U.S. patent application number 17/530402 was filed with the patent office on 2022-03-10 for compositions and methods for cancer expressing pde3a or slfn12.
This patent application is currently assigned to The Broad Institute, Inc.. The applicant listed for this patent is Bayer Pharma Aktiengesellschaft, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.. Invention is credited to Alex Burgin, Luc De Waal, Heidi Greulich, Matthew Meyerson, Ulrike Sack, Monica Schenone, Xiaoyun Wu.
Application Number | 20220071995 17/530402 |
Document ID | / |
Family ID | |
Filed Date | 2022-03-10 |
United States Patent
Application |
20220071995 |
Kind Code |
A1 |
De Waal; Luc ; et
al. |
March 10, 2022 |
COMPOSITIONS AND METHODS FOR CANCER EXPRESSING PDE3A OR SLFN12
Abstract
The present invention features improved methods of identifying
patients having cancer (e.g., melanoma, adenocarcinoma, lung,
cervical, liver or breast cancer) using biomarkers (e.g., PDE3A,
SLFN12) that correlate with drug sensitivity and consequently
treating a stratified patient population with an agent of the
invention (e.g., DNMDP, zardaverine, and anagrelide).
Inventors: |
De Waal; Luc; (Boston,
MA) ; Meyerson; Matthew; (Boston, MA) ;
Greulich; Heidi; (Boston, MA) ; Schenone; Monica;
(Cambridge, MA) ; Burgin; Alex; (Cambridge,
MA) ; Wu; Xiaoyun; (Cambridge, MA) ; Sack;
Ulrike; (Monheim Am Rhein, DE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Broad Institute, Inc.
Dana-Farber Cancer Institute, Inc.
Bayer Pharma Aktiengesellschaft |
Cambridge
Boston
Berlin |
MA
MA |
US
US
DE |
|
|
Assignee: |
The Broad Institute, Inc.
Cambridge
MA
Dana-Farber Cancer Institute, Inc.
Boston
MA
Bayer Pharma Aktiengesellschaft
Berlin
|
Appl. No.: |
17/530402 |
Filed: |
November 18, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15752130 |
Feb 12, 2018 |
11207320 |
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PCT/US2016/046912 |
Aug 12, 2016 |
|
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17530402 |
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62204875 |
Aug 13, 2015 |
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International
Class: |
A61K 31/50 20060101
A61K031/50; G01N 33/574 20060101 G01N033/574; A61P 35/00 20060101
A61P035/00; A61K 9/00 20060101 A61K009/00; A61K 31/519 20060101
A61K031/519 |
Goverment Interests
STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED
RESEARCH
[0002] This invention was made with Government support under Grant
No. 3U54HG005032 awarded by the National Institutes of Health. The
Government has certain rights in the invention.
Claims
1-3. (canceled)
4. A method of identifying a subject having a cancer cell
responsive to PDE3A modulation, the method comprising detecting an
increase in a PDE3A and/or SLFN12 polypeptide or polynucleotide
level in a biological sample of the subject relative to a
reference, thereby identifying said subject as having a cancer
responsive to PDE3A modulation.
5. A method of identifying a subject having a cancer that is
resistant to PDE3A modulation, the method comprising detecting a
decrease in the level of a SLFN12 polypeptide or polynucleotide
level in a biological sample of the subject relative to a
reference, thereby identifying said subject as having a cancer
resistant to PDE3A modulation.
6. The method of claim 4, wherein the level of PDE3A or SLFN12 is
detected by a method selected from the group consisting of
immunoblotting, mass spectrometry, and immunoprecipitation.
7. The method of claim 4, wherein the level of PDE3A or SLFN12
polynucleotide is detected by a method selected from the group
consisting of quantitative PCR, Northern Blot, microarray, mass
spectrometry, and in situ hybridization.
8. The method of claim 4, wherein the cancer cell is a melanoma,
endometrium, lung, hematopoetic/lymphoid, ovarian, cervical,
soft-tissue sarcoma, leiomyosarcoma, urinary tract, pancreas,
thyroid, kidney, glioblastoma, or breast cancer cell.
9. The method of claim 4, wherein the cancer cell is not a B-cell
proliferative type cancer.
10. The method of claim 4, wherein the cancer cell is not multiple
myeloma.
11-13. (canceled)
14. The method of claim 4, wherein the biological sample is a
tissue sample comprising a cancer cell.
15. A kit for identifying a subject having cancer responsive to
PDE3A modulation, the kit comprising a first capture reagent that
binds a PDE3A polypeptide or polynucleotide and a second capture
reagent that binds SLFN12 polypeptide or polynucleotide.
16. A kit for decreasing cancer cell proliferation in a subject
pre-selected as responsive to a PDE3A modulator, the kit comprising
an effective amount of DNMDP, zardaverine, and/or anagrelide, or a
pharmaceutically acceptable salt thereof.
17-18. (canceled)
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is the U.S. national phase application,
pursuant to 35 U.S.C. .sctn. 371, of PCT International Application
Serial No.: PCT/US2016/046912, filed Aug. 12, 2016, designating the
United States and published in English, which claims priority to
and the benefit of U.S. Provisional Application No. 62/204,875,
filed Aug. 13, 2015, the disclosure of which is incorporated herein
by reference in its entirety.
BACKGROUND OF THE INVENTION
[0003] Cancer kills over 550,000 people in the United States and
over 8 million people world-wide each year. New agents, including
small molecules, molecules that impact tissue-specific growth
requirements, and immunomodulatory agents, have been shown to
benefit a subset of patients whose cancers have unique genomic
mutations or other characteristics. Unfortunately, many cancer
patients are still left without effective therapeutic options.
[0004] One approach to identify new anti-cancer agents is
phenotypic screening to discover novel small molecules displaying
strong selectivity between cancer cell lines, followed by
chemogenomics to identify the cell features associated with drug
response. In the 1990s, Weinstein and colleagues demonstrated that
the cytotoxic profile of a compound can be used to identify
cellular characteristics, such as gene-expression profiles and DNA
copy number that correlate with drug sensitivity. The ability to
identify the features of cancer cell lines that mediate their
response to small molecules has strongly increased in recent years
with automated high-throughput chemosensitivity testing of large
panels of cell lines coupled with comprehensive genomic and
phenotypic characterization of the cell lines. Phenotypic
observations of small-molecule sensitivity can be linked to
expression patterns or somatic alterations, as in the case of
SLFN11 expression in cancer cell lines sensitive to irinotecan
treatment, and an EWS-FLI1 rearrangement in cancer cell lines
sensitive to PARP inhibitors, respectively.
[0005] Methods of characterizing malignancies at a molecular level
are useful for stratifying patients, thereby quickly directing them
to effective therapies. Improved methods for characterizing the
responsiveness of subjects having cancer are urgently required.
SUMMARY OF THE INVENTION
[0006] As described below, the present invention features methods
of identifying patients having a cancer (e.g., melanoma,
adenocarcinoma, lung, cervical, liver, endometrium, lung,
hematopoetic/lymphoid, ovarian, cervical, soft-tissue sarcoma,
leiomyosarcoma, urinary tract, pancreas, thyroid, kidney,
glioblastoma, or breast cancer) that is sensitive to treatment with
a phosphodiesterase 3A (PDF-3A) modulator (e.g.,
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e, zardaverine, and anagrelide) by detecting co-expression of PDE3A
and Schlafen 12 (SLFN12) polynucleotides or polypeptides in a
cancer cell derived from such patients.
[0007] In one embodiment, the present invention provides a method
of killing or reducing the survival of a cancer cell selected as
responsive to a phosphodiesterase 3A (PDE3A) modulator. The method
includes the step of contacting the cell with a PDE3A modulator,
where the cell was selected as having an increase in PDE3A and/or
Schlafen 12 (SLFN12) polypeptide or polynucleotide relative to a
reference, thereby reducing the survival of the cancer cell. In
another embodiment, the present invention provides a method of
reducing cancer cell proliferation in a subject pre-selected as
having a cancer that is responsive to a PDE3A modulator. The method
comprises administering to the subject a PDE3A modulator, wherein
the subject is pre-selected by detecting an increase in PDE3A
and/or SLFN12 polypeptide or polynucleotide levels relative to a
reference, thereby reducing cancer cell proliferation in the
subject. In one embodiment, the subject is pre-selected by
detecting an increase in PDE3A and/or SLFN12 polypeptide or
polynucleotide levels. In some embodiments, the PDE3A modulator is
selected from the group consisting of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP), zardaverine, and anagrelide.
[0008] In another embodiment, the present invention provides a
method of identifying a subject having a cancer responsive to PDE3A
modulation. The method includes the step of detecting an increase
in the level of a PDE3A and/or SLFN12 polypeptide or polynucleotide
in a biological sample of the subject relative to a reference,
thereby identifying the subject as responsive to PDE3A modulation.
In one embodiment, an increase in the level of PDE3A and SFLN1
polypeptide or polynucleotide is detected.
[0009] In some embodiments, the increase in the level of PDE3A
and/or SLFN12 polypeptide is detected by a method selected from the
group consisting of immunoblotting, mass spectrometry, and
immunoprecipitation. In some other embodiments, the increase in the
level of PDE3A, and/or SLFN12 polynucleotide is detected by a
method selected from the group consisting of quantitative PCR,
Northern Blot, microarray, mass spectrometry, and in situ
hybridization. In some embodiments, the activity of PDE3A is
reduced. The PDE3A modulator may be administered orally. The PDE3A
modulator may be administered by intravenous injection.
[0010] In some embodiments, the cancer cell is a melanoma,
endometrium, lung, hematopoetic/lymphoid, ovarian, cervical,
soft-tissue sarcoma, leiomyosarcoma, urinary tract, pancreas,
thyroid, kidney, glioblastoma, or breast cancer. In some other
embodiments, the cancer cell is not a B-cell proliferative type
cancer. In some embodiments, the cancer cell is not multiple
myeloma. In some embodiments, the biological sample is a tissue
sample.
[0011] In another aspect, the present invention provides a kit for
identifying a subject having cancer as responsive to PD3A
modulation, the kit comprising a capture reagent that binds PDE3A
and/or a capture reagent that binds SLFN12. In one embodiment, the
kit comprises a capture reagent that binds PDE3A and a capture
reagent that binds SLFN12.
[0012] In yet another aspect, the present invention provides a kit
for decreasing cancer cell proliferation in a subject pre-selected
as responsive to a PDE3A modulator, the kit comprising DNMDP,
zardaverine, and/or anagrelide.
[0013] The invention provides methods for treating subjects having
cancer identified as responsive to treatment with a PDE3A modulator
by detecting co-expression of PDE3A and/or Schlafen 12 (SLFN12)
polynucleotides or polypeptides in the cancer. Compositions and
articles defined by the invention were isolated or otherwise
manufactured in connection with the examples provided below. Other
features and advantages of the invention will be apparent from the
detailed description, and from the claims.
