 9:1017-1024). Triple-negative breast cancer refers to the
lack of detectable markers for the estrogen receptor (ER),
progesterone receptor (PR), and Her2/neu amplification.
[0006] Treatment of patients with triple-negative breast cancer has
been challenging due to the heterogeneity of the disease and the
absence of well-defined molecular targets (Pegram et al. (1998) J
Clin. Oncol. 16:2659-2671; Wiggans et al. (1979) Cancer Chemother.
Pharmacol. 3:45-48; Carey et al. (2007) Clin. Cancer Res.
13:2329-2334). Triple-negative breast cancer tumors are generally
larger in size, are of higher grade, have lymph node involvement at
diagnosis, and are biologically more aggressive than other types of
breast cancer tumors (Haffty (2006) J. Clin. Oncol. 24:5652-5657).
Despite having higher rates of clinical response to presurgical
(neoadjuvant) chemotherapy, triple-negative breast cancer patients
have a higher rate of distant recurrence and a poorer prognosis
than women with other breast cancer subtypes (Haffty (2006) J.
Clin. Oncol. 24:5652-5657; Dent et al. (2007) Clin. Cancer Res.
13:4429-4434). These tumors do not respond to the most effective
and least toxic therapies, including hormonal therapy (tamoxifen)
or herceptin. Less than 30% of women with metastatic
triple-negative breast cancer survive 5 years, and almost all die
of their disease despite adjuvant chemotherapy, which is the
mainstay of treatment (Dent et al. (2007) Clin. Cancer Res.
13:4429-4434).
SUMMARY
[0007] The presently disclosed subject matter relates to methods of
inhibiting cancer stem cells using HMGA1 inhibitors. In an aspect,
the presently disclosed subject matter provides a method of
inhibiting at least one cancer stem cell, the method comprising
contacting the at least one cancer stem cell with an effective
amount of at least one HMGA1 inhibitor. In some embodiments,
inhibiting the at least one cancer stem cell is selected from the
group consisting of: i) inhibiting proliferation of the at least
one cancer stem cell; ii) inhibiting self-renewal of the at least
one cancer stem cell; iii) inhibiting anchorage-independent growth
of the at least one cancer stem cell; iv) inhibiting migration of
the at least one cancer stem cell; v) inhibiting invasion of the at
least one cancer stem cell; vi) reprogramming the at least one
cancer stem cell from a stem-like state that is refractory to
apoptosis to a non stem-like state that is susceptible to
apoptosis; and vii) combinations thereof. In some embodiments, at
least one cancer stem cell is in an aggressive and/or poorly
differentiated metastatic tumor, and inhibiting the at least one
cancer stem cell inhibits at least one of: i) growth of the
aggressive and/or poorly differentiated metastatic tumor; ii)
proliferation of the aggressive and/or poorly differentiated
metastatic tumor; iii) migration of the aggressive and/or poorly
differentiated metastatic tumor; iv) invasion of the aggressive
and/or poorly differentiated metastatic tumor; v) initiation of new
aggressive and/or poorly differentiated metastatic tumors; and vi)
combinations thereof. In some embodiments, at least one cancer stem
cell expresses greater levels of HMGA1 as compared to non-stem
cancer cells in the aggressive and/or poorly differentiated
metastatic tumor. In some embodiments, at least one cancer stem
cell is selected from the group consisting of a triple-negative
breast cancer cell, a pancreatic ductal adenocarcinoma cell, a
colorectal cancer cell, and a leukemia cell. In some embodiments,
at least one HMGA1 inhibitor reduces the expression level and/or
activity of HMGA1. In some embodiments, at least one HMG1 inhibitor
is an RNA interfering agent. In some embodiments, at least one
HMGA1 inhibitor is an shRNA. In some embodiments, the shRNA targets
the nucleotide sequence of SEQ ID NO:1. In some embodiments, the
method includes contacting the at least one cancer stem cell with a
chemotherapeutic agent. In some embodiments, the chemotherapeutic
agent is gemcitabine. In some embodiments, at least one cancer stem
cell is contacted in a subject. In some embodiments, the subject is
a human subject.
[0008] In certain aspects, the presently disclosed subject matter
provides a method of treating an aggressive and/or poorly
differentiated metastatic cancer in a subject in need thereof
comprising administering a therapeutically effective amount of at
least one HMGA1 inhibitor to the subject. In some embodiments, the
aggressive and/or poorly differentiated metastatic cancer is
selected from the group consisting of triple-negative breast
cancer, pancreatic ductal adenocarcinoma cell, colorectal cancer
cell, and leukemia. In some embodiments, the aggressive and/or
poorly differentiated metastatic cancer comprises at least one
cancer stem cell that overexpresses HMGA1 protein. In some
embodiments, the method includes selecting the subject for
treatment of the aggressive and/or poorly differentiated metastatic
cancer with the at least one HMGA1 inhibitor. In some embodiments,
selecting the subject for treatment of the aggressive and/or poorly
differentiated metastatic cancer comprises: (i) obtaining a
biological sample comprising cells from the aggressive and/or
poorly differentiated metastatic cancer; (ii) assaying the level of
HMGA1 expression in the cells from the aggressive and/or poorly
differentiated metastatic cancer; (iii) comparing the level of
HMGA1 expression in the cells to the level of HMGA1 expression in a
normal control cell; and (iv) selecting the subject for treatment
of the aggressive and/or poorly differentiated metastatic cancer
with the at least one HMGA1 inhibitor if the level of HMGA1
expression in the cells is greater than the level of HMGA1
expression in the normal control cell. In some embodiments, the
biological sample is selected from the group consisting of a breast
tissue sample, a pancreatic tissue sample, a colon tissue sample,
and a bone marrow tissue sample. In some embodiments, at least some
of the cells from the aggressive and/or poorly differentiated
metastatic cancer comprise cancer stem cells. In some embodiments,
the at least one HMGA1 inhibitor reduces the expression level
and/or activity of HMGA1. In some embodiments, the at least one
HMGA1 inhibitor is formulated for delivery in a nanoparticle. In
some embodiments, the at least one HMG1 inhibitor is an RNA
interfering agent. In some embodiments, the at least one HMGA1
inhibitor is an shRNA. In some embodiments, the shRNA targets the
nucleotide sequence of SEQ ID NO:1. In some embodiments, the shRNA
is formulated for delivery in a nanoparticle. In some embodiments,
the subject is a human subject. In some embodiments, the method
includes administering an effective amount of a chemotherapeutic
agent to the subject. In some embodiments, the chemotherapeutic
agent is gemcitabine.
[0009] In other aspects, the presently disclosed subject matter
provides a method of selecting a subject with an aggressive and/or
poorly differentiated metastatic cancer for treatment with at least
one HMGA1 inhibitor, the method comprising: (a) obtaining a
biological sample from the subject, wherein the biological sample
comprises cells from the aggressive and/or poorly differentiated
metastatic cancer; (b) determining the level of expression of HMGA1
in the biological sample; (c) comparing the level of expression of
HMGA1 in the biological sample with the level of expression of
HMGA1 in a control sample; and (d) selecting the subject with
aggressive and/or poorly differentiated metastatic cancer for
treatment with at least one HMGA1 inhibitor when the level of HMGA1
expression in the biological sample is greater than the level of
HMGA1 expression in the control sample. In some embodiments, the
biological sample is selected from the group consisting of a breast
tissue sample, a pancreatic tissue sample, a colon tissue sample,
and a bone marrow tissue sample. In some embodiments, the
aggressive and/or poorly differentiated metastatic cancer is
selected from the group consisting of triple-negative breast
cancer, pancreatic ductal adenocarcinoma cell, colorectal cancer
cell, and leukemia. In some embodiments, subject is a human
subject. In some embodiments, the method includes treating the
subject with aggressive and/or poorly differentiated metastatic
cancer by administering an effective amount of at least one HMGA1
inhibitor (e.g., an shRNA, e.g., targeting SEQ ID NO:1) to the
subject. In some embodiments, the method includes administering an
effective amount of at least one chemotherapeutic agent to the
subject.
[0010] Certain aspects of the presently disclosed subject matter
having been stated hereinabove, which are addressed in whole or in
part by the presently disclosed subject matter, other aspects will
become evident as the description proceeds when taken in connection
with the accompanying Examples and Figures as best described herein
below.
[0011] The practice of the present invention will typically employ,
unless otherwise indicated, conventional techniques of cell
biology, cell culture, molecular biology, transgenic biology,
microbiology, recombinant nucleic acid (e.g., DNA) technology,
immunology, and RNA interference (RNAi) which are within the skill
of the art. Non-limiting descriptions of certain of these
techniques are found in the following publications: Ausubel, F., et
al., (eds.), Current Protocols in Molecular Biology, Current
Protocols in Immunology, Current Protocols in Protein Science, and
Current Protocols in Cell Biology, all John Wiley & Sons, N.Y.,
edition as of December 2008; Sambrook, Russell, and Sambrook,
Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, 2001; Harlow, E. and Lane,
D., Antibodies--A Laboratory Manual, Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, 1988; Freshney, R. I., "Culture of
Animal Cells, A Manual of Basic Technique", 5th ed., John Wiley
& Sons, Hoboken, N.J., 2005. Non-limiting information regarding
therapeutic agents and human diseases is found in Goodman and
Gilman's The Pharmacological Basis of Therapeutics, 11th Ed.,
McGraw Hill, 2005, Katzung, B. (ed.) Basic and Clinical
Pharmacology, McGraw-Hill/Appleton & Lange; 10th ed. (2006) or
11th edition (July 2009). Non-limiting information regarding genes
and genetic disorders is found in McKusick, V. A.: Mendelian
Inheritance in Man. A Catalog of Human Genes and Genetic Disorders.
Baltimore: Johns Hopkins University Press, 1998 (12th edition) or
the more recent online database: Online Mendelian Inheritance in
Man, OMIM.TM.. McKusick-Nathans Institute of Genetic Medicine,
Johns Hopkins University (Baltimore, Md.) and National Center for
Biotechnology Information, National Library of Medicine (Bethesda,
Md.), as of May 1, 2010, World Wide Web URL:
http://www.ncbi.nlm.nih.gov/omim/ and in Online Mendelian
Inheritance in Animals (OMIA), a database of genes, inherited
disorders and traits in animal species (other than human and
mouse), at http://omia.angis.org.au/contact.shtml. All patents,
patent applications, and other publications (e.g., scientific
articles, books, websites, and databases) mentioned herein are
incorporated by reference in their entirety. In case of a conflict
between the specification and any of the incorporated references,
the specification (including any amendments thereof, which may be
based on an incorporated reference), shall control. Standard
art-accepted meanings of terms are used herein unless indicated
otherwise. Standard abbreviations for various terms are used
herein.
BRIEF DESCRIPTION OF THE FIGURES
[0012] Having thus described the presently disclosed subject matter
in general terms, reference will now be made to the accompanying
Figures, which are not necessarily drawn to scale, and wherein:
[0013] FIG. 1A, FIG. 1B, FIG. 1C, FIG. 1D and FIG. 1E show that
silencing HMGA1 expression halts cell growth and induces dramatic
changes in cell morphology and gene expression: FIG. 1A)
lentiviral-mediated delivery of shRNA to HMGA1 (denoted shHMGA1)
results in a marked decrease in HMGA1 mRNA and protein in
triple-negative breast cancer cell lines (MDA-MB-231, Hs578T); FIG.
1B) proliferation is disrupted in cancer cell lines following
silencing of HMGA1; FIG. 1C) mesenchymal, fibroblast-like cancer
cells undergo dramatic morphologic changes within 4 days after
treatment with shHMGA1; striking changes were observed in
MDA-MB-231 (top panels) and Hs578T cells (bottom panels); bar: 50
um; FIG. 1D) alterations in EMT genes with silencing of HMGA1; and
FIG. 1E) migration and invasion is decreased with silencing of
HMGA1. *P<0.05; **P<0.01;
[0014] FIG. 2A, FIG. 2B, FIG. 2C and FIG. 2D show that silencing
HMGA1 interferes with orthotopic tumorigenicity and metastatic
progression: FIG. 2A) silencing HMGA1 impairs orthotopic
tumorigenicity; tumor volumes.+-.standard deviations are shown; no
tumors formed from shHMGA1 cells when 10.sup.4 cells were implanted
(for injections with 10.sup.4 cells, n=3 for control or shHMGA1
cells; for injections with 10.sup.5 cells, n=5 for control and n=8
for shHMGA1 cells; and for injections with 10.sup.7 cells, n=3 for
control and shHMGA1 cells; FIG. 2B) metastatic progression is
almost completely abrogated in cells that do not express HMGA1;
this graph shows the number metastatic foci to the lung 5 weeks
following implantation of MDA-MB-231 cells (10.sup.7) into mammary
fat pads following treatment with control shRNA or shHMGA1; FIG.
2C) the top photographs show the lungs 8 weeks following
implantation into mammary fat pads; there are coalescing sheets of
metastatic tumor cells in the lungs of mice injected with control
cells (left) as compared to mice injected with shHMGA1 cells
(right); due to the widespread tumor cells, individual foci could
not be counted; bar: 50 um; and FIG. 2D) the bottom panels show
multiple, discreet foci in the lungs 5 weeks following implantation
of control cells into mammary fat pads (left) as compared to mice
injected with shHMGA1 cells (right). *P<0.05; **P<0.0001;
[0015] FIG. 3A, FIG. 3B and FIG. 3C show that silencing HMGA1
blocks mammosphere formation and depletes tumor-initiator cells:
FIG. 3A) silencing HMGA1 blocks mammosphere formation in MDA-MB-231
cells (1.degree., 2.degree., 3.degree.) and Hs578T cells
(1.degree.); FIG. 3B) photographs of mammospheres following
treatment of breast cancer cells with control or shHMGA1; silencing
HMGA1 significantly inhibits mammosphere formation in MDA-MB-231
and Hs578T cells; bars: 200 um (large panels) and 50 um (insets);
and FIG. 3C) tumor numbers at limiting dilutions show that
silencing HMGA1 depletes the tumor initiator/cancer stem cells in
MDA-MB-231 cells; note that no tumors formed following injection of
10.sup.4 cells treated with shHMGA1, while tumors formed in all
cases when control cells were injected; both tumor frequency and
tumor volumes (.+-.standard deviations) are shown. *P<0.05;
**P<0.01;
[0016] FIG. 4A and FIG. 4B show that the HMGA1 signature is
enriched in pluripotent stem cells, including embryonic and induced
pluripotent stem cells: FIG. 4A shows the HMGA signature derived
from genes with the greatest expression changes in the control
versus HMGA1 knock-down cells displayed as a heat map. Green
depicts down-regulation in expression, while red depicts
up-regulation; black denotes little or no change in expression. The
HMGA1 signature overlaps with pluripotent stem cell genes that
distinguish human embryonic stem cells (hESCs) and induced
pluripotent stem cells (iPSCs) from fibroblasts and embryoid bodies
(EB). Genes (n=63) were selected for the greatest changes in
expression in the breast cancer cell lines with HMGA1 knock-down as
compared to the control breast cancer lines (FIG. 5). In a
hierarchical clustering of fibroblasts, hESCs, iPSCs, and EBs
derived from the hESCs, these genes distinguish samples by type.
The majority of the HMGA1 signature genes, represented in blue
along the left margin, are significantly differentially expressed
between fibroblasts and human pluripotent stem cells (hESC/iPSCs;
p<0.001); and FIG. 4B shows a HMGA1 network derived from the
list of differentially expressed genes using Ingenuity Pathway
Analysis (IPA) with microarray gene expression data from control
and HMGA1 knock-down in MDA-MB-231 cells. From among 63
differentially expressed genes as the focus gene set, the
highest-scoring network was Embryonic Development, Tissue
Development, and Cellular Development (score=69). Red nodes
indicate up-regulation; green nodes indicate down-regulation.
Arrows and lines denote interactions between specific genes within
the network. A, activation; E, expression regulation; I,
inhibition; L, proteolysis; LO, localization; M, biochemical
modification; MB, membership of a group or complex; P,
phosphorylation; PD, protein-DNA interaction; PP, protein-protein
interaction; PR, protein-RNA interaction; RB, regulation of
binding; RE, reaction; T, transcription; TR, translocation;
[0017] FIG. 5A and FIG. 5B show that silencing HMGA1 in MDA-MB-231
blocks the formation of foci to the lung following tail vein
injections: FIG. 5A depicts lung foci enumerated 3 weeks following
tail vein injections of control or shHMGA1 MDA-MB-231 cells (n=3
for control mice; n=4 for shHMGA1 mice); and FIG. 5B is a graph of
the mean number of tumor foci.+-.standard deviation, which shows a
striking decrease in foci following injection of shHMGA1 MDA-MB-231
cells as compared to controls (p=0.007);
[0018] FIG. 6A, FIG. 6B, FIG. 6C and FIG. 6D show that silencing
HMGA1 in MDA-MB-231 results in significant repression in HMGA1 mRNA
and protein, with alterations in gene expression: FIG. 6A
demonstrates that independent replicate experiments of MDA-MB-231
cells with or without HMGA1 knock-down result in silencing HMGA1 at
the level of mRNA; FIG. 6B demonstrates that HMGA1 protein is also
repressed following treatment with siRNA; FIG. 6C is a validation
of genes in the HMGA1 signature which shows that gene expression
assessed by quantitative RT-PCR (qRT-PCR) parallels that of the
microarray results; and FIG. 6D is a table comparing differential
expression of the HMGA1 signature identified by microarray and
qRT-PCR;
[0019] FIG. 7 shows the HMGA1 network derived from differentially
expressed genes in MDA-MB-231 with or without HMGA1 knock-down.
From among 63 differentially expressed genes as the focus gene set,
the second highest-scoring network was Cardiovascular Disease, Cell
Death and Survival, and Nervous System Development and Function
(score=46). Colors, arrows, lines and abbreviations are described
under FIG. 4B. NF-.kappa.B, ERK, and MAPK are major nodes, which
have been identified in prior studies of global gene expression
profiles mediated by HMGA1 (Schuldenfrei et al. (2011) BMC Genomics
12:549);
[0020] FIG. 8 demonstrates the oncogenic pathways activated by
HMGA;
[0021] FIG. 9 demonstrates the targeting of HMGA1 in cancer stem
cells;
[0022] FIG. 10A, FIG. 10B, and FIG. 10C demonstrate that HMGA1
correlates with poor differentiation and decreased survival in
pancreatic cancer; FIG. 10A shows a well-differentiated tumor with
low levels of HMGA1 immunoreactivity; FIG. 10B shows a high-grade,
poorly differentiated tumor with high immunoreactivity. Patient
survival (FIG. 10C) is decreased with high levels of HMGA1;
[0023] FIG. 11 demonstrates HMGA1 expression levels in different
pancreatic ductal adenocarcinoma cell (PDAC) lines; gene expression
was assessed via quantitative RT-PCR (qRT-PCR);
[0024] FIG. 12A and FIG. 12B demonstrate that HMGA1 is silenced by
short hairpin RNA as seen by expression levels (via qRT-PCR) of
HMGA1 with (red) and without (blue) shHMGA1; FIG. 12B shows protein
levels by Western blot;
[0025] FIG. 13 demonstrates that silencing HMGA1 via shHMGA
disrupts cell proliferation in three PDAC cell lines (red),
including two patient-derived cell lines, as compared to the
control (blue);
[0026] FIG. 14A and FIG. 14B demonstrate that silencing HMGA1
alters morphology of pancreatic ductal adenocarcinoma cells. FIG.
14A shows morphology of control cells not treated with the HMGA1
shRNA (spindle-shaped, mesenchymal cells) as compared to the
morphology of pancreatic ductal adenocarcinoma cells treated with
shRNA targeting HMGA1 (rounded, more cuboidal-shaped cells; FIG.
14B);
[0027] FIG. 15A, FIG. 15B and FIG. 15C demonstrate that silencing
HMGA1 via shHMGA blocks 3D sphere formation (FIG. 15A), PDAC colony
formation (FIG. 1B), and migration and invasion (FIG. 15C);
[0028] FIG. 16A, FIG. 16B, and FIG. 16C demonstrate that silencing
is cytotoxic in acute myeloid leukemia (AML) cell lines and that
silencing in colorectal cancer cells halts proliferation and alters
cell morphology. FIG. 16A shows silencing of HMGA1 in three AML
cell lines and FIG. 16B shows marked cytotoxicity in HMGA1
knock-down cells. FIG. 16C shows that silencing HMGA1 in colorectal
cancer cells halts proliferation and alters cell morphology;
[0029] FIG. 17 demonstrates nanoparticle shRNA treatment in PDAC
cell line 10.7 xenografts. The PDAC cell line was injected into
mice on tumors allowed to grow. By day 30, mice were treated with
nanoparticles to deliver shRNA to the tumors; and
[0030] FIG. 18A, FIG. 18B, and FIG. 18C demonstrate vacuolated
cytoplasm of most tumor cells, individual cell death (arrows) and
area of necrosis (outlined) in a shHMGA1 treated tumor.
[0031] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawings will be provided by the Office upon
request and payment of the necessary fee.
DETAILED DESCRIPTION
[0032] The presently disclosed subject matter now will be described
more fully hereinafter with reference to the accompanying Figures,
in which some, but not all embodiments of the presently disclosed
subject matter are shown. Like numbers refer to like elements
throughout. The presently disclosed subject matter may be embodied
in many different forms and should not be construed as limited to
the embodiments set forth herein; rather, these embodiments are
provided so that this disclosure will satisfy applicable legal
requirements. Indeed, many modifications and other embodiments of
the presently disclosed subject matter set forth herein will come
to mind to one skilled in the art to which the presently disclosed
subject matter pertains having the benefit of the teachings
presented in the foregoing descriptions and the associated Figures.
Therefore, it is to be understood that the presently disclosed
subject matter is not to be limited to the specific embodiments
disclosed and that modifications and other embodiments are intended
to be included within the scope of the appended claims.
[0033] Emerging evidence suggests that tumor cells metastasize by
co-opting stem cell transcriptional networks, although the
molecular underpinnings of this process are poorly understood.
Recent studies have identified the high mobility group A1 (HMGA1)
oncogene (Entrez Gene ID: 3159) as a key factor enriched in
embryonic stem cells, adult stem cells, and refractory or
high-grade/poorly differentiated tumors (Ben-Porath et al. (2008)
Nat. Genet. 40:499-507; Resar (2010) Cancer Research 70:436-439;
Chou et al. (2011) Cell Res. 21:518-529; Zhou et al. (2001) Proc.
Natl. Acad. Sci. USA 98:13966-13971; Karp et al. (2011) Blood
117:3302-3310; Nelson et al. (2011) Leuk Lymphoma 52:1999-2006;
Schuldenfrei et al. (2011) BMC Genomics 12:549; Belton et al.
(2012) PloS One 7:e30034; Shah and Resar (2012) Histol.
Histopathol. 27:567-579; Wood et al. (2000) Mol. Cell. Biol.
20:5490-5502; Pedulla et al. (2001) Gene 271:51-58; Reeves and
Beckerbauer (2001) Biochim. Biophys. Acta 1519:13-29; Reeves et al.
(2001) Mol. Cell. Biol. 21:575-594; Dolde et al. (2002) Breast
Cancer Research and Treatment 71:181-191; Dhar et al. (2004)
Oncogene 23:4466-4476; Takaha et al. (2004) The Prostate
60:160-167; Hommura et al. (2004) Mol. Cancer Res. 2:305-314; Xu et
al. (2004) Cancer Res. 64:3371-3375; Tesfaye et al. (2007) Cancer
Res. 67:3998-4004; Fusco and Fedele (2007) Nat. Rev. Cancer
7:899-910; Di Cello et al. (2008) Molecular Cancer Therapuetics
7:2090-2095; Hillion et al. (2008) Cancer Res. 68:10121-10127;
Hillion et al. (2009) Mol. Cancer Res. 7:1803-1812; Hristov et al.
(2010)Mod. Pathol. 23: 98-104; Reeves (2010) Biochim. Biophys. Acta
1799:3-14; Di Cello et al. (2013) Leuk. Lymphoma 54:1762-1768;
Williams et al. (2013)Anal. Bioanal. Chem. 405:5013-5030; Pomeroy
et al. (2002) Nature 415: 436-442; Flohr et al. (2003) Histol.
Histopathol. 18: 999-1004; Shah et al. (2012) PLoS One 7:
e48533).
[0034] The HMGA1 gene encodes the HMGA1a and HMGA1b chromatin
remodeling proteins, which result from alternatively spliced
messenger RNA (Resar (2010) Cancer Research 70:436-439; Reeves and
Beckerbauer (2001) Biochim. Biophys. Acta 1519:13-29; Fusco and
Fedele (2007) Nat. Rev. Cancer 7:899-910; Reeves (2010) Biochim.