Definitions
[0014] Unless defined otherwise, all technical and scientific terms
used herein have the meaning commonly understood by a person
skilled in the art to which this invention belongs. The following
references provide one of skill with a general definition of many
of the terms used in this invention: Singleton et al., Dictionary
of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge
Dictionary of Science and Technology (Walker ed., 1988); The
Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer
Verlag (1991); and Hale & Marham, The Harper Collins Dictionary
of Biology (1991). As used herein, the following terms have the
meanings ascribed to them below, unless specified otherwise.
[0015] By "Anagrelide" (IUPAC Name 6,7-dichloro-1,5-dihydroimidazo
(2,1-b)quinazolin-2(3H)-one) is meant a small molecule
phosphodiesterase inhibitor having the following structure:
##STR00001##
[0016] By "Cilostamide" (IUPAC Name
N-cyclohexyl-N-methyl-4-[(2-oxo-1H-quinolin-6-yl)oxy]butanamide) is
meant a small molecule inhibitor having the following
structure:
##STR00002##
[0017] By "Cilostazol" (IUPAC Name
6-[4-(1-cyclohexyl-1H-tetrazol-5-yl)butoxy]-3,4-dihydro-2(1H)-quinolinone-
) is meant a small molecule inhibitor having the following
structure:
##STR00003##
[0018] By "DNDMP" (IUPAC Name
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e) is meant a small molecule inhibitor having the following
structure:
##STR00004##
[0019] By "Forskolin" (IUPAC Name
(3R,4aR,5S,6S,6aS,10S,10aR,10bS)-6,10,10b-Trihydroxy-3,4a,7,7,10a-pentame-
thyl-1-oxo-3-vinyldodecahydro-1H-benzo[f]chromen-5-ylacetate) is
meant a small molecule inhibitor having the following
structure:
##STR00005##
[0020] By "Levosimendan" (IUPAC Name
(E)-2-cyano-1-methyl-3-(4-(4-methyl-6-oxo-1,4,5,6-tetrahydropyridazin-3-y-
l)phenyl)guanidine) is meant a small molecule inhibitor having the
following structure:
##STR00006##
[0021] By "Milrinone" (IUPAC Name
2-methyl-6-oxo-1,6-dihydro-3,4'-bipyridine-5-carbonitrile) is meant
a small molecule inhibitor having the following structure:
##STR00007##
[0022] By "Papaverine" (IUPAC Name
1-(3,4-dimethoxybenzyl)-6,7-dimethoxyisoquinoline) is meant a small
molecule inhibitor having the following structure:
##STR00008##
[0023] By "Siguazodan" (IUPAC Name
(E)-2-cyano-1-methyl-3-(4-(4-methyl-6-oxo-1,4,5,6-tetrahydropyridazin-3-y-
l)phenyl)guanidine) is meant a small molecule inhibitor having the
following structure:
##STR00009##
[0024] By "Sildenafil" (IUPAC Name
1-[4-ethoxy-3-(6,7-dihydro-1-methyl-7-oxo-3-propyl-1H-pyrazolo[4,3-d]pyri-
midin-5-yl)phenylsulfonyl]-4-methylpiperazine) is meant a small
molecule inhibitor having the following structure:
##STR00010##
[0025] By "Trequinsin" (IUPAC Name
9,10-dimethoxy-3-methyl-2-(2,4,6-trimethylphenyl)imino-6,7-dihydropyrimid-
o[6,1-a]isoquinolin-4-one) is meant a small molecule inhibitor
having the following structure:
##STR00011##
[0026] By "Vardenifil" (IUPAC Name
4-[2-ethoxy-5-(4-ethylpiperazin-1-yl)sulfonyl-phenyl]-9-methyl-7-propyl-3-
,5,6,8-tetrazabicyclo[4.3.0]nona-3,7,9-trien-2-one) is meant a
small molecule inhibitor having the following structure:
##STR00012##
[0027] By "Zardaverine (IUPAC Name
3-[4-(Difluoromethoxy)-3-methoxyphenyl]-1H-pyridazin-6-one)" is
meant a small molecule inhibitor having the following
structure:
##STR00013##
[0028] In some other embodiments, any one of the compounds
Cilostamide, Cilostazol, DNDMP, Levosimendan, Milrinone,
Papaverine, Siguazodan, Sildenafil, Trequinsin, Vardenifil, and
Zardaverine is a small molecule phosphodiesterase inhibitor. In
another embodiment, forskolin may be used in a method of the
invention.
[0029] By "PDE3A polypeptide" is meant a protein or fragment
thereof having at least 85% amino acid sequence identity to the
sequence provided at NCBI Ref No. NP_000912.3 that catalyzes the
hydrolysis of cyclic adenosine monophosphate (cAMP) and cyclic
guanosine monophosphate (cGMP). An exemplary human full-length
PDE3A amino acid sequence is provided below:
TABLE-US-00001 (SEQ ID NO.: 3)
MAVPGDAARVRDKPVHSGVSQAPTAGRDCHHRADPASPRDSGCRGCWGDtV
LQPLRSSRKLSSALCAGSLSFLLALLVRLVRGEVGCDLEQCKEAAAAEEEE
AAPGAEGGVFPGPRGGAPGGGARLSPWLQPSALLFSLLCAFFWMGLYLLRA
GVRLPLAVALLAACCGGEALVQIGLGVGEDHLLSLPAAGVVLSCLAAATWL
VLRLRLGVLMIALTSAVRTVSLISLERFKVAWRPYLAYLAGVLGILLARYV
EQILPQSAEAAPREHLGSQLIAGTKEDIPVFKRRRRSSSVVSAEMSGCSSK
SHRRTSLPCIPREQLMGHSEWDHKRGPRGSQSSGTSITVDIAVMGEAHGLI
TDLLADPSLPPNVCTSLRAVSNLLSTQLTFQAIHKPRVNPVTSLSENYTCS
DSEESSEKDKLAIPKRLRRSLPPGLLRRVSSTWTTTTSATGLPTLEPAPVR
RDRSTSIKLQEAPSSSPDSWNNPVMMTLTKSRSFTSSYAISAANHVKAKKQ
SRPGALAKISPLSSPCSSPLQGTPASSLVSKISAVQFPESADTTAKQSLGS
HRALTYTQSAPDLSPQILTPPVICSSCGRPYSQGNPADEPLERSGVATRTP
SRTDDTAQVTSDYETNNNSDSSDIVQNEDETECLREPLRKASACSTYAPET
MMFLDKPILAPEPLVMDNLDSIMEQLNTWNFPIFDLVENIGRKCGRILSQV
SYRLFEDMGLFEAFKIPIREFMNYFHALEIGYRDIPYHNRIHATDVLHAVW
YLTTQPIPGLSTVINDHGSTSDSDSDSGFTHGHMGYVFSKTYNVTDDKYGC
LSGNIPALSLMALYVAAAMHDYDHPGRTNAFLVATSAPQAVLYNDRSVLEN
HHAAAAWNLFMSRPEYNFLINLDHVEFKHFRELVIEAILATDLKKHFDFVA
KFNGKVNDDVGIDWTNENDRLLVCQMCIKLADINGPAKCKELHLQWTDGIV
NEFYEQGDEEASLGLPISPFMDRSAPQLANLQESFISHIVGPLCNSYDSAG
LMPGKWVEDSDESGDTDDPEEEEEEAPAPNEEETCENNESPKKKTFKRRKI
YCQITQHLLQNHKMWKKVIEEEQRLAGIENQSLDQTPQSHSSEQIQAIKEE
EEEKGKPRGEEIPTQKPDQ
Three PDE3A isoforms are known: PDE3A1, PDE3A2, and PDE3A3. PDE3A1
comprises amino acids 146-1141, PDE3A2 isoform 2 comprises amino
acids 299-1141, and PDE3A3 comprises amino acids 483-1141 of the
full-length PDE3A amino acid sequence.
[0030] By "PDE3A polynucleotide" is meant any nucleic acid
molecule, including DNA and RNA, encoding a PDE3A polypeptide or
fragment thereof. An exemplary PDE3A nucleic acid sequence is
provided at NCBI Ref: NM 000921.4:
TABLE-US-00002 (SEQ ID NO.: 4) 1 gggggccact gggaattcag tgaagagggc
accctatacc atggcagtgc ccggcgacgc 61 tgcacgagtc agggacaagc
ccgtccacag tggggtgagt caagccccca cggcgggccg 121 ggactgccac
catcgtgcgg accccgcatc gccgcgggac tcgggctgcc gtggctgctg 181
gggagacctg gtgctgcagc cgctccggag ctctcggaaa ctttcctccg cgctgtgcgc
241 gggctccctg tcctttctgc tggcgctgct ggtgaggctg gtccgcgggg
aggtcggctg 301 tgacctggag cagtgtaagg aggcggcggc ggcggaggag
gaggaagcag ccccgggagc 361 agaagggggc gtattccagg ggcctcgggg
aggtgctccc gggggcggtg cgcggctcag 421 ccccCggctg cagccctcgg
cgctgctctt cagtctcctg tgtgccttct tctggatggg 481 cttgtacctc
ctgcgcgccg gggtgcgcct gcctctggct gtcgcgctgc tggccgcctg 541
ctgcgggggg gaagcgctcg tccagattgg gctgggcgtc ggggaggatc acttactctc
601 actccccgcc gcgggggtgg tgctcagctg cttggccgcc gcgacatggc
tggtgctgag 661 gctgaggctg ggcgtcctca tgatcgcctt gactagcgcg
gtcaggaccg tgtccctcat 721 ttccttagag aggttcaagg tcgcctggag
accttacctg gcgtacctgg ccggcgtgct 781 ggggatcctc ttggccaggt
acgtggaaca aatcttgccg cagtccgcgg aggcggctcc 841 aagggagcat
ttggggtccc agctgattgc tgggaccaag gaagatatcc cggtgtttaa 901
gaggaggagg cggtccagct ccgtcgtgtc cgccgagatg tccggctgca gcagcaagtc
961 ccatcggagg acctccctgc cctgtatacc gagggaacag ctcatggggc
attcagaatg 1021 ggaccacaaa cgagggccaa gaggatcaca gtcttcagga
accagtatta ctgtggacat 1081 cgccgtcatg ggcgaggccc acggcctcat
taccgacctc ctggcagacc cttctcttcc 1141 accaaacgtg tgcacatcct
tgagagccgt gagcaacttg ctcagcacac agctcacctt 1201 ccaggccatt
cacaagccca gagtgaatcc cgtcacttcg ctcagtgaaa actatacctg 1261
ttctgactct gaagagagct ctgaaaaaga caagcttgct attccaaagc gcctgagaag
1321 gagtttgcct cctggcttgt tgagacgagt ttcttccact tggaccacca
ccacctcggc 1381 cacaggtcta cccaccttgg agcctgcacc agtacggaga
gaccgcagca ccagcatcaa 1441 actgcaggaa gcaccttcat ccagtcctga
ttcttggaat aatccagtga tgatgaccct 1501 caccaaaagc agatccttta
cttcatccta tgctatttct gcagctaacc atgtaaaggc 1541 taaaaagcaa
agtcgaccag gtgccctcgc taaaatttca cctctttcat cgccctgctc 1621
ctcacctctc caagggactc ctgccagcag cctggtcagc aaaatttctg cagtgcagtt
1681 tccagaatct gctgacacaa ctgccaaaca aagcctaggt tctcacaggg
ccttaactta 1741 cactcagagt gccccagacc tatccectca aatcctgact
ccacctgtta tatgtagcag 1801 ctgtggcaga ccatattccc aagggaatcc
tgctgatgag cccctggaga gaagtggggt 1861 agccactcgg acaccaagta
gaacagatga cactgctcaa gttacctctg attatgaaac 1921 caataacaac
agtgacagca gtgacattgt acagaatgaa gatgaaacag agtgcctgag 1981
agagcctctg aggaaagcat cggcttgcag cacctatgct cctgagacca tgatgtttct
2041 ggacaaacca attcttgctc ccgaacctct tgtcatggat aacctggact
caattatgga 2101 gcagctaaat acttggaatt ttccaatttt tgatttagtg
gaaaatatag gaagaaaatg 2161 tggccgtatt cttagtcagg tatcttacag
actttttgaa gacatgggcc tctttgaagc 2221 ttttaaaatt ccaattaggg
aatttatgaa ttattttcat gctttggaga ttggatatag 2281 ggatattcct
tatcataaca gaatccatgc cactgatgtt ttacatgctg tttggtatct 2341
tactacacag cctattccag gcctctcaac tgtgattaat gatcatggtt caaccagtga
2401 ttcagattct gacagtggat ttacacatgg acatatggga tatgtattct
caaaaacgta 2461 taatgtgaca gatgataaat acggatgtct gtctgggaat
atccctgcct tggagttgat 2521 ggcgctgtat gtggctgcag ccatgCacga
ttatgatcat ccaggaagga ctaatgcttt 2581 cctggttgca actagtgctc
ctcaggcggt gctatataac gatcgttcag ttttggagaa 2641 tcatcacgca
gctgctgcat ggaatctttt catgtcccgg ccagagtata acttcttaat 2701
taaccttgac catgtggaat ttaagcattt ccgtttcctt gtcattgaag caattttggc
2761 cactgacctg aagaaacact ttgacttcgt agccaaattt aatggcaagg
taaatgatga 2821 tgttggaata gattggacca atgaaaatga tcgtctactg
gtttgtcaaa tgtgtataaa 2881 gttggctgat atcaatggtc cagctaaatg
taaagaactc catcttcagt ggacagatgg 2941 tattgtcaat gaattttatg
aacagggtga tgaagaggcc agccttggat tacccataag 3001 ccccttcatg
gatcgttctg ctcctcagct ggccaacctt caggaatcct tcatctctca 3061
cattgtgggg cctctgtgca actcctatga ttcagcagga ctaatgcctg gaaaatgggt
3121 ggaaganagc gatgagtcag gagatactga tgacccagaa gaagaggagg
aagaagcacc 3181 agcaccaaat gaagaggaaa cctgtgaaaa taatgaatct
ccaaaaaaga agactttcaa 3241 aaggagaaaa atctactgcc aaataactca
gcacctctta cagaaccaca agatgtggaa 3301 gaaagtcatt gaagaggagc
aacggttggc aggcatagaa aatcaatccc tggaccagac 3361 ccctcagtcg
cactcttcag aacagatcca ggctatcaag gaagaagaag aagagaaagg 3421
gaaaccaaga ggcgaggaga taccaaccca aaagccagac cagtgacaat ggatagaatg
3481 ggctgtgttt ccaaacagat tgacttgtca aagactctct tcaagccagc
acaacattta 3541 gacacaacac tgtagaaatt tgagatgggc aaatggctat
tgcattttgg gattcttcgc 3601 attttgtgtg tatattttta cagtgaggta
cattgttaaa aactttttgc tcaaagaagc 3661 tttcacattg caacaccagc
ttctaaggat tttttaagga gggaatatat atgtgtgtgt 3721 gtatataagc
tcccacatag atacatgtaa aacatattca cacccatgca cgcacacaca 3781
tacacactga aggccacgat tgctggctcc acaatttagt aacatttata ttaagatata
3841 tatatagtgg tcactgtgat ataataaatc ataaaggaaa ccaaatcaca
aaggagatgg 3901 tgtggcttag caaggaaaca gtgcaggaaa tgtaggttac
caactaagca gcttttgctc 3961 ttagtactga gggatgaaag ttccagagca
ttatttgaat tctgatacat cctgccaaca 4021 ctgtgtgtgt gtgtgtgtgt
gtgtgtgtgt gtgtgtgtgt gtgtgaaaga gagacagaag 4081 ggaatggttt
gagagggtgc ttgtgtgcat gtgtgtgcat atgtaaagag atttttgtgg 4141
tttaagtaac tcagaatagc tgtagcaaat gactgaatac atgtgaacaa acagaaggaa
4201 gttcactctg gagtgtcttt gggaggcagc cattccaaat gccctcctcc
atttagcttc 4261 aataaagggc cttttgctga tggagggcac tcaagggctg
ggtgagaggg ccacgtgttt 4321 ggtattacat tactgctatg caccacttga
aggagctcta tcaccagcct caaacccgaa 4381 agactgaggc attttccagt
ctacttgcct aatgaatgta taggaactgt ctatgagtat 4441 ggatgtcact
caactaagat caaatcacca tttaagggga tggcattctt tatacctaaa 4501
cacctaagag ctgaagtcag gtcttttaat caggttagaa ttctaaatga tgccagagaa
4561 ggcttgggaa attgtaCttc agCgtgatag Cctgtgtett cttaatttgc
tgcaaaatat 4621 gtggtagaga aagaaaagga aacagaaaaa tcactctggg
ttatatagca agagatgaag 4681 gagaatattt caacacaggg tttttgtgtt
gacataggaa aagcctgatt cttggcaact 4741 gttgtagttt gtctttcagg
ggtgaaggtc ccactgacaa cccctgttgt ggtgttccac 4801 acgctgtttg
ttggggtagc ttccatcggc agtctggccc attgtcagtc atgcttcttc 4861
tggccgggga gattatagag agattgtttg aagattgggt tattattgaa agtctttttt
4921 tttgtttgtt ttgttttggt ttgtttgttt atctacactt gtttatgctg
tgagccaaac 4981 ctctatttaa aaagttgata ctcactttca atattttatt
tcatattatt atatatgtca 5041 tgatagttat cttgatgtaa atabgaagat
ttttttgttt ctgtagatag taaactcttt 5101 ttttaaaaaa ggaaaaggga
aacattttta taaagttata ttttaatcac catttttata 5161 cattgtagtt
ctctccaagc ccagtaagag aatgatgatt catttgcatg gaggtcgatg 5221
gacaaccaat catctacctt ttctaattta aatgataatc tgatatagtt ttattgccag
5281 ttaaatgagg atgctgcaaa gcatgttttt tcactagtaa cttttgctaa
ctgaatgaat 5341 tctgggtcca tatctcccag atgaaaaact gttaaccaat
accatatttt atagttggtg 5401 tccatttctt tccaacantg tttgttatga
ttcttccttg agtacttata tacagacctg 5461 ctcattatct aaacaatctt
accttctaag taaaccttga ttgtgatttc cagtttttat 5521 tttctctgac
gtagtagaaa ggaatgttta cattaaaaat acttttgttt ctcataaatg 5581
gatattgtac tccccccttt caaagcatta ttttacaata attcatggca ttttaaaaaa
5641 taaggcaaag ataatacgac aaaaaatata catggtttca aggcaaattc
tccaataagt 5701 tggaaaatgt aaaaaggatc aagtggatgc agcctctacc
taaataatta aaatatattt 5761 cagtatattt ctgaattaac accaggtctt
cattatttag aacttactaa attgttttca 5821 ttttcttagt tttacctgtg
tatctccatg tttgcaaaaa ttactataag tcaaattttg 5881 ccagtgaatt
taactatttt tctttccttg caattaaggg gaaaaaagca tttatcttat 5941
cttctcatac cccttgcatc taagtactta gcaaagtcaa tattttccca ttttccaaat
6001 gcgtccatct ctaacataaa tattaattga acatagagct atgtttggag
tgagtggact 6061 ggcaggacag ttggaagtcc atcacagtct attgacagtt
tcatcaaagc tgtataytcc 6121 aactagtggg gcagcttggc tactatggtg
gaagtctcag caaactgcct ggttttgttt 6181 gtttgttttg ttttaaggta
caggaaataa gaggaataat agtggccaaa gcaattagaa 6241 catcttcatt
ccagaactgt gttcagcaat ccaggcagat tgatacattt ttctttaaaa 6301
ataaattgct attacagcta gacgtcaatt gggataaata aagggatgaa gatccactaa
6361 gtttgtgact ttcatacaca cccagtacat ctcaaaggat gctaagggac
attttctgcc 6421 agtagagttc tccccctttt tggtgacagc aatattatta
tgttcacatc taactccaga 6481 gcttacttcc tgtggtgcca atgtatttgt
tgcaatttac tacattttta tatgagccta 6541 tttataggtg ccattaaact
caggtctttc aaatgaaaga gtttctagcc cacttaggga 6601 aaaagataat
tgtttagaaa accataaaat caatggtagg aaaagttgga actggttacc 6661
tggatgccat ggttctctgt taaataaagt aagagaccag gtgtattctg agtgtcatca
6721 gtgttatttt cagcatgcta ataaatgtct ttccggttat atatctatct
aaattaacct 6781 ttaaaatatt ggtttccttg ataaaagcac cacttttgct
tttgttagct gtaatatttt 6841 ttgtcattta gataagacct ggtttggctc
tcaataaaag atgaagacag tagctctgta 6901 cagggatata tctatattag
tcttcatctg atgaatgaag aaattttctc atattatgtt 6961 caagaaagta
tttacttcct aaaaatagaa ttcccgattc tgtctatttt ggttgaatac 7021
cagaacaaat ctttccgttg caatcccagt aaaacgaaag aaaaggaata tcttacagac
7081 tgttcatatt agatgtatgt agactgttaa tttgcaattt ccccatattt
cctgcctatc 7141 ttacccagat aactttettt gaaggtaaaa gctgtgcaaa
aggcatgaga ctcaggccta 7201 ctctttgttt aaatgatgga aaaatataaa
ttattttcta agtaataaaa gtataaaaat 7261 tatcattata aataaagtct
aaagtttgaa attattaatt taaaaaaaaa aaaaaaaaa
[0031] By "Schlafen 12 (SLFN12) polypeptide" is meant a protein or
fragment thereof having at least 85% amino acid sequence identity
to the sequence provided at NCBI Ref No. NP_060512.3 that interacts
with PDE3A when bound to anagrelide, zardaverine or DNMDP and
related compounds. An exemplary human SLFN12 amino acid sequence is
provided below:
TABLE-US-00003 (SEQ ID NO: 5)
MNISVDLETNYAELVLDVGRVTLGENSRKKMKDCKLRKKQNESVSRAMCAL
LNSGGGVIKAEIENEDYSYTKDGIGLDLENSFSNILLFVPEYLDFMQNGNY
FLIFVKSWSLNTSGLRITTLSSNLYKRDITSAKVMNATAALEFLKDMKKTR
GRLYLRPELLAKRPCVDIQEENNMKALAGVFFDRTELDRKEKLTFTESTHV
EIKNFSTEKLLQRIKETLPQYVSAFANTDGGYLFIGLNEDKEIIGFKAEMS
DLDDLEREIEKSIRKMPVHHFCMEKKKTNYSCKELGVYDKGSLCGYVCALR
VERFCCAVFAKEPDSWHVKDNRVMQLTRKEWIQFMVEAEPKFSSSYEEVIS
QINTSLPAPHSWPLLEWQRQRHHCPGLSGRITYTPENLCRKLFLQHEGLKQ
LICEEMDSVRKGSLIFSRSWSVDLGLQENHKVLCDALLISQDSPPVLYTFH
MVQDERFKGYSTQTALTLKQKLAKTGGYTKKVCVMTKIFYLSPEGMTSCQY
DLRSQVTYPRSYYFTRRKYLLKALFKALKRLKSLRDQFSFAENLYQIIGID
CFQKNDKKMFKSCRRLT
[0032] By "Schlafen 12 (SLFN12) polynucleotide" is meant any
nucleic acid molecule, including DNA and RNA, encoding a SLFN12
polypeptide or fragment thereof. An exemplary SLFN12 nucleic acid
sequence is provided at NCBI Ref: NM_018042.4:
TABLE-US-00004 (SEQ ID NO.: 6) 1 tttgtaactt cacttcagcc tcccattgat
cgctttctgc aaccattcag actgatctcg 61 ggctcctatt tcatttacat
tgtgtgcaca ccaagtaacc agtgggaaaa ctttagaggg 121 tacttaaacc
ccagaaaatt ctgaaaccgg gctcttgagc cgctatcctc gggcctgctc 181
ccaccctgtg gagtgcactt tcgttttcaa taaatctctg cttttgttgc ttcattcttt
241 ccttgctttg tttgtgtgtt tgtccagttc tttgttcaac acgccaagaa
cctggacact 301 cttcactggt aacatatttt ggcaagccaa ccaggagaaa
agaatttctg cttggacact 361 gcatagctgc tgggaaaatg aacatcagtg
ttgatttgga aacgaattat gccgagttgg 421 ttctagatgt gggaagagtc
actcttggag agaacagtag gaaaaaaatg aaggattgta 481 aactgagaaa