Biophys. Acta 1799:3-14). These low molecular weight (thus high
mobility group) protein isoforms bind to the minor groove of
chromatin at AT-rich regions. HMGA1 proteins modulate gene
expression by altering chromatin structure and orchestrating the
assembly of transcription factor complexes to enhanceosomes within
enhancer or promoter regions throughout the genome. These proteins
are highly expressed during embryogenesis with low or absent levels
in adult tissues.
[0035] HMGA1 is overexpressed in all aggressive cancers studied to
date, and high levels portend a poor prognosis in diverse tumors
(Ben-Porath et al. (2008) Nat. Genet. 40:499-507; Resar (2010)
Cancer Research 70:436-439; Chou et al. (2011) Cell Res.
21:518-529; Zhou et al. (2001) Proc. Natl. Acad. Sci. USA
98:13966-13971; Karp et al. (2011) Blood 117:3302-3310; Nelson et
al. (2011) Leuk Lymphoma 52:1999-2006; Schuldenfrei et al. (2011)
BMC Genomics 12:549; Belton et al. (2012) PloS One 7:e30034; Shah
and Resar (2012) Histol. Histopathol. 27:567-579; Wood et al.
(2000) Mol. Cell. Biol. 20:5490-5502; Pedulla et al. (2001) Gene
271:51-58; Reeves and Beckerbauer (2001) Biochim. Biophys. Acta
1519:13-29; Reeves et al. (2001)Mol. Cell. Biol. 21:575-594; Dolde
et al. (2002) Breast Cancer Research and Treatment 71:181-191; Dhar
et al. (2004) Oncogene 23:4466-4476; Takaha et al. (2004) The
Prostate 60:160-167; Hommura et al. (2004) Mol. Cancer Res.
2:305-314; Xu et al. (2004) Cancer Res. 64:3371-3375; Tesfaye et
al. (2007) Cancer Res. 67:3998-4004; Fusco and Fedele (2007) Nat.
Rev. Cancer 7:899-910; Di Cello et al. (2008) Molecular Cancer
Therapuetics 7:2090-2095; Hillion et al. (2008) Cancer Res.
68:10121-10127; Hillion et al. (2009) Mol. Cancer Res. 7:1803-1812;
Hristov et al. (2010) Mod. Pathol. 23: 98-104; Reeves (2010)
Biochim. Biophys. Acta 1799:3-14; Di Cello et al. (2013) Leuk.
Lymphoma 54:1762-1768; Williams et al. (2013)Anal. Bioanal. Chem.
405:5013-5030; Pomeroy et al. (2002) Nature 415: 436-442; Flohr et
al. (2003) Histol. Histopathol. 18: 999-1004). In fact, HMGA1
proteins are the most abundant nonhistone chromatin binding
proteins found in cancer cells. A recent landmark paper
demonstrated that HMGA1 is essential for the cellular reprogramming
of somatic cells to induced pluripotent stem cells by the four
Yamanaka factors (Oct4, Sox2, Klf4, cMyc) (Shah et al. (2012) PLoS
One 7: e48533). HMGA1 induces expression of key stem cell
transcriptional networks in normal embryonic stem cells and during
cellular reprogramming. The presently disclosed subject matter
relates in part to the discovery that HMGA1 is a central factor in
reprogramming cancer stem cells. In particular, it was discovered
that the HMGA1 gene drives metastatic progression in
triple-negative breast cancer cells (MDA-MB-231, Hs578T) by
reprogramming cancer cells to a stem-like state. Silencing HMGA1
expression in invasive, aggressive breast cancer cells dramatically
halted cell growth and resulted in striking morphologic changes
from mesenchymal-like, spindle-shaped cells to cuboidal,
epithelial-like cells. Mesenchymal genes (Vimentin, Twist) were
repressed, while E-cadherin was induced in knock-down cells.
Silencing HMGA1 also blocked oncogenic properties, including
proliferation, migration, invasion, and orthotopic tumorigenesis.
Metastatic progression following mammary implantation was almost
completely abrogated in the HMGA1 knock-down cells. Moreover,
silencing HMGA1 inhibited the stem cell properties and depleted
breast cancer initiator/cancer stem cells. An HMGA1 signature in
triple-negative breast cancer cells was also discovered that was
highly enriched in embryonic stem cells. Accordingly, in some
embodiments, the presently disclosed subject matter provides
methods for inhibiting cancer stem cells and growth of aggressive
and/or poorly differentiated metastatic tumors, by inhibiting the
expression of the high mobility group A1 (HMGA1) gene.
I. Methods of Inhibiting Cancer Stem Cells
[0036] It has been found that silencing HMGA1 reprograms aggressive
stem-like cancer cells into non stem-like cells with slow growth
and altered properties. Accordingly, in some embodiments, the
presently disclosed subject matter provides a method of inhibiting
at least one cancer stem cell, the method comprising contacting at
least one cancer stem cell with an effective amount of at least one
HMGA1 inhibitor. Cancer stem cells (CSCs) are cancer cells that
possess characteristics associated with normal stem cells,
specifically the ability to differentiate into multiple cell types.
CSCs may generate tumors through the stem cell processes of
self-renewal and differentiation and are proposed to persist in
tumors as a distinct population. In addition, they appear to be
highly drug-resistant cells.
[0037] As used herein, an HMGA1 inhibitor is an agent that inhibits
target gene expression (i.e., HMGA1 gene expression). As used
herein, "inhibition of target gene expression" includes any
decrease in expression or protein activity or level of the target
gene (HMGA1 gene) or protein encoded by the target gene (HMGA1
protein). The decrease may be of at least 10%, 20%, 30%, 40%, 50%,
60%, 70%, 80%, 90%, 95% or 99% or more as compared to the
expression of a target gene or the activity or level of the protein
encoded by a target gene which has not been targeted by an RNA
interfering agent. Certain exemplary methods of assaying for HMGA1
gene expression or HGMA1 protein activity include, but are not
limited to, those methods disclosed herein as well as assays known
to those skilled in the art (see, e.g., Liau et al. (2006) Cancer
Res. 66:11613-11622; Liu et al. (2012) Biotechnol. Appl. Biochem.
59:1-5).
[0038] HMGA1 inhibitors for use in the presently disclosed methods
include RNA interfering agents. An "RNA interfering agent" as used
herein, is defined as any agent which interferes with or inhibits
expression of a target gene, e.g., a marker of the presently
disclosed subject matter, by RNA interference (RNAi). Such RNA
interfering agents include, but are not limited to, nucleic acid
molecules including RNA molecules which are homologous to the
target gene, e.g., a marker of the presently disclosed subject
matter, or a fragment thereof, short interfering RNA (siRNA), and
small molecules which interfere with or inhibit expression of a
target gene by RNA interference (RNAi). In some embodiments, at
least one HMG1 inhibitor is an RNA interfering agent.
[0039] "RNA interference (RNAi)" is an evolutionally conserved
process whereby the expression or introduction of RNA of a sequence
that is identical or highly similar to a target gene results in the
sequence specific degradation or specific post-transcriptional gene
silencing (PTGS) of messenger RNA (mRNA) transcribed from that
targeted gene (see Coburn & Cullen (2002) J. Virol. 76:9225),
thereby inhibiting expression of the target gene (see, e.g., U.S.
Patent Application Nos: 20030153519A1; 20030167490A1; and U.S. Pat.
Nos. 6,506,559; 6,573,099). In one embodiment, the RNA is double
stranded RNA (dsRNA). This process has been described in plants,
invertebrates, and mammalian cells. In nature, RNAi is initiated by
the dsRNA-specific endonuclease Dicer, which promotes processive
cleavage of long dsRNA into double-stranded fragments termed
siRNAs. siRNAs are incorporated into a protein complex that
recognizes and cleaves target mRNAs. RNAi can also be initiated by
introducing nucleic acid molecules, e.g., synthetic siRNAs or RNA
interfering agents, to inhibit or silence the expression of target
genes.
[0040] The presently disclosed subject matter also contemplates
"short interfering RNA" (siRNA), also referred to herein as "small
interfering RNA." Such a molecule is defined as an agent which
functions to inhibit expression of a target gene, e.g., by RNAi. As
used herein, the term siRNA is intended to be equivalent to any
term in the art defined as a molecule capable of mediating
sequence-specific RNAi. Such equivalents include, for example,
double-stranded RNA (dsRNA), microRNA (mRNA), short hairpin RNA
(shRNA), short interfering oligonucleotide, and
post-transcriptional gene silencing RNA (ptgsRNA). An siRNA may be
chemically synthesized, may be produced by in vitro transcription,
or may be produced within a host cell. In one embodiment, siRNA is
a double stranded RNA (dsRNA) molecule of about 15 to about 40
nucleotides in length, preferably about 15 to about 28 nucleotides,
more preferably about 19 to about 25 nucleotides in length, and
more preferably about 19, 20, 21, or 22 nucleotides in length, and
may contain a 3' and/or 5' overhang on each strand having a length
of about 0, 1, 2, 3, 4, or 5 nucleotides. The length of the
overhang is independent between the two strands, i.e., the length
of the overhang on one strand is not dependent on the length of the
overhang on the second strand. Preferably the siRNA is capable of
promoting RNA interference through degradation or specific
post-transcriptional gene silencing (PTGS) of the target messenger
RNA (mRNA).
[0041] In another embodiment, an siRNA is a small hairpin (also
called stem loop) RNA (shRNA). In one embodiment, these shRNAs are
composed of a short (e.g., 19-25 nucleotide) antisense strand,
followed by a 5-9 nucleotide loop, and the analogous sense strand.
Alternatively, the sense strand may precede the nucleotide loop
structure and the antisense strand may follow. These shRNAs may be
contained in plasmids, retroviruses, and lentiviruses and expressed
from, for example, the pol III U6 promoter, or another promoter
(see, e.g., Stewart et al. (2003) RNA 9:493-501). In a particular
embodiment, the siRNA is an shRNA that targets the nucleotide
sequence of SEQ ID NO:1 (see, e.g., Liau et al. (2006) Cancer Res.
66:11613-11622).
[0042] As used herein, inhibition of at least one cancer stem cell
includes, but is not limited to, inhibition of oncogenic properties
associated with both tumor initiation (orthotopic tumorigenesis)
and tumor progression (migration, invasion, and metastatic
progression), for example, inhibition of growth of cancer stem
cells as compared to the growth of untreated or mock treated cells,
inhibition of metastases, induction of cancer cell senescence,
induction of cancer cell death, and reduction of tumor size.
[0043] As used herein, the term "contacting" means any action that
results in at least one HMGA1 inhibitor of the presently disclosed
subject matter physically contacting at least one cell, such as a
cancer stem cell. It thus may comprise exposing the cell(s) to the
HMGA1 inhibitor in an amount sufficient to result in contact of at
least one HMGA1 inhibitor with at least one cell. The method can be
practiced in vitro or ex vivo by introducing, and preferably
mixing, the HMGA1 inhibitor and cells in a controlled environment,
such as a culture dish or tube. The method can be practiced in
vivo, in which case contacting means exposing at least one cell in
a subject to at least one HMGA1 inhibitor of the presently
disclosed subject matter, such as administering the HMGA1 inhibitor
to a subject via any suitable route. According to the presently
disclosed subject matter, contacting may comprise introducing,
exposing, and the like, the HMGA1 inhibitor at a site distant to
the cells to be contacted, and allowing the bodily functions of the
subject, or natural (e.g., diffusion) or man-induced (e.g.,
swirling) movements of fluids to result in contact of the HMGA1
inhibitor and cell(s). In general, the term "effective amount"
refers to the amount of an agent, such as an HMGA1 inhibitor, to
elicit the desired biological response, such as inhibition of a
cancer stem cell.
[0044] In addition, "a therapeutically effective amount," of a
therapeutic agent refers to the amount of the agent necessary to
elicit the desired biological response. As will be appreciated by
those of ordinary skill in this art, the effective amount of an
agent may vary depending on such factors as the desired biological
endpoint, the agent to be delivered, the composition of the
pharmaceutical composition, the target tissue or cell, and the
like. More particularly, the term "effective amount" refers to an
amount sufficient to produce the desired effect, e.g., to reduce or
ameliorate the severity, duration, progression, or onset of a
disease, disorder, or condition (e.g., aggressive and/or poorly
differentiated metastatic cancer), or one or more symptoms thereof;
prevent the advancement of a disease, disorder, or condition, cause
the regression of a disease, disorder, or condition; prevent the
recurrence, development, onset or progression of a symptom
associated with a disease, disorder, or condition, or enhance or
improve the prophylactic or therapeutic effect(s) of another
therapy. Accordingly, as used herein, treatment of aggressive
and/or poorly differentiated metastatic cancer, includes, but is
not limited to, reduction in cancer growth or tumor burden,
induction of cancer cell senescence, induction of apoptosis of
cancer cells, induction of cancer cell death, inhibition of
angiogenesis, enhancement of cancer cell apoptosis, and inhibition
of metastases.
[0045] In some embodiments, inhibiting at least one cancer stem
cell is selected from the group consisting of i) inhibiting
proliferation of the at least one cancer stem cell; ii) inhibiting
self-renewal of the at least one cancer stem cell; iii) inhibiting
anchorage-independent growth of the at least one cancer stem cell;
iv) inhibiting migration of the at least one cancer stem cell; v)
inhibiting invasion of the at least one cancer stem cell; vi)
reprogramming the at least one cancer stem cell from a stem-like
state that is refractory to apoptosis to a non stem-like state that
is susceptible to apoptosis; and vii) combinations thereof. As used
herein, the term "proliferation" refers to an increase in the
number of cells as a result of cell growth and cell division. Thus,
inhibiting proliferation of a cancer stem cell means to reduce its
ability to undergo cell growth and/or cell division. "Self-renewal"
refers to the process by which stem cells divide to make more stem
cells, thereby perpetuating the stem cell pool. Self-renewal is
division with maintenance of the undifferentiated state. Some
cancer arises from mutations that inappropriately activate
self-renewal programs. "Migration" refers to the ability of a cell
to move. "Invasion" refers to the ability of cells to become motile
and to navigate through the extracellular matrix within a tissue or
to infiltrate neighboring tissues. Cancer cells that become
invasive may disseminate to secondary sites and form metastases.
"Anchorage-independent growth" refers to the ability of a cell to
have colony forming capacity in semisolid media, which is connected
with tumor cell aggressiveness in vivo. "Reprogramming" a cell
refers to causing a change in the cell, for example, by changing a
cancer stem cell from a cell that is refractory or resistant to
apoptosis (e.g., as a result of exposure to a chemotherapeutic
agent) to a state where the cell is susceptible to apoptosis. As
used herein, "apoptosis", also referred to as programmed cell
death, refers to the process of cell self-destruction.
[0046] In some embodiments, at least one cancer stem cell is in an
aggressive and/or poorly differentiated metastatic tumor, and
inhibiting the at least one cancer stem cell inhibits at least one
of: i) growth of the aggressive and/or poorly differentiated
metastatic tumor; ii) proliferation of the aggressive and/or poorly
differentiated metastatic tumor; iii) migration of the aggressive
and/or poorly differentiated metastatic tumor; iv) invasion of the
aggressive and/or poorly differentiated metastatic tumor; v)
initiation of new aggressive and/or poorly differentiated
metastatic tumors; and vi) combinations thereof. As used herein,
the term "aggressive" in the context of a tumor/cancer means that
the tumor/cancer exhibits rapid growth, is more likely to have
spread by the time it has been diagnosed, and is more refractory
than other non-aggressive forms of the tumor/cancer in that it is
more likely to recur after treatment as compared to the
non-aggressive form of the tumor/cancer. As used herein, the term
"poorly differentiated" refers to a cell that is abnormal looking
as compared to a normal cell. Poorly differentiated cells in a
tumor are an indicator of a more aggressive tumor. A "metastatic
tumor" or "metastatic cancer" is a tumor or cancer that has spread
from the place where it first started to another place in the
body.
[0047] HMGA1 is overexpressed in bulk tumor mass of aggressive
and/or poorly differentiated metastatic cancers with the highest
levels of HMGA1 overexpression occurring in the cancer stem cells
of the aggressive and/or poorly differentiated metastatic cancer.
Accordingly, in some embodiments, at least one cancer stem cell
expresses greater levels of HMGA1 as compared to non-stem cancer
cells in the aggressive and/or poorly differentiated metastatic
tumor. In some embodiments, at least one cancer stem cell expresses
greater levels of HMGA1 as compared to normal tissue or precursor
lesions. In some embodiments, an aggressive and/or poorly
differentiated metastatic tumor expresses greater levels of HMGA1
as compared to normal tissue or precursor lesions. As used herein,
the term "greater levels" means a level of HMGA1 in a sample that
is higher than the level of expression of HMGA1 in a control sample
by at least 1.5 fold, 1.6 fold, 1.7 fold, 1.8 fold, 1.9 fold, 2.0
fold, 2.1 fold, 2.2 fold, 2.3 fold, 2.4 fold, 2.5 fold, 2.6 fold,
2.7 fold, 2.8 fold, 2.9 fold, 3.0 fold, 3.1 fold, 3.2 fold, 3.3
fold, 3.4 fold, 3.5 fold, 3.6 fold, 3.7 fold, 3.8 fold, 3.9 fold,
4.0 fold, 4.1 fold, 4.2 fold, 4.3 fold, 4.4 fold, 4.5 fold, 4.6
fold, 4.7 fold, 4.8 fold, 4.9 fold, 5.0 fold or more. In other
embodiments, the term "greater levels" means a level of HMGA1 in a
sample that is higher than the level of HMGA1 in a control sample
by at least 10 fold, 20 fold, 50 fold, 100 fold, 200 fold, 300
fold, 400 fold or more.
[0048] A "cancer" in a patient refers to the presence of cells
possessing characteristics typical of cancer-causing cells, for
example, uncontrolled proliferation, loss of specialized functions,
immortality, significant metastatic potential, significant increase
in anti-apoptotic activity, rapid growth and proliferation rate,
and certain characteristic morphology and cellular markers. In some
circumstances, cancer cells will be in the form of a tumor; such
cells may exist locally within an animal, or circulate in the blood
stream as independent cells. Cancer as used herein includes newly
diagnosed or recurrent cancers, including without limitation,
blastomas, carcinomas, gliomas, leukemias, lymphomas, melanomas,
myeloma, and sarcomas. Cancer as used herein includes, but is not
limited to, head cancer, neck cancer, head and neck cancer, lung
cancer, breast cancer, prostate cancer, colorectal cancer,
esophageal cancer, stomach cancer, leukemia/lymphoma, uterine
cancer, skin cancer, endocrine cancer, urinary cancer, pancreatic
cancer, gastrointestinal cancer, ovarian cancer, cervical cancer,
and adenomas. In some embodiments, the cancer comprises Stage 0
cancer. In some embodiments, the cancer comprises Stage I cancer.
In some embodiments, the cancer comprises Stage II cancer. In some
embodiments, the cancer comprises Stage III cancer. In some
embodiments, the cancer comprises Stage IV cancer. In some
embodiments, the cancer is refractory and/or metastatic. In some
embodiments, at least one cancer stem cell is selected from the
group consisting of a triple-negative breast cancer cell, a
pancreatic ductal adenocarcinoma cell, a colorectal cancer cell,
and a leukemia cell.
[0049] In some embodiments, at least one HMGA1 inhibitor reduces
the expression level and/or activity of HMGA1. As used herein, the
term "expression level" refers to the amount of a mRNA or protein
detected. Levels can be detected at the transcriptional level, the
translational level, and the post-translational level, for example.
"mRNA expression levels" refers to the amount of mRNA detected in a
sample and "protein expression levels" refers to the amount of
protein detected in a sample.
[0050] In some embodiments, the methods further comprise contacting
at least one cancer stem cell with a chemotherapeutic agent. A
"chemotherapeutic agent" is used to connote a compound or
composition that is administered in the treatment of cancer.
Chemotherapeutic agents useful in methods, compositions, and kits
disclosed herein include, but are not limited to, alkylating agents
such as thiotepa, temozolomide, and cyclophosphamide; alkyl
sulfonates such as busulfan, improsulfan and piposulfan; aziridines
such as benzodopa, carboquone, meturedopa, and uredopa;
ethylenimines and methylamelamines including altretamine,
triethylenemelamine, trietylenephosphoramide,
triethylenethiophosphaoramide and trimethylolomelamime; nitrogen
mustards such as chlorambucil, chlornaphazine, cholophosphamide,
estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide
hydrochloride, melphalan, novembichin, phenesterine, prednimustine,
trofosfamide, uracil mustard; nitrosureas such as carmustine,
chlorozotocin, fotemustine, lomustine, nimustine, ranimustine;
antibiotics such as aclacinomysins, actinomycin, authramycin,
azaserine, bleomycins, cactinomycin, calicheamicin, carabicin,
caminomycin, carzinophilin, chromomycins, dactinomycin,
daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin,
epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins,
mycophenolic acid, nogalamycin, olivomycins, peplomycin,
potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin,
streptozocin, tubercidin, ubenimex, zinostatin, zorubicin;
anti-metabolites such as methotrexate and 5-fluorouracil (5-FU);
folic acid analogues such as denopterin, methotrexate, pteropterin,
trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine,
thiamiprine, thioguanine; pyrimidine analogs such as ancitabine,
azacitidine, 6-azauridine, carmofur, cytosine arabinoside,
dideoxyuridine, doxifluridine, enocitabine, floxuridine, 5-FU;
androgens such as calusterone, dromostanolone propionate,
epitiostanol, mepitiostane, testolactone; anti-adrenals such as
aminoglutethimide, mitotane, trilostane; folic acid replenishers
such as folinic acid; aceglatone; aldophosphamide glycoside;
aminolevulinic acid; amsacrine; bestrabucil; bisantrene;
edatraxate; defofamine; demecolcine; diaziquone; elformithine;
elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea;
lentinan; lonidamine; mitoguazone; mitoxantrone; mopidamol;
nitracrine; pentostatin; phenamet; pirarubicin; podophyllinic acid;
2-ethylhydrazide; procarbazine; PSK; razoxane; sizofuran;
spirogermanium; tenuazonic acid; triaziquone;
2,2',2''-trichlorotriethylamine; urethan; vindesine; dacarbazine;
mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;
arabinoside (Ara-C); taxoids, e.g. paclitaxel and docetaxel;
chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; platinum
analogs such as cisplatin and carboplatin; vinblastine; platinum;
etoposide; ifosfamide; mitomycin C; mitoxantrone; vincristine;
vinorelbine; navelbine; novantrone; teniposide; daunomycin;
aminopterin; xeloda; ibandronate; CPT11; topoisomerase inhibitor
RFS 2000; difluoromethylornithine; retinoic acid; esperamicins;
capecitabine; immune system blockers, e.g. rapamycin; amino acid
modifiers, e.g. asparaginase; and pharmaceutically acceptable
salts, acids or derivatives of any of the above. Chemotherapeutic
agents also include anti-hormonal agents that act to regulate or
inhibit hormone action on tumors such as anti-estrogens including
for example tamoxifen, raloxifene, aromatase inhibiting
4(5)-imidazoles, 4-hydroxytamoxifen, trioxifene, keoxifene,
LY117018, onapristone, and toremifene (Fareston); and
anti-androgens such as flutamide, nilutamide, bicalutamide,
leuprolide, and goserelin; and pharmaceutically acceptable salts,
acids or derivatives of any of the above.
[0051] In some embodiments, the chemotherapeutic agent is a
topoisomerase inhibitor. Topoisomerase inhibitors are chemotherapy
agents that interfere with the action of a topoisomerase enzyme
(e.g., topoisomerase I or II). Topoisomerase inhibitors include,
but are not limited to, doxorubicin HCl, daunorubicin citrate,
mitoxantrone HCl, actinomycin D, etoposide, topotecan HCl,
teniposide, and irinotecan, as well as pharmaceutically acceptable
salts, acids, or derivatives of any of these.
[0052] In some embodiments, the chemotherapeutic agent is an
anti-metabolite. An anti-metabolite is a chemical with a structure
that is similar to a metabolite required for normal biochemical
reactions, yet different enough to interfere with one or more
normal functions of cells, such as cell division. Anti-metabolites
include, but are not limited to, gemcitabine, fluorouracil,
capecitabine, methotrexate sodium, ralitrexed, pemetrexed, tegafur,
cytosine arabinoside, thioguanine, 5-azacytidine, 6-mercaptopurine,
azathioprine, 6-thioguanine, pentostatin, fludarabine phosphate,
and cladribine, as well as pharmaceutically acceptable salts,
acids, or derivatives of any of these.
[0053] In certain embodiments, the chemotherapeutic agent is an
antimitotic agent, including, but not limited to, agents that bind
tubulin. In some embodiments, the agent is a taxane. In certain
embodiments, the agent is paclitaxel or docetaxel, or a
pharmaceutically acceptable salt, acid, or derivative of paclitaxel
or docetaxel. In certain alternative embodiments, the antimitotic
agent comprises a vinca alkaloid, such as vincristine, binblastine,
vinorelbine, or vindesine, or pharmaceutically acceptable salts,
acids, or derivatives thereof. In some embodiments, the
chemotherapeutic agent is gemcitabine.