aaagcagaat gaaagtgtct cacgagctat gtgtgctctg ctcaattctg 541
gagggggagt gatcaaggct gaaattgaga atgaagacta tagttataca aaagatggaa
601 taggactaga tttggaaaat tcttttagta acattctgtt atttgttcct
gagtacttag 661 acttcatgca gaatggtaac tactttctga tttttgtgaa
gtcatggagc ttgaacacct 721 ctggtctgcg gattaccacc ttgagctcca
atttgtacaa aagagatata acatctgcaa 781 aagtcatgaa tgccactgct
gcactggagt tcctcaaaga catgaaaaag actagaggga 841 gattgtattt
aagaccagaa ttgctggcaa agaggccctg tgttgatata caagaagaaa 901
ataacatgaa ggccttggcc ggggtttttt ttgatagaac agaacttgat cggaaagaaa
961 aattgacctt tactgaatcc acacatgttg aaattaaaaa cttctcgaca
gaaaagttgt 1021 tacaacgaat taaagagatt ctccctcaat atgtttctgc
atttgcaaat actgatggag 1081 gatatttgtt cattggttta aatgaagata
aagaaataat tggctttaaa gcagagatga 1141 gtgacctcga tgacttagaa
agagaaatcg aaaagtccat taggaagatg cctgtgcatc 1201 acttctgtat
ggagaagaag aagataaatt attcatgcaa attccttgga gtatatgata 1261
aaggaagtct ttgtggatat gtctgtgcac tcagagtgga gcgcttctgc tgtgcagtgt
1321 ttgctaaaga gcctgattcc tggcatgtga aagataaccg tgtgatgcag
ttgaccagga 1381 aggaatggat ccagttcatg gtggaggctg aaccaaaatt
ttccagttca tatgaagagg 1441 tgatctctca aataaatacg tcattacctg
ctcoccacag ttggcctctt ttggaatggc 1501 aacggcagag acatcactgt
ccagggctat caggaaggat aacgtatact ccagaaaacc 1561 tttgcagaaa
actgttctta caacatgaag gacttaagca attaatatgt gaagaaatgg 1621
actctgtcag aaagggctca ctgatcttct ctaggagctg gtctgtggat ctgggcttgc
1681 aagagaacca caaagtcctc tgtgatgctc ttctgatttc ccaggacagt
cctccagtcc 1741 tatacacctt ccacatggta caggatgagg agtttaaagg
ctattctaca caaactgccc 1801 taaccttaaa gcagaagctg gcaaaaattg
gtggttacac taaaaaagtg tgtgtcatga 1861 caaagatctt ctacttgagc
cctgaaggca tgacaagctg ccagtatgat ttaaggtcgc 1921 aagtaattta
ccctgaatcc tactatttta caagaaggaa atacttgctg aaagcccttt 1981
ttaaagcctt aaagagactc aagtctctga gagaccagtt ttcctttgca gaaaatctat
2041 accagataat cggtatagat tgctttcaga agaatgataa aaagatgttt
aaatcttgtc 2101 gaaggctcac ctgatggaaa atggactggg ctactgagat
atttttcatt atatatttga 2161 taacattctc taattctgtg aaaatatttc
tttgaaaact ttgcaagtta agcaacttaa 2221 tgtgatgttg gataattggg
ttttgtctat tttcacttct ccctaaataa tcttcacaga 2281 tattgtttga
gggatattag gaaaattaat ttgttaactc gtctgtgcac agtattattt 2341
actctgtctg tagttcctga ataaattttc ttccatgctt gaactgggaa aattgcaaca
2401 cttttattct taatgacaac agtgaaaatc tcccagcata tacctagaaa
acaattataa 2461 cttacaaaag attatccttg atgaaactca gaatttccac
agtgggaatg aataagaagg 2521 caaaactcat
[0033] In some aspects, the compound is an isomer. "Isomers" are
different compounds that have the same molecular formula.
"Stereoisomers" are isomers that differ only in the way the atoms
are arranged in space. As used herein, the term "isomer" includes
any and all geometric isomers and stereoisomers, for example,
"isomers" include geometric double bond cis- and trans-isomers,
also termed E- and Z-isomers; R- and S-enantiomers; diastereomers,
(d)-isomers and (l)-isomers, racemic mixtures thereof; and other
mixtures thereof, as falling within the scope of this
invention.
[0034] Geometric isomers can be represented by the symbol which
denotes a bond that can be a single, double or triple bond as
described herein. Provided herein are various geometric isomers and
mixtures thereof resulting from the arrangement of substituents
around a carbon-carbon double bond or arrangement of substituents
around a carbocyclic ring. Substituents around a carbon-carbon
double bond are designated as being in the "Z" or "E" configuration
wherein the terms "Z" and "E" are used in accordance with IUPAC.
standards. Unless otherwise specified, structures depicting double
bonds encompass both the "E" and "Z" isomers.
[0035] Substituents around a carbon-carbon double bond
alternatively can be referred to as "cis" or "trans," where "cis"
represents substituents on the same side of the double bond and
"trans" represents substituents on opposite sides of the double
bond. The arrangement of substituents around a carbocyclic ring can
also be designated as "cis" or "trans." The term "cis" represents
substituents on the same side of the plane of the ring, and the
term "trans" represents substituents on opposite sides of the plane
of the ring. Mixtures of compounds wherein the substituents are
disposed on both the same and opposite sides of plane of the ring
are designated "cis/trans."
[0036] The term "enantiomers" refers to a pair of stereoisomers
that are non-superimposable mirror images of each other. An atom
having an asymmetric set of substituents can give rise to an
enantiomer. A mixture of a pair of enantiomers in any proportion
can be known as a "racemic" mixture. The term "(.+-.)" is used to
designate a racemic mixture where appropriate. "Diastereoisomers"
are stereoisomers that have at least two asymmetric atoms, but
which are not mirror-images of each other. The absolute
stereochemistry is specified according to the Cahn-Ingold-Prelog
R-S system. When a compound is an enantiomer, the stereochemistry
at each chiral carbon can be specified by either R or S. Resolved
compounds whose absolute configuration is unknown can be designated
(+) or (-) depending on the direction (dextro- or levorotatory)
which they rotate plane polarized light at the wavelength of the
sodium D line. Certain of the compounds described herein contain
one or more asymmetric centers and can thus give rise to
enantiomers, diastereomers, and other stereoisomeric forms that can
be defined, in terms of absolute stereochemistry at each asymmetric
atom, as (R)- or (S)-. The present chemical entities,
pharmaceutical compositions and methods are meant to include all
such possible isomers, including racemic mixtures, optically
substantially pure forms and intermediate mixtures.
[0037] Optically active (R)- and (S)-isomers can be prepared, for
example, using chiral synthons or chiral reagents, or resolved
using conventional techniques. Enantiomers can be isolated from
racemic mixtures by any method known to those skilled in the art,
including chiral high pressure liquid chromatography (HPLC), the
formation and crystallization of chiral salts, or prepared by
asymmetric syntheses.
[0038] Optical isomers can be obtained by resolution of the racemic
mixtures according to conventional processes, e.g., by formation of
diastereoisomeric salts, by treatment with an optically active acid
or base. Examples of appropriate acids are tartaric,
diacetyltartaric, dibenzoyltartaric, ditoluoyltartaric, and
camphorsulfonic acid. The separation of the mixture of
diastereoisomers by crystallization followed by liberation of the
optically active bases from these salts affords separation of the
isomers. Another method involves synthesis of covalent
diastereoisomeric molecules by reacting disclosed compounds with an
optically pure acid in an activated form or an optically pure
isocyanate. The synthesized diastereoisomers can be separated by
conventional means such as chromatography, distillation,
crystallization or sublimation, and then hydrolyzed to deliver the
enantiomerically enriched compound. Optically active compounds can
also be obtained by using active starting materials. In some
embodiments, these isomers can be in the form of a free acid, a
free base, an ester or a salt.
[0039] In certain embodiments, the compound of the invention can be
a tautomer. As used herein, the term "tautomer" is a type of isomer
that includes two or more interconvertible compounds resulting from
at least one formal migration of a hydrogen atom and at least one
change in valency (e.g., a single bond to a double bond, a triple
bond to a single bond, or vice versa). "Tautomerization" includes
prototropic or proton-shift tautomerization, which is considered a
subset of acid-base chemistry. "Prototropic tautomerization" or
"proton-shift tautomerization" involves the migration of a proton
accompanied by changes in bond order. The exact ratio of the
tautomers depends on several factors, including temperature,
solvent, and pH. Where tautomerization is possible (e.g., in
solution), a chemical equilibrium of tautomers can be reached.