[0054] In some embodiments, at least one cancer stem cell is
contacted in a subject. In some embodiments, the subject is a human
subject.
II. Methods of Treating Aggressive and/or Poorly Differentiated
Metastatic Cancer
[0055] In some embodiments, an aggressive and/or poorly
differentiated metastatic cancer cell may be contacted with an
HGMA1 inhibitor within a subject, and such contact may result in
treatment of aggressive and/or poorly differentiated metastatic
cancer in the subject. In some embodiments, at least some of the
cells from the aggressive and/or poorly differentiated metastatic
cancer comprise cancer stem cells. Accordingly, the presently
disclosed subject matter also provides methods of treating
aggressive and/or poorly differentiated metastatic cancer in a
subject in need thereof. In such embodiments, the methods include
administering a therapeutically effective amount of at least one
HMGA1 inhibitor to a subject in need thereof to treat aggressive
and/or poorly differentiated metastatic cancer. In some
embodiments, the aggressive and/or poorly differentiated metastatic
cancer is selected from the group consisting of triple-negative
breast cancer, pancreatic ductal adenocarcinoma cell, colorectal
cancer cell, and leukemia. In some embodiments, the aggressive
and/or poorly differentiated metastatic cancer comprises at least
one cancer stem cell that overexpresses HMGA1 protein.
[0056] The presently disclosed methods may further comprise
selecting the subject for treatment of the aggressive and/or poorly
differentiated metastatic cancer with at least one HMGA1 inhibitor.
In some embodiments, selecting the subject for treatment of the
aggressive and/or poorly differentiated metastatic cancer
comprises: (i) obtaining a biological sample comprising cells from
the aggressive and/or poorly differentiated metastatic cancer; (ii)
assaying the level of HMGA1 expression in the cells from the
aggressive and/or poorly differentiated metastatic cancer; (iii)
comparing the level of HMGA1 expression in the cells to the level
of HMGA1 expression in a normal control cell; and (iv) selecting
the subject for treatment of the aggressive and/or poorly
differentiated metastatic cancer with the at least one HMGA1
inhibitor if the level of HMGA1 expression in the cells is greater
than the level of HMGA1 expression in the normal control cell.
[0057] The terms "sample," "subject sample," "biological sample,"
and the like, encompass a variety of sample types obtained from a
subject, individual, or subject and can be used in a diagnostic or
monitoring assay. The subject sample may be obtained from a healthy
subject, a diseased subject or a subject having associated symptoms
of cancer. Moreover, a sample obtained from a subject can be
divided and only a portion may be used for diagnosis. Further, the
sample, or a portion thereof, can be stored under conditions to
maintain sample for later analysis. The definition specifically
encompasses blood and other liquid samples of biological origin
(including, but not limited to, peripheral blood, serum, plasma,
cerebrospinal fluid, urine, saliva, stool and synovial fluid),
solid tissue samples such as a biopsy specimen or tissue cultures
or cells derived therefrom and the progeny thereof. In a specific
embodiment, a sample comprises a cancer tissue sample. The
definition also includes samples that have been manipulated in any
way after their procurement, such as by centrifugation, filtration,
precipitation, dialysis, chromatography, treatment with reagents,
washed, or enriched for certain cell populations. The terms further
encompass a clinical sample, and also include cells in culture,
cell supernatants, tissue samples, organs, and the like. Samples
may also comprise fresh-frozen and/or formalin-fixed,
paraffin-embedded tissue blocks, such as blocks prepared from
clinical or pathological biopsies, prepared for pathological
analysis or study by immunohistochemistry. In some embodiments, the
biological sample is selected from the group consisting of a breast
tissue sample, a pancreatic tissue sample, a colon tissue sample,
and a bone marrow tissue sample.
[0058] In some embodiments, at least one HMGA1 inhibitor is
formulated for delivery in a nanoparticle. As used herein, the term
"nanoparticle," refers to a particle having at least one dimension
in the range of about 1 nm to about 1000 nm, including any integer
value between 1 nm and 1000 nm (including about 1, 2, 5, 10, 20,
50, 60, 70, 80, 90, 100, 200, 500, and 1000 nm and all integers and
fractional integers in between).
[0059] As used herein, the term "subject" treated by the presently
disclosed methods in their many embodiments is desirably a human
subject, although it is to be understood that the methods described
herein are effective with respect to all vertebrate species, which
are intended to be included in the term "subject." Accordingly, a
"subject" can include a human subject for medical purposes, such as
for the diagnosis or treatment of an existing disease, disorder,
condition or the prophylactic diagnosis or treatment for preventing
the onset of a disease, disorder, or condition or an animal subject
for medical, veterinary purposes, or developmental purposes.
Suitable animal subjects include mammals including, but not limited
to, primates, e.g., humans, monkeys, apes, gibbons, chimpanzees,
orangutans, macaques and the like; bovines, e.g., cattle, oxen, and
the like; ovines, e.g., sheep and the like; caprines, e.g., goats
and the like; porcines, e.g., pigs, hogs, and the like; equines,
e.g., horses, donkeys, zebras, and the like; felines, including
wild and domestic cats; canines, including dogs; lagomorphs,
including rabbits, hares, and the like; and rodents, including
mice, rats, guinea pigs, and the like. An animal may be a
transgenic animal. In some embodiments, the subject is a human
including, but not limited to, fetal, neonatal, infant, juvenile,
and adult subjects. Further, a "subject" can include a patient
afflicted with or suspected of being afflicted with a disease,
disorder, or condition. Thus, the terms "subject" and "patient" are
used interchangeably herein. Subjects also include animal disease
models (e.g., rats or mice used in experiments, and the like).
[0060] As described herein, the presently disclosed HMGA1 inhibitor
can be administered to a subject for therapy by any suitable route
of administration, including orally, nasally, transmucosally,
ocularly, rectally, intravaginally, parenterally, including
intramuscular, subcutaneous, intramedullary injections, as well as
intrathecal, direct intraventricular, intravenous, intra-articular,
intra-sternal, intra-synovial, intra-hepatic, intralesional,
intracranial, intraperitoneal, intranasal, or intraocular
injections, intracistemally, topically, as by powders, ointments or
drops (including eyedrops), including buccally and sublingually,
transdermally, through an inhalation spray, or other modes of
delivery known in the art.
[0061] The phrases "systemic administration," "administered
systemically," "peripheral administration" and "administered
peripherally" as used herein mean the administration of at least
one HMGA1 inhibitor such that it enters the patient's system and,
thus, is subject to metabolism and other like processes, for
example, subcutaneous administration.
[0062] The phrases "parenteral administration" and "administered
parenterally" as used herein mean modes of administration other
than enteral and topical administration, usually by injection, and
includes, without limitation, intravenous, intramuscular,
intarterial, intrathecal, intracapsular, intraorbital, intraocular,
intracardiac, intradermal, intraperitoneal, transtracheal,
subcutaneous, subcuticular, intraarticular, subcapsular,
subarachnoid, intraspinal and intrasternal injection and
infusion.
[0063] Regardless of the route of administration selected,
compositions comprising an HMGA1 inhibitor may be formulated into
pharmaceutically acceptable dosage forms. One skilled in the art
can select appropriate formulation components, such as carriers,
buffers, adjuvants, etc., according to the route of administration
and/or the subject being treated.
[0064] Actual dosage levels of an HMGA1 inhibitor can be varied so
as to obtain an amount of the active ingredient that is effective
to achieve the desired therapeutic response for a particular
subject, composition, route of administration, and disease,
disorder, or condition without being toxic to the subject. The
selected dosage level will depend on a variety of factors including
the activity of the particular composition employed, the route of
administration, the time of administration, the rate of excretion
of the particular composition being employed, the duration of the
treatment, other drugs, and/or materials used in combination with
the particular composition employed, the age, sex, weight,
condition, general health and prior medical history of the patient
being treated, and like factors well known in the medical arts.
Accordingly, a physician having ordinary skill in the art can
readily determine and prescribe the effective amount of the
presently disclosed composition required. Accordingly, the dosage
range for administration will be adjusted by the physician as
necessary, as described more fully elsewhere herein.
III. Methods of Selecting a Subject with Aggressive and/or Poorly
Differentiated Metastatic Cancer
[0065] In some embodiments, the presently disclosed method is a
method of selecting a subject with an aggressive and/or poorly
differentiated metastatic cancer for treatment with at least one
HMGA1 inhibitor, the method comprising: (a) obtaining a biological
sample from the subject, wherein the biological sample comprises
cells from the aggressive and/or poorly differentiated metastatic
cancer; (b) determining the level of expression of HMGA1 in the
biological sample; (c) comparing the level of expression of HMGA1
in the biological sample with the level of expression of HMGA1 in a
control sample; and (d) selecting the subject with aggressive
and/or poorly differentiated metastatic cancer for treatment with
at least one HMGA1 inhibitor when the level of HMGA1 expression in
the biological sample is greater than the level of HMGA1 expression
in the control sample.
IV. Methods of Diagnosing an Aggressive and/or Poorly
Differentiated Metastatic Cancer
[0066] The presently disclosed subject matter also provides methods
of diagnosing an aggressive and/or poorly differentiated metastatic
cancer in a subject in need thereof. In such embodiments, the
methods comprise: (a) obtaining a biological sample from the
subject, wherein the biological sample comprises cells suspected of
being aggressive and/or poorly differentiated metastatic cancer
cells; (b) determining the level of expression of two or more genes
selected from Table 1 in the biological sample; and (c) comparing
the level of expression of the two or more genes in the biological
sample with the level of expression of the two or more genes in a
control sample; wherein a significant difference in the level of
expression of the two or more genes in the biological sample
compared to the level of expression of the two or more genes in the
control sample indicates that the biological sample comprises at
least one aggressive and/or poorly differentiated metastatic cancer
cell.
TABLE-US-00001 TABLE 1 Differentially Expressed Genes Induced By
HMGA1 Gene Entrez Gene ID Direction SLC17A5 26503 Down Expressed
PGRMC1 10857 Down Expressed TMCO1 54499 Up Expressed SLC9A6 10479
Down Expressed ARL2BP 23568 Down Expressed DRAM2 128338 Down
Expressed PLAT 5327 Down Expressed SEPT2 4735 Down Expressed PSG4
5672 Up Expressed RPS10P7 376693 Down Expressed INPP5A 3632 Down
Expressed CAMK2N1 55450 Down Expressed OR6X1 390260 Up Expressed
TGFBR2 7048 Up Expressed SLC37A2 219855 Down Expressed GRB2 2885
Down Expressed B3GALT5 10317 Down Expressed TAF9B 51616 Down
Expressed HIST1H4L 8368 Down Expressed FOS 2353 Up Expressed SRPX
8406 Down Expressed LIPA 3988 Down Expressed HM4GA1 3159 Down
Expressed CNDP2 55748 Down Expressed BOK 666 Down Expressed ABCA1
19 Down Expressed MSRB3 253827 Up Expressed WSB2 55884 Down
Expressed CLIP1 6249 Down Expressed WIPF1 7456 Down Expressed MYEOV
26579 Down Expressed SLC26A2 1836 Up Expressed WDFY1 57590 Up
Expressed SYPL1 6856 Down Expressed STEAP3 55240 Down Expressed
C5orf28 64417 Up Expressed IRAK2 3656 Down Expressed NFIB 4781 Up
Expressed LOC100134868 100134868 Up Expressed IPMK 253430 Down
Expressed ICK 22858 Down Expressed PORCN 64840 Down Expressed SFXN1
94081 Up Expressed APOL6 80830 Down Expressed C12orf49 79794 Down
Expressed PIGO 84720 Down Expressed AKAP6 9472 Up Expressed ULBP3
79465 Down Expressed GPR45 11250 Down Expressed RACGAP1 29127 Down
Expressed MT1E 4493 Down Expressed C3orf34 84984 Up Expressed STX19
415117 Down Expressed GRAMD3 65983 Up Expressed SLC1A3 6507 Up
Expressed HMGCS1 3157 Up Expressed SEC24D 9871 Up Expressed MAP3K13
9175 Down Expressed GPR110 266977 Down Expressed TSPAN11 441631
Down Expressed OR6F1 343169 Down Expressed PLAU 5328 Down Expressed
ALDH1A3 220 Down Expressed
[0067] As used herein, the term "biomarker" refers to any gene, RNA
or protein whose level of expression in a cell or tissue is altered
in some way compared to that of a normal or healthy cell or tissue.