Tautomerizations (i.e., the reaction providing a tautomeric pair)
can be catalyzed by acid or base, or can occur without the action
or presence of an external agent. Exemplary tautomerizations
include, but are not limited to, keto-to-enol; amide-to-imide;
lactam-to-lactim; enamine-to-imine; and enamine-to-(a different)
enamine tautomerizations. A specific example of keto-enol
tautomerization is the interconversion of pentane-2,4-dione and
4-hydroxypent-3-en-2-one tautomers. Another example of
tautomerization is phenol-keto tautomerization. A specific example
of phenol-keto tautomerization is the interconversion of
pyridin-4-ol and pyridin-4(1H)-one tautomers.
[0040] All chiral, diastereomeric, racemic, and geometric isomeric
forms of a structure are intended, unless specific stereochemistry
or isomeric form is specifically indicated. All processes used to
prepare compounds of the present invention and intermediates made
therein are considered to be part of the present invention. All
tautomers of shown or described compounds are also considered to be
part of the present invention.
[0041] By "agent" is meant any small molecule chemical compound,
antibody, nucleic acid molecule, or polypeptide, or fragments
thereof.
[0042] By "ameliorate" is meant decrease, suppress, attenuate,
diminish, arrest, or stabilize the development or progression of a
disease.
[0043] By "alteration" is meant a change (increase or decrease) in
the expression levels or activity of a gene or polypeptide as
detected by standard art known methods such as those described
herein. As used herein, an alteration includes an about 10% change
in expression levels, preferably an about 25% change, more
preferably an about 40% change, and most preferably an about 50% or
greater change in expression levels.
[0044] By "analog" is meant a molecule that is not identical, but
has analogous functional or structural features. For example, a
polypeptide analog retains the biological activity of a
corresponding naturally-occurring polypeptide, while having certain
biochemical modifications that enhance the analog's function
relative to a naturally occurring polypeptide. Such biochemical
modifications could increase the analog's protease resistance,
membrane permeability, or half-life, without altering, for example,
ligand binding. An analog may include an unnatural amino acid.
[0045] In this disclosure, "comprises," "comprising," "containing"
and "having" and the like can have the meaning ascribed to them in
U.S. Patent law and can mean "includes," "including," and the like;
"consisting essentially of" or "consists essentially" likewise has
the meaning ascribed in U.S. Patent law and the term is open-ended,
allowing for the presence of more than that which is recited so
long as basic or novel characteristics of that which is recited is
not changed by the presence of more than that which is recited, but
excludes prior art embodiments.
[0046] "Detect" refers to identifying the presence, absence or
amount of the analyte to be detected. In particular embodiments,
the analyte is a PDE3A or SLFN12 polypeptide.
[0047] By "disease" is meant any condition or disorder that damages
or interferes with the normal function of a cell, tissue, or organ.
Examples of diseases include melanoma, adenocarcinoma, lung cancer,
cervical cancer, liver cancer and breast cancer.
[0048] By "effective amount" is meant the amount of a compound
described herein required to ameliorate the symptoms of a disease
relative to an untreated patient. The effective amount of active
compound(s) used to practice the present invention for therapeutic
treatment of a disease varies depending upon the manner of
administration, the age, body weight, and general health of the
subject. Ultimately, the attending physician or veterinarian will
decide the appropriate amount and dosage regimen. Such amount is
referred to as an "effective" amount. In one embodiment, the
compound is DNMDP, zardaverine, or anagrelide.
[0049] The invention provides a number of targets that are useful
for the development of highly specific drugs to treat or a disorder
characterized by the methods delineated herein. In addition, the
methods of the invention provide a facile means to identify
therapies that are safe for use in subjects. In addition, the
methods of the invention provide a route for analyzing virtually
any number of compounds for effects on a disease described herein
with high-volume throughput, high sensitivity, and low
complexity.
[0050] By "fragment" is meant a portion of a polypeptide or nucleic
acid molecule. This portion contains, preferably, at least about
10%, about 20%, about 30%, about 40%, about 50%, about 60%, about
70%, about 80%, or about 90% of the entire length of the reference
nucleic acid molecule or polypeptide. A fragment may contain about
10, about 20, about 30, about 40, about 50, about 60, about 70,
about 80, about 90, about 100, about 200, about 300, about 400,
about 500, about 600, about 700, about 800, about 900, or about
1000 nucleotides or amino acids.
[0051] "Hybridization" means hydrogen bonding, which may be
Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding,
between complementary nucleobases. For example, adenine and thymine
are complementary nucleobases that pair through the formation of
hydrogen bonds.
[0052] By "marker" or "biomarker" is meant any protein or
polynucleotide having an alteration in expression level or activity
(e.g., at the protein or mRNA level) that is associated with a
disease or disorder. In particular embodiments, a marker of the
invention is PDE3A or SLFN12.
[0053] By "modulator" is meant any agent that binds to a
polypeptide and alters a biological function or activity of the
polypeptide. A modulator includes, without limitation, agents that
reduce or eliminate a biological function or activity of a
polypeptide (e.g., an "inhibitor"). For example, a modulator may
inhibit a catalytic activity of a polypeptide. A modulator
includes, without limitation, agents that increase or decrease
binding of a polypeptide to another agent. For example, a modulator
may promote binding of a polypeptide to another polypeptide. In
some embodiments, a modulator of PDE3A polypeptide is DNMDP. In
some other embodiments, the modulator of PDE3A polypeptide is
anagrelide or zardaverine.
[0054] By "reference" is meant a standard or control condition.
[0055] Nucleic acid molecules useful in the methods of the
invention include any nucleic acid molecule that encodes a
polypeptide of the invention or a fragment thereof. Such nucleic
acid molecules need not be 100% identical with an endogenous
nucleic acid sequence, but will typically exhibit substantial
identity. Polynucleotides having "substantial identity" to an
endogenous sequence are typically capable of hybridizing with at
least one strand of a double-stranded nucleic acid molecule.
Nucleic acid molecules useful in the methods of the invention
include any nucleic acid molecule that encodes a polypeptide of the
invention or a fragment thereof. Such nucleic acid molecules need
not be 100% identical with an endogenous nucleic acid sequence, but
will typically exhibit substantial identity. Polynucleotides having
"substantial identity" to an endogenous sequence are typically
capable of hybridizing with at least one strand of a
double-stranded nucleic acid molecule. By "hybridize" is meant pair
to form a double-stranded molecule between complementary
polynucleotide sequences (e.g., a gene described herein), or
portions thereof, under various conditions of stringency. (See,
e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399;
Kimmel, A. R. (1987) Methods Enzymol. 152:507).
[0056] For example, stringent salt concentration will ordinarily be
less than about 750 mM NaCl and 75 mM trisodium citrate, preferably
less than about 500 mM NaCl and 50 mM trisodium citrate, and more
preferably less than about 250 mM NaCl and 25 mM trisodium citrate.
Low stringency hybridization can be obtained in the absence of
organic solvent, e.g., formamide, while high stringency
hybridization can be obtained in the presence of at least about 35%
formamide, and more preferably at least about 50% formamide.
Stringent temperature conditions will ordinarily include
temperatures of at least about 30.degree. C., more preferably of at
least about 37.degree. C., and most preferably of at least about
42.degree. C. Varying additional parameters, such as hybridization
time, the concentration of detergent, e.g., sodium dodecyl sulfate
(SDS), and the inclusion or exclusion of carrier DNA, are well
known to those skilled in the art. Various levels of stringency are
accomplished by combining these various conditions as needed, in a
preferred: embodiment, hybridization will occur at 30.degree. C. in
750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In a more
preferred embodiment, hybridization will occur at 37.degree. C. in
500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and
100 .mu.g/ml denatured salmon sperm DNA (ssDNA). In a most
preferred embodiment, hybridization will occur at 42.degree. C. in
250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and
200 .mu.g/ml ssDNA. Useful variations on these conditions will be
readily apparent to those skilled in the art.
[0057] For most applications, washing steps that follow
hybridization will also vary in stringency. Wash stringency
conditions can be defined by salt concentration and by temperature.
As above, wash stringency can be increased by decreasing salt
concentration or by increasing temperature. For example, stringent
salt concentration for the wash steps will preferably be less than
about 30 mM NaCl and 3 mM trisodium citrate, and most preferably
less than about 15 mM NaCl and 1.5 mM trisodium citrate. Stringent
temperature conditions for the wash steps will ordinarily include a
temperature of at least about 25.degree. C., more preferably of at
least about 42.degree. C., and even more preferably of at least
about 68.degree. C. In a preferred embodiment, wash steps will
occur at 25.degree. C. in 30 mM NaCl, 3 mM trisodium citrate, and
0.1% SDS. In a more preferred embodiment, wash steps will occur at
42 C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In
amore preferred embodiment, wash steps will occur at 68.degree. C.
in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional
variations on these conditions will be readily apparent to those
skilled in the art. Hybridization techniques are well known to
those skilled in the art and are described, for example, in Benton
and Davis (Science 196:180, 1977); Grunstein and Hogness (Proc.
Natl. Acad. Sci., USA 72:3961, 1975); Ausubel et al. (Current
Protocols in Molecular Biology, Wiley Interscience, New York,
2001); Berger and Kimmel (Guide to Molecular Cloning Techniques,
1987, Academic Press, New York); and Sambrook et al., Molecular
Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press,
New York.
[0058] By "substantially identical" is meant a polypeptide or
nucleic acid molecule exhibiting at least 50% identity to a
reference amino acid sequence (for example, any one of the amino
acid sequences described herein) or nucleic acid sequence (for
example, any one of the nucleic acid sequences described herein).
Preferably, such a sequence is at least 60%, more preferably 80% or
85%, and more preferably 90%, 95% or even 99% identical at the
amino acid level or nucleic acid to the sequence used for
comparison.
[0059] Sequence identity is typically measured using sequence
analysis software (for example, Sequence Analysis Software Package
of the Genetics Computer Group, University of Wisconsin
Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705,
BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software
matches identical or similar sequences by assigning degrees of
homology to various substitutions, deletions, and/or other
modifications. Conservative substitutions typically include
substitutions within the following groups: glycine, alanine;
valine, isoleucine, leucine; aspartic acid, glutamic acid,
asparagine, glutamine; serine, threonine; lysine, arginine; and
phenylalanine, tyrosine. In an exemplary approach to determining
the degree of identity, a BLAST program may be used, with a
probability score between e.sup.-3 and e.sup.-100 indicating a
closely related sequence.
[0060] By "subject" is meant a mammal, including, but not limited
to, a human or non-human mammal, such as a bovine, equine, canine,
ovine, or feline.
[0061] Ranges provided herein are understood to be shorthand for
all of the values within the range. For example, a range of 1 to 50
is understood to include any number, combination of numbers, or
sub-range from the group consisting 1, 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, or 50.
[0062] As used herein, the terms "treat," treating," "treatment,"
and the like refer to reducing or ameliorating a disorder and/or
symptoms associated therewith. It will be appreciated that,
although not precluded, treating a disorder or condition does not
require that the disorder, condition or symptoms associated
therewith be completely eliminated.
[0063] Unless specifically stated or obvious from context, as used
herein, the term "or" is understood to be inclusive. Unless
specifically stated or obvious from context, as used herein, the
terms "a", "an", and "the" are understood to be singular or
plural.
[0064] Unless specifically stated or obvious from context, as used
herein, the term "about" is understood as within a range of normal
tolerance in the art, for example within 2 standard deviations of
the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%,
5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated
value. Unless otherwise clear from context, all numerical values
provided herein are modified by the term about.
[0065] The recitation of a listing of chemical groups in any
definition of a variable herein includes definitions of that
variable as any single group or combination of listed groups. The
recitation of an embodiment for a variable or aspect herein
includes that embodiment as any single embodiment or in combination
with any other embodiments or portions thereof.
[0066] Any compositions or methods provided herein can be combined
with one or more of any of the other compositions and methods
provided herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0067] FIGS. 1A-1D show identification and characterization of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP), a potent and selective cancer cell cytotoxic agent. FIG.
1A is a scatterplot of 1924 compounds showing mean survival of TP53
mutant NCI-H1734 cells, which is a non-small cell lung cancer cell
line, and TP53 wild-type A549 cells, another lung cancer cell line,
after 48 hours of treatment at concentrations of 10 .mu.M. DNMDP is
indicated with a large arrowhead. Other compounds that selectively
killed NCI-H1734 cells are indicated with a small arrow. Positive
control staurosporine is indicated with a long arrow. FIG. 1B is a
linear graph showing a panel of cell lines that was treated with
the indicated concentrations of DNMDP for 48 hours. FIG. 1C is a
linear graph showing the HeLa cell line that was treated with
indicated concentrations of the separated enantiomers of DNMDP for
48 hours. The (R)-enantiomer had a 500-fold lower EC.sub.50
compared to the (S)-enantiomer. FIG. 1D is a structure of
(R)-DNMDP.
[0068] FIG. 2 shows that DNMDP selectively killed NCI-H1734 and did
not affect cell viability in A549. NCI-H1734 and A549 cell lines
were treated with indicated compounds and concentrations for 48
hours.
[0069] FIG. 3 shows the synthesis scheme of
(R)-6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H-
)-one (R)-DNMDP) and analogues. Reaction conditions are as follows:
(a) Ac.sub.2O, (91%); (b) 90% HNO.sub.3, H.sub.2SO.sub.4, (19%);
(c) NaOH, MeOH/H.sub.2O, (100%), then CH.sub.3CHO, NaBH(OAc).sub.3,
(7%); (d) (BrCH.sub.2CH.sub.2).sub.2O, K.sub.2CO.sub.3, DMF, (46%);
(e) CH.sub.3CHO, NaBH.sub.3CN, MeOH, (82%).
[0070] FIGS. 4A-4C show super-critical fluid (SCF) chromatographs
of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) (top to bottom: ES+, diode array, ES- traces). FIG. 4A
are three chromatographs showing Peak 1 (CRO separation); FIG. 4B
are three chromatographs showing Peak 2 (CRO separation); FIG. 4C
are three chromatographs showing synthesized (R)-DNMDP (5:95 ratio
peaks 1:2 by uv).
[0071] FIGS. 5A-5C show that Phosphodiesterase 3A (PDE3A)
expression correlated with sensitivity to
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP), but inhibition of PDE3A mediated cAMP hydrolysis did not
correlate with cytotoxicity. FIG. 5A is a scatterplot showing
correlation between DNMDP sensitivity and expression of 18,988
genes in 766 genomically characterized cell lines. Cell lines were
treated for 72 hours with concentrations ranging from 66.4 .mu.M-2
nM in 2-fold step dilutions. The Z-score for Pearson correlation
between PDE3A expression and sensitivity to DNMDP is 8.5. FIG. 5B
is a scatterplot showing results from cell lines from panel A that
were treated with 480 compounds. DNMDP showed the best correlation
between PDE3A expression and sensitivity. FIG. 5C is a scatterplot
showing published PDE3 inhibitor IC.sub.50 values and EC.sub.50
values of HeLa cells treated with indicated compounds up to 10
.mu.M for 48 hours. DNMDP IC.sub.50 concentration for PDE3A
inhibition was determined in FIG. 7B.
[0072] FIGS. 6A-6C show chemical structures of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP), siguazodan and levosimendan, respectively.
[0073] FIGS. 7A and 7B are graphs showing determination of
Phosphodiesterase 3A (PDE3A) in vitro IC.sub.50 of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP). FIG. 7A shows PDE3A in vitro inhibition with indicated
concentrations of positive control trequinsin (IC.sub.50 curve was
performed by Caliper). FIG. 7B shows PDE3A in vitro inhibition with
indicated concentrations of DNMDP (IC.sub.50 curve was performed by
Caliper).
[0074] FIGS. 8A and 8B are graphs showing that induction of cAMP
signaling did not phenocopy cytotoxicity induced by
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2n)-on-
e (DNMDP). Forskolin: FSK. FIG. 8A shows cAMP concentrations that
were measured 1 hour after treatment with indicated compounds and
concentration in HeLa cells. FIG. 8B shows viability of HeLa cells
that were treated with indicated compounds and concentrations for
48 hours.
[0075] FIGS. 9A-9C show that non-lethal Phosphodiesterase 3 (PDE3)
inhibitors rescued cell death induced by
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) by competing for the binding of PDE3A. FIG. 9A is a
scatterplot showing viability of HeLa cells that were treated with
1600 bioactive compounds at a concentration of 20 .mu.M in
combination with 30 nM (EC70) of DNMDP for 48 hours. The viability
was calculated as a percentage of the untreated DMSO control. FIG.
9B is a linear graph showing viability of HeLa cells that were
treated with DNMDP in combination with indicated concentrations of
non-lethal PDE3 and pan-PDE inhibitors for 48 hours. FIG. 9C shows
a SDS-PAGE gel depicting the result of affinity purification
performed on 200 .mu.g of HeLa cell lysate using a DNMDP
linker-analogue tethered to a solid phase with the same rescue
characteristic as non-lethal PDE3 inhibitors. Indicated compounds
were co-incubated with the linker-analogue. The affinity purified
fraction was run on an SDS-PAGE gel and probed for PDE3A.
[0076] FIGS. 10A and 10B show the structure and rescue phenotype of
linker-compound tert-butyl
(R)-(2-(2-(2-(ethyl(4-(4-methyl-6-oxo-1,4,5,6-tetrahydropyridazin-3-yl)ph-
enyl)amino)ethoxy) ethoxy)ethyl)carbamate (DNMDP)-2L. FIG. 10A
shows the structure of DNMDP-2L. FIG. 10B is a graph showing the
viability of HeLa cells that were treated with indicated compounds
and concentrations for 48 hours.
[0077] FIGS. 11A-11C show that Phosphodiesterase 3A (PDE3A) was not
essential in sensitive cell lines, but was required for relaying
the cytotoxic signal. FIG. 11A is a Western blot. HeLa cells were
infected with Cas9 and indicated guide RNAs (sgRNA) against PDE3A.
Western blots were probed for PDE3A at indicated time points. FIG.
11B is a bar graph showing percent rescue of HeLa cells that were
infected with indicated sgRNAs for two weeks and treated with 1
.mu.M of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) for 48 hours. Percent rescue was normalized to the
Cas9-only control. FIG. 11C is a plot showing viability of cells
infected with indicated sgRNAs and treated with various
concentrations of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP).
[0078] FIGS. 12A and 12B are a Western blot and a graph showing
that reduction of Phosphodiesterase 3A (PDE3A) protein level caused
resistance to
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-
-one (DNMDP). In FIG. 12A HeLa cells were treated with scrambled
control siRNA or a combination of four different siRNAs targeting
PDE3A. Cells were lysed at indicated time-points and immunoblotted
for PDE3A and Actin. FIG. 12B is a linear graph showing viability
of HeLa cells that were treated with indicated concentrations of
DNMDP analogue 3 for 48 hours.
[0079] FIGS. 13A-13C show that Phosphodiesterase 3A (PDE3A)
immunoprecipitation in the presence of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) revealed novel SIRT7 and SLFN12 interaction. FIG. 13A
shows a schematic overview of the affinity enrichment followed by
quantitative proteomics of PDE3A performed in HeLa cells. All cells
were treated for four hours prior to lysis with 10 .mu.M of
indicated compounds. The presence of all compounds was maintained
throughout the experiment including washing steps. FIG. 13B is a
scatterplot showing log.sub.2 ratios for proteins that were
enriched in anti-PDE3A immunoprecipitates in the DMSO treated HeLa
cells compared to anti-PDE3A immuno precipitates in the presence of
blocking peptide specific to the PDE3A antibody; each dot
represents a protein. FIG. 13C is a scatterplot showing Log.sub.2
ratios of changes of proteins bound to PDE3A in the presence of
DNMDP versus trequinsin. Each dot represents the average of two
replicates per condition for an individual protein. In all cases,
the data plotted passed the Bland-Altman test with 95% confidence
interval for reproducibility.
[0080] FIGS. 14A-14C show results of replicate PDE3A-protein
interaction studies using PDE3A as bait under different conditions.
Each scatterplot showed log.sub.2 ratios of two replicates for
proteins that were enriched by PDE3A under different conditions
over enrichment by PDE3A in the presence of blocking peptide. Each
dot represents the log.sub.2 ratio for that particular protein,
medium gray dots correspond to a Benjamini-Hochberg adjusted p
value <0.01, light gray dots represent proteins that fall
outside of the Blandt-Altman test for reproducibility within a 95%
confidence interval. In FIG. 14A protein enrichment was
accomplished by immunoprecipitation using anti-PDE3A. In FIG. 14B
protein enrichment was accomplished by immunoprecipitation using
anti-PDE3A in the presence of DNMDP. In FIG. 14C protein enrichment
was accomplished by immunoprecipitation using anti-PDE3A in the
presence of trequinsin.
[0081] FIGS. 15A-15E show that cell lines with dual expression of
SLFN12 and PDE3A were significantly enriched for DNMDP-sensitive
cell lines. FIG. 15A is a scatterplot showing mRNA robust multichip
average (RMA) expression values for PDE3A and SLFN12 from the
Cancer Cell Line Encyclopedia (CCLE) database (a detailed genetic
characterization of a large panel of human cancer cell lines) with
sensitive cell lines indicated (Barretina et al., Nature 483,
603-607, 2012). 21 sensitive cell lines were binned in three groups
of 7 based on area under the curve (AUC) rank. FIG. 15B is a bar
graph showing results of a Fisher's exact test on DNMDP sensitivity
of cell lines with high expression of both SLFN12 and PDE3A (RMA
Log 2>5) compared to other cell lines. The top half of the bar
on the right indicates melanoma cell lines. FIG. 15C is a
scatterplot showing mRNA RPKM+1 expression values for PDE3A and
SLFN12 from RNA sequencing data. FIG. 15D is a bar graph showing
qPCR expression changes of SLFN12 in HeLa cells transduced with
shSLFN12 normalized to GAPDH. FIG. 15E is a plot showing viability
of HeLa cells transduced with indicated shRNA reagents and treated
with indicated concentrations of DNMDP for 72 hours.