Biomarkers of the presently disclosed subject matter are selective
for an aggressive and/or poorly differentiated metastatic cancer
and comprise two or more genes comprising embryonic development
genes, tissue development genes, cellular development genes, cell
death and survival genes, cell movement genes, or a combination
thereof. In particular, biomarkers of the presently disclosed
subject matter that are selective for aggressive and/or poorly
differentiated metastatic cancer include 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,
61, 62 or 63 genes selected from Table 1 in the biological
sample.
[0068] In some embodiments, the significant difference in
expression of two or more genes in the biological sample compared
to the control sample comprises increased expression of TMCO1,
PSG4, OR6X1, TGFBR2, FOS, MSRB3, SLC26A2, WDFY1, C5orf28, NFIB,
LOC100134868, SFXN1 AKAP6, C3orf34, GRAMD3, SLC1A3, HMGCS1, and/or
SEC24D in the biological sample.
[0069] In some embodiments, the significant difference in
expression of two or more genes in the biological sample compared
to the control sample comprises decreased expression of SLC17A5,
PGRMC1, SLC9A6, ARL2BP, DRAM2, PLAT, SEPT2, RPS10P7, INPP5A,
CAMK2N1, SLC37A2, GRB2, B3GALT5, TAF9B, HIST1H4L, SRPX, LIPA,
HMGA1, CNDP2, BOK, ABCA1, WSB2, CLIP1, WIPF1, MYEOV, SYPL1, STEAP3,
IRAK2, IPMK, ICK, PORCN, APOL6, C12orf49, PIGO, ULBP3, GPR45,
RACGAP1, MT1E, STX19, MAP3K13, GPR110, TSPAN11, OR6F1, PLAU, and/or
ALDH1A3 in the biological sample.
[0070] In another embodiment, the significant difference in
expression of two or more genes in the biological sample compared
to the control sample comprises increased expression of TGF.beta.1,
FOS, cMYC, STAT3, and/or TMCO1 in the biological sample and/or
decreased expression of ARL2BP, PGRMC1, and/or GRB2 in the
biological sample.
[0071] As used herein, the term "level of expression" of a
biomarker refers to the amount of biomarker detected. Levels of
biomarker can be detected at the transcriptional level, the
translational level, and the post-translational level, for example.
As used herein, the term "diagnosing" refers to the process of
attempting to determine or identify a disease or disorder.
[0072] As used herein, the term "comparing" refers to making an
assessment of how the proportion or level of one or more biomarkers
in a sample from a subject relates to the proportion or level of
the corresponding one or more biomarkers in a standard or control
sample. For example, "comparing" may refer to assessing whether the
proportion or level of one or more biomarkers in a sample from a
subject is the same as, more or less than, or different from the
proportion or level of the corresponding one or more biomarkers in
a standard or control sample. More specifically, the term may refer
to assessing whether the proportion or level of one or more
biomarkers in a sample from a subject is the same as, more or less
than, different from or otherwise corresponds (or not) to the
proportion or level of predefined biomarker levels that correspond
to, for example, a subject having an aggressive and/or poorly
differentiated metastatic cancer. In a specific embodiment, the
term "comparing" refers to assessing whether the level of one or
more biomarkers of the presently disclosed subject matter in a
sample from a subject is the same as, more or less than, different
from or otherwise correspond (or not) to levels of the same
biomarkers in a control sample (e.g., predefined levels that
correlate to individuals without an aggressive and/or poorly
differentiated metastatic cancer, standard biomarker levels, and
the like).
[0073] As used herein, the terms "indicates" or "correlates" (or
"indicating" or "correlating," or "indication" or "correlation,"
depending on the context) in reference to a parameter, e.g., a
modulated proportion or level in a sample from a subject, may mean
that the subject has an aggressive and/or poorly differentiated
metastatic cancer. In specific embodiments, the parameter may
comprise the level of one or more biomarkers of the presently
disclosed subject matter. A particular set or pattern of the
amounts of one or more biomarkers may indicate that a subject has
an aggressive and/or poorly differentiated metastatic cancer. In
other embodiments, a particular set or pattern of the amounts of
one or more biomarkers may be correlated to a subject being
unaffected (i.e., indicates a subject does not have an aggressive
and/or poorly differentiated metastatic cancer). In certain
embodiments, "indicating," or "correlating," as used according to
the presently disclosed subject matter, may be by any linear or
non-linear method of quantifying the relationship between levels of
biomarkers to a standard, control or comparative value for the
assessment of the diagnosis, prediction of an aggressive and/or
poorly differentiated metastatic cancer, assessment of efficacy of
clinical treatment, identification of a subject that may respond to
a particular treatment regime or pharmaceutical agent, monitoring
of the progress of treatment, and in the context of a screening
assay, for the identification of a therapeutic to treat an
aggressive and/or poorly differentiated metastatic cancer.
[0074] A "subject" can include a subject afflicted with or
suspected of being afflicted with a condition or disease. The
subject may have mild, intermediate or severe disease. The subject
may be treatment naive, responding to any form of treatment, or
refractory. The subject may be an individual in need of treatment
or in need of diagnosis based on particular symptoms or family
history.
[0075] As used herein, the term "subject at risk" of getting a
disease refers to estimating that a subject will have a disease or
disorder in the future based on the subject's current symptoms,
family history, lifestyle choices, and the like.
[0076] As used herein, the term "disease" refers to any condition,
dysfunction or disorder that damages or interferes with the normal
function of a cell, tissue, or organ.
[0077] The terms "measuring" and "determining" are used
interchangeably throughout, and refer to methods which include
obtaining a subject sample and/or detecting the level of a
biomarker(s) in a sample. In one embodiment, the terms refer to
obtaining a subject sample and detecting the level of one or more
biomarkers in the sample. In another embodiment, the terms
"measuring" and "determining" mean detecting the level of one or
more biomarkers in a subject sample. Measuring can be accomplished
by methods known in the art and those further described herein. The
term "measuring" is also used interchangeably throughout with the
term "detecting."
[0078] Various methodologies of the presently disclosed subject
matter include a step that involves comparing a value, level,
feature, characteristic, property, and the like, to a "suitable
control," referred to interchangeably herein as an "appropriate
control" or a "control sample." A "suitable control," "appropriate
control" or a "control sample" is any control or standard familiar
to one of ordinary skill in the art useful for comparison purposes.
In one embodiment, a "suitable control" or "appropriate control" is
a value, level, feature, characteristic, property, and the like,
determined in a cell, organ, or subject, e.g., a control or normal
cell, organ, or subject, exhibiting, for example, normal traits.
For example, the biomarkers of the presently disclosed subject
matter may be assayed for levels in a sample from an unaffected
individual (UI) or a normal control individual (NC) (both terms are
used interchangeably herein). In another embodiment, a "suitable
control" or "appropriate control" is a value, level, feature,
characteristic, property, and the like, determined prior to
performing a therapy (e.g., a cancer treatment) on a subject. In
yet another embodiment, a transcription rate, mRNA level,
translation rate, protein level, biological activity, cellular
characteristic or property, genotype, phenotype, and the like, can
be determined prior to, during, or after administering a therapy
into a cell, organ, or subject. In a further embodiment, a
"suitable control" or "appropriate control" is a predefined value,
level, feature, characteristic, property, and the like. A "suitable
control" can be a profile or pattern of levels of one or more
biomarkers of the presently disclosed subject matter that
correlates to the presence of an aggressive and/or poorly
differentiated metastatic cancer, to which a subject sample can be
compared. The subject sample can also be compared to a negative
control, i.e., a profile that correlates to not having an
aggressive and/or poorly differentiated metastatic cancer.
V. General Definitions
[0079] Although specific terms are employed herein, they are used
in a generic and descriptive sense only and not for purposes of
limitation. Unless otherwise defined, all technical and scientific
terms used herein have the same meaning as commonly understood by
one of ordinary skill in the art to which this presently described
subject matter belongs.
[0080] Following long-standing patent law convention, the terms
"a," "an," and "the" refer to "one or more" when used in this
application, including the claims. Thus, for example, reference to
"a subject" includes a plurality of subjects, unless the context
clearly is to the contrary (e.g., a plurality of subjects), and so
forth.
[0081] Throughout this specification and the claims, the terms
"comprise," "comprises," and "comprising" are used in a
non-exclusive sense, except where the context requires otherwise.
Likewise, the term "include" and its grammatical variants are
intended to be non-limiting, such that recitation of items in a
list is not to the exclusion of other like items that can be
substituted or added to the listed items.
[0082] For the purposes of this specification and appended claims,
unless otherwise indicated, all numbers expressing amounts, sizes,
dimensions, proportions, shapes, formulations, parameters,
percentages, parameters, quantities, characteristics, and other
numerical values used in the specification and claims, are to be
understood as being modified in all instances by the term "about"
even though the term "about" may not expressly appear with the
value, amount or range. Accordingly, unless indicated to the
contrary, the numerical parameters set forth in the following
specification and attached claims are not and need not be exact,
but may be approximate and/or larger or smaller as desired,
reflecting tolerances, conversion factors, rounding off,
measurement error and the like, and other factors known to those of
skill in the art depending on the desired properties sought to be
obtained by the presently disclosed subject matter. For example,
the term "about," when referring to a value can be meant to
encompass variations of, in some embodiments, .+-.100% in some
embodiments .+-.50%, in some embodiments .+-.20%, in some
embodiments .+-.10%, in some embodiments .+-.5%, in some
embodiments .+-.1%, in some embodiments .+-.0.5%, and in some
embodiments .+-.0.1% from the specified amount, as such variations
are appropriate to perform the disclosed methods or employ the
disclosed compositions.
[0083] Further, the term "about" when used in connection with one
or more numbers or numerical ranges, should be understood to refer
to all such numbers, including all numbers in a range and modifies
that range by extending the boundaries above and below the
numerical values set forth. The recitation of numerical ranges by
endpoints includes all numbers, e.g., whole integers, including
fractions thereof, subsumed within that range (for example, the
recitation of 1 to 5 includes 1, 2, 3, 4, and 5, as well as
fractions thereof, e.g., 1.5, 2.25, 3.75, 4.1, and the like) and
any range within that range.
EXAMPLES
[0084] The following Examples have been included to provide
guidance to one of ordinary skill in the art for practicing
representative embodiments of the presently disclosed subject
matter. In light of the present disclosure and the general level of
skill in the art, those of skill can appreciate that the following
Examples are intended to be exemplary only and that numerous
changes, modifications, and alterations can be employed without
departing from the scope of the presently disclosed subject matter.
The synthetic descriptions and specific examples that follow are
only intended for the purposes of illustration, and are not to be
construed as limiting in any manner to make compounds of the
disclosure by other methods.
Example 1
Methods
[0085] Ethics Statement:
[0086] All animal experiments were conducted in accordance with a
protocol approved by the Johns Hopkins University Animal Care and
Use Committee (protocol #MO11M270). Mice were housed in a sterile
environment where they had free access to food and water as
outlined in the institutional guidelines.
[0087] Cell Culture and Proliferation Assay:
[0088] Cells (MDA-MB-231 and Hs578T) were cultured as recommended
(ATCC). For proliferation assays, cells were seeded (7,500/well)
and counted using an automated cell counter (Nexcelom). Each
experiment was done in triplicate and performed at least twice.
[0089] RNA Interference:
[0090] The short-hairpin RNA interference vector for HMGA1 targets
5'-CAACTCCAGGAAGGAAACCAA-3' (SEQ ID NO:1) and has been described
elsewhere (Liau et al. (2006) Cancer Res. 66:11613-11622). Virus
was prepared as previously described. The empty vector was used as
a negative control as described (Belton et al. (2012) PloS One
7:e30034). Polyclonal, transduced cells were selected and
maintained in puromycin (1 ug/ml). To ensure that the effects of
silencing HMGA were not a result of a single clone, independent,
polyclonal transductions were done at least twice for each
experiment. All functional experiments were performed in duplicate
or triplicate and replicated after a repeat transduction experiment
and polyclonal selection of shRNA or control cells. Repression of
HMGA1 was confirmed in each case at the level of gene expression
(qRT-PCR) and Western analysis.
[0091] Migration and Invasion Assays:
[0092] Invasion assays were performed as previously described
(Hillion et al. (2009) Mol. Cancer Res. 7:1803-1812) with the
following modifications. Briefly, 15,000 cells were resuspended in
serum-free media (500 ul) and placed in the upper chamber of a
24-well BD BioCoat.TM. Matrigel.TM. Invasion Chamber coated with
Matrigel. Invasion was calculated as the percentage of total cells
that invaded into the bottom chamber containing complete media with
serum. Migration was performed similarly, except that Matrigel was
omitted.