[0082] FIGS. 16A and 16B are scatter plots showing that SLFN12
expression was amongst the top genes correlating with DNMDP
sensitivity. FIG. 16A shows the correlation between DNMDP
sensitivity and expression of 18,988 genes in 766 genomically
characterized cell lines. Cell lines were treated for 72 hours with
concentrations ranging from 66.4 .mu.M-2 nM in 2-fold step
dilutions.
[0083] FIG. 16B is a scatterplot showing a correlation between
DNMDP sensitivity and expression of 18,988 genes in 766 genomically
characterized cell lines. Expression levels were corrected for
PDE3A expression as described earlier (Kim et al., Genetica 131,
151-156, 2007). Cell lines were treated for 72 hours with
concentrations ranging from 66.4 .mu.M-2 nM in 2-fold step
dilutions.
[0084] FIGS. 17A-7B show that DNMDP induces apoptosis in HeLa
cells. FIG. 17A is a plot showing viability of HeLa cells treated
for 48 hours with indicated concentrations of DNMDP. Caspase-Glo
represents Caspase 3/7 activity indicating induction of apoptosis.
CellTiter-Glo reflects viability. FIG. 17B is an immunoblot. HeLa
cells were treated for 36 hours with indicated compounds and
concentrations. HeLa cells were harvested and immunoblotted for
PARP-cleavage products, indicative of apoptosis.
[0085] FIG. 18 is a scatterplot of PDE3A mRNA expression and
sensitivity to DNMDP of 766 cancer cell lines.
[0086] FIG. 19 is an immunoblot showing that DNMDP induces
interaction between PDE3A and SIRT7 and SLFN12 in HeLa cells. HeLa
cells were transfected with indicated plasmids and treated with
indicated compounds with a final concentration of 10 .mu.M for four
hours. Endogenous PDE3A was immunoprecipitated and immunoblotted
for V5 to identify novel interaction with SIRT7 and SLFN12 (upper
two panels). Immunoprecipitate input was immunoblotted for PDE3A
and V5 (lower two panels). V5-SLFN12 was undetectable in whole cell
lysate.
[0087] FIG. 20 is an immunoblot showing confirmation of mass
spectrometric results herein using affinity reagents. FIG. 20 shows
that DNMDP and (weakly) anagrelide, but not trequinsin, induced
PDE3A and SFLN12 complex formation.
[0088] FIG. 21 is a set of tables showing that SLFN12 is lost in
cells that have acquired resistance to DNMDP.
[0089] FIG. 22 is a plot showing sensitization of a DNMDP-resistant
cell line by expression of SLFN12 or expression of SFLN12 and
PDE3A.
[0090] FIG. 23 is a scatter plot showing sensitivity of
Leiomyosarcomas (LMS) to PDE3A modulation based on SLFN12
expression level.
[0091] Table 1 shows sensitivity data of 766 cancer cell lines
treated with DNMDP. Cell lines were treated for 72 hours with
concentrations ranging from 66.4 .mu.M-2 nM in 2-fold step
dilutions.
[0092] Table 2 shows results from panel of 19 phosphodiesterase
inhibition reactions perforated by Caliper. DNMDP concentration was
100 nM.
[0093] Table 3 shows RPKM values of SLFN12 and PDE3A expression in
multiple healthy tissue types.
[0094] Table 4 showing Leiomyosarcoma sensitivity to DNMDP
[0095] Table 5 shows binding of DNMDP to PDE3A(677-1141).
[0096] Compositions and articles defined by the invention were
isolated or otherwise manufactured in connection with the examples
provided below. Other features and advantages of the invention will
be apparent from the detailed description, and from the claims.
DETAILED DESCRIPTION
[0097] As described below, the present invention features improved
methods of identifying patients having cancer (e.g., melanoma,
endometrium, lung, hematopoetic/lymphoid, ovarian, cervical,
soft-tissue sarcoma, leiomyosarcoma, urinary tract, pancreas,
thyroid, kidney, glioblastoma, or breast cancer)) that is sensitive
to treatment with a phosphodiesterase 3A (PDE3A) modulator by
detecting co-expression of PDE3A and Schlafen 12 (SLFN12)
polypeptides or polynucleotides in a cancer cell derived from such
patients. The invention is based at least in part on the discovery
that sensitivity to phosphodiesterase 3A modulators, such as
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e, or DNMDP, in 766 cancer cell lines correlated with expression of
the phosphodiesterase 3A gene, PDE3A. Like DNMDP, a subset of PDE3A
inhibitors kill selected cancer cells while others do not; these
cell-sparing PDE3A inhibitors instead block DNMDP induced
cytotoxicity. Furthermore, PDE3A depletion leads to DNMDP
resistance. DNMDP binding to PDE3A promotes an interaction between
PDE3A and Sirtuin 7 (SIRT7) and Schlafen 12 (SLFN12), suggesting a
neomorphic activity, and SLFN12 and PDE3A co-expression correlated
with DNMDP sensitivity. These results indicate that PDE3A
modulators are promising cancer therapeutic agents and demonstrate
the power of chemogenomics in small-molecule discovery and
target-identification.
[0098] Accordingly, the invention provides methods of selecting a
subject as having a cancer that responds to a PDE3A modulator,
where the selection method involves detecting co-expression of
PDE3A and Schlafen 12 (SLFN12) polypeptides or polynucleotides, in
a cancer cell derived from such subjects.
PDE3A Modulator
[0099] The identification of PDE3A modulators was made in
connection with a phenotypic screen designed to identify cytotoxic
small molecules in a mutant tp53 background. A chemogenomics
approach complements target-driven drug development programs, which
consists of extensive in vitro and in vivo target validation, and
can also be referred to as reverse chemogenomics (Zheng et al.,
Curr Issues Mol Biol 4, 33-43, 2002). Many U.S. Food and Drug
Administration (FDA)-approved targeted therapies have been
developed this way, among them small-molecule kinase inhibitors
that target oncogenic somatic driver mutations (Moffat et al., Nat
Rev Drug Discov 13, 588-602, 2014). However, the discovery and
development of targeted therapies is often hampered by limitations
in knowledge of the biological function of the target, its
mechanism of action, and the available chemical matter to
selectively inhibit the target.
[0100] Phenotypic screening can discover novel targets for cancer
therapy whose specific molecular mechanism is often elucidated by
future studies (Swinney et al., Nat Rev Drug Discov 10, 507-519,
2011). In recent years, two classes of anti-cancer drugs found by
unbiased phenotypic screening efforts have been approved by the
FDA. Lenalidomide and pomalidomide were found to be modulators of
an E3-ligase that alter the affinity of its target, leading to
degradation of lineage specific transcription factors (Kronke et
al., Science 343, 301-305, 2014; Lu et al., Science 343, 305-309,
2014), whereas romidepsin and vorinostat were later identified as
histone deacetylase (HDAC) inhibitors (Moffat et al., Nat Rev Drug
Discov 13, 588-602, 2014; Nakajima et al., Exp. Cell Res. 241,
126-133, 1998, Marks et al., Nat Biotechnol 25, 84-90, 2007).
[0101] Tumor suppressor alterations are suitable targets for
phenotypic screening as they are not S directly targetable with
small molecules, although synthetic lethal approaches such as
olaparib treatment of BRCA1/BRCA2 mutant cancers have proven to be
effective. According to current knowledge, the tp53 tumor
suppressor gene is the most frequently mutated across human cancer,
with somatic mutations detected in 36% of 4742 cancers subjected to
whole exome sequencing. Despite many attempts, no compounds that
selectively kill tp53 mutant cells have been identified.
[0102] A phenotypic screen developed to identify small molecules
causing synthetic lethality in tp53 mutant cancer cells enabled the
serendipitous discovery of a class of cancer-selective cytotoxic
agents which act as modulators of phosphodiesterase 3A (PDE3A), as
described herein below. Cyclic nucleotide phosphodiesterases
catalyze the hydrolysis of second messenger molecules cyclic
adenosine monophosphate (cAMP) and cyclic guanosine monophosphate
(cGMP), and are important in many physiological processes. Several
phosphodiesterase inhibitors have been approved for clinical
treatment, including PDE3 inhibitors milrinone, cilostazol, and
levosimendan for cardiovascular indications and inhibition of
platelet coagulation, as well as the PDE3 inhibitor anagrelide for
thrombocythemia. PDE5 inhibitors, e.g. vardenafil, are used for
smooth muscle disorders including erectile dysfunction and
pulmonary arterial hypertension, and the PDE4 inhibitor roflumilast
reduces exacerbations from chronic obstructive pulmonary disease
(COPD).
[0103] Phosphodiesterase inhibitors act by direct inhibition of
their targets or by allosteric modulation; for example, structural
analysis of PDE4 has led to the design of PDE4D and PDE4B
allosteric modulators (Burgin et al., Nat Biotechnol 28, 63-70,
2010; Gurney et al., Neurotherapeutics 12, 49-56, 2015). The data
provided herein below indicates that the cancer cytotoxic
phosphodiesterase modulator DNMDP likely acts through a similar
allosteric mechanism.
[0104] Accordingly, the invention provides methods for identifying
subjects that have a malignancy that is likely to respond to PDE3A
modulator treatment based on the level of PDE3A and SLFN12
expression in a subject biological sample comprising a cancer cell.
In some embodiments, the PDE3A modulator is DNMDP. In some other
embodiments, the PDE3A modulator is anagrelide or zardaverine.
Compound Forms and Salts
[0105] The compounds of the present invention include the compounds
themselves, as well as their salts and their prodrugs, if
applicable. A salt, for example, can be formed between an anion and
a positively charged substituent (e.g., amino) on a compound
described herein. Suitable anions include chloride, bromide,
iodide, sulfate, nitrate, phosphate, citrate, methanesulfonate,
trifluoroacetate, and acetate. Likewise, a salt can also be formed
between a cation and a negatively charged substituent (e.g.,
carboxylate) on a compound described herein. Suitable cations
include sodium ion, potassium ion, magnesium ion, calcium ion, and
an ammonium cation such as tetramethylammonium ion. Examples of
prodrugs include C.sub.1-6 alkyl esters of carboxylic acid groups,
which, upon administration to a subject, are capable of providing
active compounds.
[0106] Pharmaceutically acceptable salts of the compounds of the
present disclosure include those derived from pharmaceutically
acceptable inorganic and organic acids and bases. As used herein,
the term "pharmaceutically acceptable salt" refers to a salt formed
by the addition of a pharmaceutically acceptable acid or base to a
compound disclosed herein. As used herein, the phrase
"pharmaceutically acceptable" refers to a substance that is
acceptable for use in pharmaceutical applications from a
toxicological perspective and does not adversely interact with the
active ingredient.