[0093] Orthotopic Tumorigenicity and Metastatic Foci
Experiments:
[0094] Cells (suspended in 75 ul phosphate-buffered saline (PBS))
were implanted into murine (NOD-scid IL2Rgamma.sup.null) mammary
fat pads with an equal volume of Matrigel. Tumor volumes
(calculated by 4/3.pi..times.length/2.times.width/2.times.depth/2)
were monitored daily until they reached 1-1.5 cm.sup.3, after which
mice were euthanized. The presence of tumor foci within the lung
was analyzed histopathologically. For tail vein injection
experiments, cells (10.sup.6) were resuspended in PBS (150 ul).
Mice were euthanized after 3 weeks, and lungs were examined
histopathologically.
[0095] Mammosphere Assay:
[0096] Mammosphere assays were performed as previously described
(Shaw et al. (2012) J. Mammary Gland Biol. Neoplasia 17: 111-117)
and spheres (>50 um) were counted.
[0097] Western Analysis:
[0098] Western blots were performed as previously described (Belton
et al. (2012) PloS One 7:e30034; Wood et al. (2000) Mol. Cell.
Biol. 20:5490-5502), using commercial antibodies to HMGA1 (Abcam)
and .beta.-Actin (Cell Signaling), both at a 1:1000 dilution.
[0099] Gene Expression Analysis with Quantitative, Reverse
Transcription PCR:
[0100] Total RNA was isolated using the Direct-zol RNA MiniPrep kit
(Zymo) and analyzed by qRT-PCR as previously described. The
expression level of each gene was normalized to the human RPLP0
(Applied Biosystems) or/3-actin gene. Primers for ECadherin, Snail,
and Vimentin were previously described (Belton et al. (2012) PloS
One 7:e30034; Mani et al. (2008) Cell 133:704-715).
[0101] HMGA1 Knock-Down and Gene Expression Profile Analysis:
[0102] HMGA1 was knocked-down in MDA-MB-231 cells using siRNA as
previously described (Belton et al. (2012) PloS One 7:e30034;
Tesfaye et al. (2007) Cancer Res. 67:3998-4004; Hillion et al.
(2009) Mol. Cancer Res. 7:1803-1812). RNA was isolated and
hybridized to the Affymetrix exon array (GeneChip Human Exon 1.0 ST
Array) as previously described. Expression data was preprocessed
using the robust microarray (RMA) algorithm (Irizarry et al. (2003)
Nucleic Acids Res. 31: e15), as implemented in the oligo software
package (Carvalho and Irizarry (2010) Bioinformatics 26: 2363-2367)
available from Bioconductor (Gentleman et al. (2004) Genome Biol.
5: R80) and annotated to the most recent human genome using the
getNetAffx function in the oligo package. Microarray data were
uploaded to Gene Expression Omnibus (GSE45483). Expression profiles
from HMGA1 knock-down cells were compared to control cells treated
with the vector RNA using Bayes modified t-tests and the limma
package from Bioconductor (Smyth (2005) "Bioinformatics and
Computational Biology Solutions using R and Bioconductor",
Springer-Verlag: 397-420). The analysis was focused on the 100 most
differentially expressed transcripts.
[0103] To compare this signature to genes expressed in a panel of
embryonic stem cells, induced pluripotent stem cells, embryoid
bodies, and fibroblasts, expression profiles were downloaded for a
43 sample study (GSE25970) (Bock et al. (2011) Cell 44: 439-452)
from the Gene Expression Omnibus (Barrett et al. (2005) Nucleic
Acids Res. 33: D562-D566). Unsupervised cluster analysis was
performed on all probes annotated to the 63 genes in the HMGA1
panel using agglomorative clustering with complete linkage.
Euclidean distance and t-tests were used to compare probe-specific
expression in stem cells and fibroblasts.
[0104] Pathway analysis of differentially expressed genes was
performed using Ingenuity Pathway Analysis (IPA, Ingenuity Systems)
as described (Schuldenfrei et al. (2011) BMC Genomics 12:549). IPA
scores were generated for each network and indicate the likelihood
that the focus genes present in the network could occur by chance
alone. A score of >3 is considered significant because it
represents a 1/1,000 chance that the network contains specific
focus genes by random chance alone (Schuldenfrei et al. (2011) BMC
Genomics 12:549).
Results
[0105] Silencing HMGA1 Halts Cell Proliferation and Reprograms
Invasive, Mesenchymal-Like Cells:
[0106] To define the role of HMGA1 in oncogenic properties and
tumor progression, HMGA1 expression was silenced using
lentiviral-mediated delivery of short hairpin RNA (shRNA) ((Shah et
al. (2012) PLoS One 7: e48533) in cell lines derived from
aggressive, triple-negative breast cancers (MDAMB-231, Hs578T; FIG.
1A). Control cells were transduced with a control lentiviral vector
(Belton et al. (2012) PloS One 7:e30034; Shah et al. (2012) PLoS
One 7: e48533). It was discovered that cell proliferation was
rapidly halted in both cell lines (FIG. 1B) within the first 4
days. Surprisingly, there was a dramatic change in cell morphology
whereby the spindle-shaped, fibroblast-like cells became cuboidal
and epithelial-like in appearance (FIG. 1C). Because these
morphologic changes are consistent with a mesenchymal-epithelial
transition, the expression of genes involved in a
mesenchymal-epithelial transition was investigated (Belton et al.
(2012) PloS One 7:e30034; Mani et al. (2008) Cell 133:704-715). In
MDA-MB-231 cells, it was found that silencing HMGA1 led to a
significant repression in the mesenchymal genes, Snail and
Vimentin, while there was an increase in the gene expressing the
epithelial marker, E-Cadherin (FIG. 1D). Similarly, in Hs578T
cells, E-Cadherin was induced when HMGA1 was silenced. Tumor
progression properties, including invasion and migration, were also
assessed. In both cell lines, there was a marked reduction in
migration and invasion in cells with silencing of HMGA1 (FIG. 1E).
Together, these findings indicate that silencing HMGA1 results in a
profound decrease in proliferation, migration, and invasion, as
well as morphologic and gene expression changes consistent with a
mesenchymal-epithelial transition.
[0107] Silencing HMGA1 Interferes with Orthotopic Tumorigenicity
and Metastatic Progression:
[0108] Next, the role of HMGA1 on tumorigenesis was assessed using
in vivo models of triple-negative breast cancer. First, tumor
growth was assessed following mammary fat pad implantation. It was
found that silencing HMGA1 in the aggressive MDA-MB-231 cells leads
to a dramatic decrease in tumor growth following mammary fat pad
implantation (FIG. 2A). Specifically, cells (10.sup.5) transduced
with control virus reached a volume of 0.53 cm.sup.3.+-.0.34 at 8
weeks following mammary fat pad implantation. In contrast, the
tumors from cells transduced with HMGA1 shRNA (shHMGA1) were
significantly smaller at 8 weeks following implantation (0.037
cm.sup.3.+-.0.058; p=0.016). Because there was a dramatic effect on
primary tumorigenesis, it was also determined if silencing HMGA1
interferes with metastatic progression. Therefore, the lungs were
evaluated histopathologically for tumor foci after necropsy.
Strikingly, almost no metastatic lesions to the lungs in the mice
implanted with the shHMGA1 cells were discovered as compared to the
mice implanted with control cells in which there were extensive,
coalescing sheets of metastatic tumor cells throughout the lungs
following mammary implantation with 10.sup.5 cells (FIG. 2B).
Metastatic progression was also assessed following mammary fat pad
implantation with a greater number of cells (10.sup.7) from a
repeat transduction experiment, and sacrificed the mice after 5
weeks. With the higher number of cells, tumors formed from all
injections (3/3 in controls and 3/3 in shHMGA1 cells (FIG. 2C).
Although tumors were slightly smaller from the shHMGA1 cells, the
difference was not significant (0.64.+-.0.27 in controls versus
0.17.+-.0.072 in shHMGA1 cells, p=0.08). Despite the similar tumor
volumes, a dramatic decrease (>100-fold) was observed in
metastatic foci in the shHMGA1 cells as compared to controls
(0.67.+-.1.15 versus >100 in all controls; p=0.00004; FIGS.
2C-2D). Lung foci was also assessed following tail vein injection
of control or shHMGA1 cells (10.sup.6) after 3 weeks. Only one lung
focus was observed after injection of the shHMGA1 cells, while
there were numerous foci in the control cells (0.25.+-.0.5 versus
99.3.+-.15.0; p=0.007; FIG. 5).
[0109] Silencing HMGA1 Blocks Mammosphere Formation and Depletes
Tumor-Initiator Cells:
[0110] Because silencing HMGA1 has profound effects on oncogenic
properties in vitro, primary tumorigenesis and metastatic
progression in vivo, and expression of genes involved in
epithelialmesenchymal transition, it was sought to determine its
role in cancer stem cell characteristics. To this end, the
epithelial stem cell property of mammosphere formation (Shaw et al.
(2012) J. Mammary Gland Biol. Neoplasia 17: 111-117) was explored
in the control and shHMGA1-treated cells (FIGS. 3A-3B). It was
found that growth of primary, secondary, and tertiary mammospheres
was significantly impaired in the MDA-MB-231 cells with silencing
of HMGA1. Similarly, it was observed that there was a significant
decrease in primary mammosphere formation in the Hs578T cells
treated with shHMGA1. (Secondary or tertiary mammospheres do not
form in control Hs578T cells, precluding analysis of these
phenotypes). Next, orthotopic implantations were performed and
tumorigenicity was assessed with limiting dilutions. As presented
above, tumors formed in both control and shHMGA1 cells when
10.sup.7 or 10.sup.5 cells were implanted. In contrast, no tumors
formed in the MDA-MB-231 cells with silencing of HMGA1 when
10.sup.4 cells were injected (0/3), while tumors formed in all
control injections (3/3; FIG. 3C). These results indicate that
silencing HMGA1 in MDA-MB-231 cells depletes the tumor-initiator or
cancer stemlike cells and further underscores the role of HMGA1 as
a key regulator of stem cell properties in aggressive,
triple-negative breast cancer cells.
[0111] HMGA1 Induces a Stem Cell Signature in Triple-Negative
Breast Cancer Cells:
[0112] To globally define the transcriptional networks regulated by
HMGA1, gene expression profile analysis was performed in MDAMB-231
cells with or without HMGA1 knock-down. To this end, siRNA was used
(Tesfaye et al. (2007) Cancer Res. 67:3998-4004; Hillion et al.
(2009) Mol. Cancer Res. 7:1803-1812) and a rapid and significant
reduction in HMGA1 expression was observed (FIG. 6A). HMGA1 mRNA
falls dramatically by 48 hours, with persistent decreases at 72
hours (FIG. 6A). There was also a marked decrease in HMGA1 protein
at 48 and 72 hours (FIG. 6B). Therefore, global gene expression
profile analysis was performed at 48 hours using an Affymetrix exon
array (GeneChip Human Exon 1.0 ST Array) with RNA from three
independent replicates of each experimental condition. To define an
HMGA1 signature in breast cancer, 100 transcripts that were most
differentially expressed were identified. These 100 transcripts
correspond to 63 unique genes. Because HMGA1 is enriched in
embryonic stem cells and functional studies showed that it is
required for cancer stem cell properties, the HMGA1 signature of 63
genes was compared to gene expression profiles from diverse
pluripotent stem cells and differentiated cells, including
embryonic stem cells (ESCs), induced pluripotent stem cells,
embryoid bodies, and fibroblasts (Bock et al. (2011) Cell 44:
439-452). As shown, un-supervised cluster analysis of these genes
separates the samples by cell type with a clear distinction between
pluripotent stem cells and differentiated cells. Moreover, the
HMGA1 signature is highly enriched in pluripotent/embryonic stem
cells (p<0.001; FIG. 4A). A subset of the HMGA1 signature genes
was validated using quantitative RT-PCR, and differential
expression similar to the microarray gene expression results was
found in all cases (FIG. 6C). These findings suggest that HMGA1
drives tumor progression by inducing stem cell transcriptional
networks.
[0113] To elucidate cellular pathways regulated by HMGA1 in breast
cancer, the HMGA1 signature was analyzed with Ingenuity Pathway
Analysis (IPA, Ingenuity Systems). From the top list of
differentially regulated genes, two pathways had significant
network scores (69 and 46, respectively; FIGS. 4B and 7). The
highest scoring network was embryonic development, tissue
development, and cellular development. The top molecular and
cellular functions were cell death and survival and cellular
movement, while the top physiologic system development and
functions included: 1. nervous system development and function, 2.
organ morphology, and 3. embryonic development. In this network,
the most down-regulated molecule was ARL2BP or ADP-ribosylation
factor (ARF)-like 2 binding protein. This protein is a member of a
functionally distinct group of RAS-related GTPases, called the ARF
family. ARL2BP protein binds to ARL2.GTP with high affinity and
plays a role in the nuclear translocation, retention and
transcriptional activity of STAT3 (Muromoto et al. (2008) Int.
Immunol. 20: 395-403). Notably, it was shown that HMGA1 induces
STAT3 expression in lymphoid tumorigenesis, and STAT3 inhibitors
are cytotoxic to the HMGA1-driven tumor cells (Hillion et al.
(2008) Cancer Res. 68:10121-10127). TMCO1 or transmembrane and
coiled-coil domains 1 protein was the most up-regulated protein in
this network. Although its function is not known, it is associated
with breast cancer cells [8882811 GEO Profiles-NCBI]. TGF.beta.1 is
a major node and this protein is upregulated in diverse cancers and
thought to promote invasion, migration, EMT and tumor progression
(Massague (2008) Cell 134: 215-230). EGFR and MAPK are other
important nodes that are activated in cancer and mediate
proliferative signals (Schuldenfrei et al. (2011) BMC Genomics
12:549). Another central node was HIF-1 alpha, a key factor
involved in angiogenesis during tumor progression and vascular
development during embryogenesis (Semenza (2012) Oncogene in press.
In addition, Myc was identified as a major node and prior studies
found that not only does cMYC induce HMGA1 expression (Wood et al.
(2000) Mol. Cell. Biol. 20:5490-5502), but HMGA1 also directly
up-regulates cMYC expression (Shah et al. (2012) PLoS One 7:
e48533). Myc also has a well-defined role in breast (Thibodeaus et
al. (2009) Breast Cancer Res. Treat. 116:281-294; Tront et al.
(2010) Cancer Res. 70:9671-9681) and other diverse cancers (Dang
(2012) Cell 2:304-307) as well as in embryonic stem cells (Dang
(2012) Cell 2:304-307; Nie et al. (2012) Cell 151:68-79. Thus, this
pathway analysis further confirms the important role for HMGA1 in
regulating embryonic stem cell networks during tumor progression in
breast cancer.
Discussion
[0114] The presently disclosed subject matter reports for the first
time that silencing HMGA1 induces a rapid and dramatic
reprogramming of highly proliferative, invasive, mesenchymal-like
breast cancer cells to more differentiated, slowly growing,
epithelial-like cells. It was found that knock-down of HMGA1 has
profound effects on oncogenic properties associated with both tumor
initiation (orthotopic tumorigenesis) and tumor progression
(migration, invasion, and metastatic progression). In fact, the in
vivo effects on metastatic progression were even more pronounced
than the effects on primary tumorigenesis, thus highlighting the
role of HMGA1 in tumor progression. The changes induced by
silencing HMGA1 are among the most striking alterations reported to
date with knockdown of HMGA1 or most other oncogenes for that
matter, both in degree and rate of onset. The profound effects
could be related to the presently disclosed efficient,
viral-mediated delivery of shRNA to repress HMGAL In addition,
triple-negative breast cancer cells may be highly dependent upon
HMGA1 and related pathways for their oncogenic properties. Indeed,
a study from the Broad Institute at MIT identified HMGA1 as a key
transcription factor enriched in triple-negative breast cancer
(Ben-Porath et al. (2008) Nat. Genet. 40:499-507). Moreover,
expression of HMGA1 and 8 additional genes predicted poor outcomes
in breast cancer, as well as brain and bladder cancer. Prior
studies using antisense or dominant-negative approaches in
triple-negative breast cancer cells (MDA-MB-231 or Hs578T) also
showed that anchorage-independent cell growth or colony formation
are inhibited by HMGA1 repression (Reeves et al. (2001) Mol. Cell.
Biol. 21:575-594; Dolde et al. (2002) Breast Cancer Research and
Treatment 71:181-191). There is also preliminary evidence
demonstrating that HMGA1 expression correlates with more advanced
nuclear grade in primary tumors (Asch & Resar, unpublished
data).
[0115] Emerging evidence further indicates that HMGA1 is important
in maintaining a de-differentiated, pluripotent stem-like state
((Shah et al. (2012) PLoS One 7: e48533). A recent landmark paper
demonstrated that HMGA1 is required for cellular reprogramming of
somatic cells to induced pluripotent stem cells (iPSCs) by the
Yamanaka factors (Flohr et al. (2003) Histol. Histopathol. 18:
999-1004). Blocking HMGA1 expression or function prevents the
derivation of iPSCs. In normal embryonic stem cells in culture and
during the reprogramming process to iPSCs, HMGA1 activates
expression of stem cell transcriptional networks. Recent studies
also found that tumor progression and an epithelial-mesenchymal
transition (EMT) involves transcriptional networks important in
stem cells (Ben-Porath et al. (2008) Nat. Genet. 40:499-507;
Schuldenfrei et al. (2011) BMC Genomics 12:549; Belton et al.
(2012) PloS One 7:e30034; Shah et al. (2012) PLoS One 7: e48533;
Mani et al. (2008) Cell 133:704-715). The first evidence linking
HMGA1 to EMT came from an important study in 2001 in MCF-7 breast
cancer cells, which demonstrated that forced expression of HMGA1
results in metastatic progression and histologic changes consistent
with EMT in the epithelial MCF-7 breast cancer cell line (Dolde et
al. (2002) Breast Cancer Research and Treatment 71:181-191). This
group also found that HMGA1 induces changes in classes of genes
involved in tumor progression. More recently, studies in colon
cancer showed that HMGA1 is required for tumor progression and stem
cell properties (Belton et al. (2012) PloS One 7:e30034). The
presently disclosed subject matter shows that HMGA1 is required for
mammosphere formation, including secondary and tertiary
mammospheres in MDA-MB-231 cells. It has also been found that
silencing HMGA1 depletes tumor initiator/cancer stem cells,
indicating that targeting HMGA1 in breast cancer therapy could have
an important impact on the cancer stem cell population, which is
believed to be the basis for refractory disease in diverse tumors.
These functional studies are corroborated by the HMGA1 signature
and pathway analysis demonstrating that HMGA1 orchestrates
transcriptional networks important in stem cells and metastatic
progression.
[0116] There is a dire need to understand the molecular
underpinnings of metastatic progression because this is the major
cause of death in patients with cancer. Although cancer is a highly
complex and heterogeneous disease, with significant heterogeneity
even within a single tumor, increasing evidence indicates that
common, central pathways exist that could serve as "Achilles heels"
or rational therapeutic targets in diverse tumors. The presently
disclosed subject matter underscores the fundamental role for HMGA1
in tumor progression in preclinical models for aggressive,
triple-negative breast cancers and provides compelling evidence
that HMGA1 is a master regulator in the evolution of primary tumors
to metastatic disease.
Example 2
[0117] The HMGA1 gene encodes the HMGA1a and HMGA1b chromatin
remodeling proteins, which regulate gene expression by altering
chromatin structure. HMGA1 plays a central role in the development
and progression of PDAC by acting as a master regulator of
transcriptional networks that maintain tumor cells in a refractory,
stem-like state (FIG. 8 and FIG. 9). It has been discovered that
HMGA1 is overexpressed in >90% of PDACs with absent levels in
precursor lesions and normal tissue. Moreover, previous work
demonstrates that high levels of HMGA1 protein correlate positively
with poor differentiation status and decreased survival. It was
also found that HMGA1 is required for reprogramming somatic cells
to induced pluripotent stem cells by the Yamanaka factors. In
addition, it was discovered that HMGA1 induces stem cell
transcriptional networks in cancer cells and normal stem cells.
Taken together, these studies suggest that HMGA1 drives poor
differentiation and metastatic progression in PDAC by inducing stem
cell genes. Previous studies indicate that knock-down of HMGA1
blocks oncogenic phenotypes in vitro and metastatic progression in
orthotopic murine models. Knock-down of HMGA1 also blocks cancer
stem cell properties and depletes cancer stem cells/tumor initiator
cells.
Results
[0118] Silencing HMGA1 with Short Hairpin RNA (shRNA) Reprograms
PDAC Cells:
[0119] HMGA1 and HMGA2 expression levels in different pancreatic
ductal adenocarcinoma cell (PDAC) lines are shown in FIG. 11. In
low-passage PDAC cells derived from patient tumors (lines 10.7,
10.05) or MiaPaCa2 commercial PDAC cell lines, it was discovered
that silencing HMGA1 using viral-mediated delivery of shRNA
drastically impairs cell growth (FIG. 10 and FIG. 12).
Surprisingly, there is also a dramatic change in morphology, with
fibroblast-like cells becoming cuboidal or epithelial-like,
consistent with a mesenchymal-epithelial transition, or MET (FIG.
11 and FIG. 14) Preliminary studies also show that colony
formation, migration, and invasion are disrupted in the HMGA1
knock-down cell. (FIG. 13 and FIG. 15B). In preliminary
experiments, xenograft tumor formation was inhibited in the HMGA1
shRNA cells. Strikingly, it was also found that silencing HMGA1
blocks stem cell properties, including 3-dimensional (3-D) sphere
formation in PDAC cells (FIG. 15C). HMGA1 knock-down also prevents
tumor formation following injection of reduced numbers of cells or
"limiting dilutions" in patient-derived PDAC cells; studies are
underway to more precisely calculate the frequency of
tumor-initiator cells in the control and wild type PDAC cells. This
latter finding indicates that the tumor initiator/cancer stem cells
(CSCs) are depleted in the HMGA1 knock-down cells. Similar findings
were observed in other cancer cells treated with shRNA targeting
HMGA1, including colorectal cancer (CRC) and leukemia cells (FIG.
16A, FIG. 16B and FIG. 16C). Tumorigenicity and additional
oncogenic assays are underway in PDAC cells. Gene expression
analysis is also planned to identify the molecular pathways that
are disrupted after silencing HMGA1.
[0120] Systemic Nanoparticle (NP) Plasmid Delivery of shRNA to
HMGA1:
[0121] The experiments shown herein demonstrate that silencing
HMGA1 in PDAC cells is an effective anti-tumor therapy. Innovative
NP platforms are being tested to systemically deliver shRNA plasmid
DNA in vivo in preclinical animal models. It was found that there
was a decrease in average tumor size in tumors treated with NP
delivery of plasmid DNA vectors encoding shRNA to target HMGA1 as
compared to control NPs (FIG. 17). On histologic examination,
necrosis appeared to be increased in the tumors treated with the
HMGA1-targeting vector (FIG. 18A and FIG. 18B).
Fluorescent-activated cell sorting (FACS) analysis following
injection of labeled DNA, however, showed that the plasmid was
delivered to only .about.5-30% of cells.
Discussion
[0122] Together, these results show that silencing HMGA1 reprograms
aggressive stem-like cancer cells into non stem-like cells with
slow growth and altered properties. Results demonstrated that
silencing HMGA1 has dramatic effects on tumor cell appearance,
proliferation and invasive properties. It was also found that
silencing HMGA1 prevents 3D sphere formation and depletes cancer
stem cells. Silencing HMGA1 also halts proliferation and blocks
hallmarks of aggressive PDA including self-renewal, migration,
invasion, and anchorage independent cell growth. It is expected
that nanoparticle delivery of specifically targeted RNA inhibitors
will function as viable therapeutic approaches to aggressive
neoplastic cancer. In addition, preliminary studies suggest that NP
delivery of plasmid DNA expressing shRNA to target HMGA1 can be
delivered to xenograft tumor cells and may impair growth.
REFERENCES
[0123] All publications, patent applications, patents, and other
references mentioned in the specification are indicative of the
level of those skilled in the art to which the presently disclosed
subject matter pertains. All publications, patent applications,
patents, and other references are herein incorporated by reference
to the same extent as if each individual publication, patent
application, patent, and other reference was specifically and
individually indicated to be incorporated by reference. It will be
understood that, although a number of patent applications, patents,
and other references are referred to herein, such reference does
not constitute an admission that any of these documents forms part
of the common general knowledge in the art.
[0124] Although the foregoing subject matter has been described in
some detail by way of illustration and example for purposes of
clarity of understanding, it will be understood by those skilled in
the art that certain changes and modifications can be practiced
within the scope of the appended claims.
Sequence CWU 1
1
1121DNAHomo sapiens 1caactccagg aaggaaacca a 21
* * * * *
References