[0107] Examples of suitable acid salts include acetate, adipate,
alginate, aspartate, benzoate, benzenesulfonate, bisulfate,
butyrate, citrate, camphorate, camphorsulfonate, digluconate,
dodecylsulfate, ethanesulfonate, formate, fumarate,
glucoheptanoate, glycolate, hemisulfate, heptanoate, hexanoate,
hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate,
lactate, maleate, malonate, methanesulfonate,
2-naphthalenesulfonate, nicotinate, nitrate, palmoate, pectinate,
persulfate, 3-phenylpropionate, phosphate, picrate, pivalate,
propionate, salicylate, succinate, sulfate, tartrate, thiocyanate,
tosylate and undecanoate. Other acids, such as oxalic, while not in
themselves pharmaceutically acceptable, may be employed in the
preparation of salts useful as intermediates in obtaining the
compounds of the present invention and their pharmaceutically
acceptable acid addition salts. Salts derived from appropriate
bases include alkali metal (e.g., sodium), alkaline earth metal
(e.g., magnesium), ammonium and N-(alkyl).sub.4.sup.+ salts. The
present invention also envisions the quaternization of any basic
nitrogen-containing groups of the compounds disclosed herein. Water
or oil-soluble or dispersible products may be obtained by such
quaternization. Salt forms of the compounds of any of the formulae
herein can be amino acid salts of carboxyl groups (e.g.,
L-arginine, -lysine, -histidine salts).
[0108] Lists of suitable salts are found in Remington's
Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton,
Pa., 1985, p. 1418; Journal of Pharmaceutical Science, 66, 2
(1977); and "Pharmaceutical Salts: Properties, Selection, and Use A
Handbook; Wermuth, C. G. and Stahl, P. H. (eds.) Verlag Helvetica
Chimica Acta, Zurich, 2002 [ISBN 3-906390-26-8] each of which is
incorporated herein by reference in their entireties.
[0109] The neutral forms of the compounds may be regenerated by
contacting the salt with a base or acid and isolating the parent
compound in the conventional manner. The parent form of the
compound differs from the various salt forms in certain physical
properties, such as solubility in polar solvents, but otherwise the
salts are equivalent to the parent form of the compound for the
purposes of the present invention.
[0110] In addition to salt forms, the present invention provides
compounds which are in a prodrug form. Prodrugs of the compounds
described herein are those compounds that undergo chemical changes
under physiological conditions to provide the compounds of the
present invention. Additionally, prodrugs can be converted to the
compounds of the present invention by chemical or biochemical
methods in an ex vivo environment. For example, prodrugs can be
slowly converted to the compounds of the present invention when
placed in a transdermal patch reservoir with a suitable enzyme or
chemical reagent. Prodrugs are often useful because, in some
situations, they may be easier to administer than the parent drug.
They may, for instance, be more bioavailable by oral administration
than the parent drug. The prodrug may also have improved solubility
in pharmacological compositions over the parent drug. A wide
variety of prodrug derivatives are known in the art, such as those
that rely on hydrolytic cleavage or oxidative activation of the
prodrug. An example, without limitation, of a prodrug would be a
compound of the present invention which is administered as an ester
(the "prodrug"), but then is metabolically hydrolyzed to the
carboxylic acid, the active entity. Additional examples include
peptidyl derivatives of a compound of the present invention.
[0111] The present invention also includes various hydrate and
solvate forms of the compounds.
[0112] The compounds of the present invention may also contain
unnatural proportions of atomic isotopes at one or more of the
atoms that constitute such compounds. For example, the compounds
may be radiolabeled with radioactive isotopes, such as for example
tritium (.sup.3H), iodine-125 (.sup.125I) or carbon-14 (.sup.14C).
All isotopic variations of the compounds of the present invention,
whether radioactive or not, are intended to be encompassed within
the scope of the present invention.
Diagnostics
[0113] The present invention features diagnostic assays for the
characterization of cancer. In one embodiment, levels of PDE3A
and/or Schlafen 12 (SLFN12) polynucleotides or polypeptides are
measured in a subject sample and used as an indicator of cancer
that is responsive to treatment with a PDE3A modulator. Levels of
PDE3A and/or Schlafen 12 polynucleotides may be measured by
standard methods, such as quantitative PCR, Northern Blot,
microarray, mass spectrometry, and in situ hybridization. Standard
methods may be used to measure levels of PDE3A and/or Schlafen 12,
polypeptides in a biological sample derived from a tumor. Such
methods include immunoassay, ELISA, western blotting using an
antibody that binds PDE3A and/or Schlafen 12 and radioimmunoassay.
Elevated levels of PDE3A and Schlafen 12 polynucleotides or
polypeptides relative to a reference are considered a positive
indicator of cancer that is responsive to treatment with a PDE3A
modulator.
Types of Biological Samples
[0114] In characterizing the responsiveness of a malignancy in a
subject to PDE3A modulator treatment, the level of PDE3A and/or
SLFN12 expression is measured in different types of biologic
samples. In one embodiment, the biologic sample is a tumor
sample.
[0115] PDE3A and/or SLFN12 expression is higher in a sample
obtained from a subject that is responsive to PDE3A modulator
treatment than the level of expression in a non-responsive subject.
In another embodiment, PDE3A and/or SLFN12 is at least about 5, 10,
20, or 30-fold higher in a subject with a malignancy than in a
healthy control. Fold change values are determined using any method
known in the art. In one embodiment, change is determined by
calculating the difference in expression of PDE3A and/or SLFN12 in
a cancer cell vs the level present in a non-responsive cancer cell
or the level present in a corresponding healthy control cell.
Selection of a Treatment Method
[0116] As reported herein below, subjects suffering from a
malignancy may be tested for PDE3A and/or SLFN12 expression in the
course of selecting a treatment method. Patients characterized as
having increased PDE3A and/or SEEN 12 relative to a reference level
are identified as responsive to PDE3A modulator treatment.
Kits
[0117] The invention provides kits for characterizing the
responsiveness or resistance of a subject to PDE3A modulator
treatment.
[0118] Also provided herein are kits that can include a therapeutic
composition containing an effective amount of a PDE3A modulator in,
e.g., unit dosage form.
[0119] In one embodiment, a diagnostic kit of the invention
provides a reagent for measuring relative expression of PDE3A and
SLFN12. Such reagents include capture molecules (e.g., antibodies
that recognize PDE3A and SLFN12 polypeptides or nucleic acid probes
that hybridize with PDE3A and SLFN12 polynucleotides).
[0120] In some embodiments, the kit comprises a sterile container
which includes a therapeutic or diagnostic composition; such
containers can be boxes, ampoules, bottles, vials, tubes, bags,
pouches, blister-packs, or other suitable container forms known in
the art. Such containers can be made of plastic, glass, laminated
paper, metal foil, or other materials suitable for holding
medicaments.
[0121] In one embodiment, a kit of the invention comprises reagents
for measuring PDE3A and/or SLFN12 levels. If desired, the kit
further comprises instructions for measuring PDE3A and/or SLFN12
and/or instructions for administering the PDE3A modulator to a
subject having a malignancy, e.g., a malignancy selected as
responsive to PDE3A modulator treatment. In particular embodiments,
the instructions include at least one of the following: description
of the therapeutic agent; dosage schedule and administration for
treatment or prevention of malignancy or symptoms thereof;
precautions; warnings; indications; counter-indications; over
dosage information; adverse reactions; animal pharmacology;
clinical studies; and/or references. The instructions may be
printed directly on the container (when present), or as a label
applied to the container, or as a separate sheet, pamphlet, card,
or folder supplied in or with the container.
[0122] The practice of the present invention employs, unless
otherwise indicated, conventional techniques of molecular biology
(including recombinant techniques), microbiology, cell biology,
biochemistry and immunology, which are well within the purview of
the skilled artisan. Such techniques are explained fully in the
literature, such as, "Molecular Cloning: A Laboratory Manual",
second edition (Sambrook, 1989); "Oligonucleotide Synthesis" (Gait,
1984); "Animal Cell Culture" (Freshney, 1987); "Methods in
Enzymology" "Handbook of Experimental immunology" (Weir, 1996);
"Gene Transfer Vectors for Mammalian Cells" (Miller and Calos,
1987); "Current Protocols in Molecular Biology" (Ausubel, 1987);
"PCR: The Polymerase Chain Reaction", (Mullis, 1994); "Current
Protocols in Immunology" (Coligan, 1991). These techniques are
applicable to the production of the polynucleotides and
polypeptides of the invention, and, as such, may be considered in
making and practicing the invention. Particularly useful techniques
for particular embodiments will be discussed in the sections that
follow.
[0123] The following examples are put forth so as to provide those
of ordinary skill in the art with a complete disclosure and
description of how to make and use the assay, screening, and
therapeutic methods of the invention, and are not intended to limit
the scope of the invention.
EXAMPLES
Example 1. Identification of a Cell-Selective Cytotoxic Small
Molecule
[0124] To identify anti-cancer compounds with cell-selective
cytotoxic activity, an unbiased chemical screen was performed in
two lung adenocarcinoma cell lines, A549 and NCI-H1734, both of
which harbor oncogenic KRAS mutations and truncating STK11
mutations, and which were TP53 wild type and mutant (R273L),
respectively. 1,924 compounds were screened from the Molecular
Libraries Small-Molecule Repository validation set in the A549 and
NCI-H1734 cell lines at a single concentration of 10 .mu.M in
384-well format in duplicate. As a proxy for cellular viability,
ATP content was measured after 48 hours of compound treatment.
[0125] Three compounds showed a selective reduction in cell
viability for the NCI-H1734 cell line compared to the A549 cell
line, with an approximately 50% reduction in the NCI-H1734 cell
line, which is >4 median absolute deviations from the median in
the negative direction, compared to a minimal change of <1
median absolute deviations from the median in the A549 cell line
(FIG. 1A). Retesting the three compounds in a dose-response
analysis validated that one compound,
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e, or DNMDP, was specifically toxic to the NCI-H1734 cell line
(FIG. 2).
[0126] Testing of additional cell lines with DNMDP showed clear
cell-selective cytotoxicity, with an EC.sub.50 between 10 and 100
nM for two additional lung adenocarcinoma cell lines, NCI-H1563 and
s NCI-H2122, and for HeLa cervical carcinoma cells, but an EC50
greater than 1 .mu.M for A549, MCF7, and PC3 cells (FIG. 1B; FIG.
1C). Caspase activity was detected by a caspase-sensitive
luciferase assay and by poly ADP ribose polymerase (PARP) cleavage
in HeLa cells upon DNMDP treatment, indicating that sensitive cells
undergo apoptosis after DNMDP exposure (FIGS. 17A-17B). To
characterize cellular sensitivity to DNMDP further, 766 genomically
characterized cancer cell lines were screened for DMNDP sensitivity
at concentrations ranging from 66.4 .mu.M to 2 nM in 2-fold
dilution steps for 72 hours. From these cell lines, 22 cell lines
were categorized as sensitive with a robust Z-score lower than -4,
which represented multiple lineages including multiple melanoma
cell lines, amongst others (Table 1).
[0127] Next, the DNMDP enantiomers were separated by chiral
super-critical fluid (SCF) chromatography. One enantiomer was
500-fold more potent in HeLa cells than the other (FIGS. 1C and D).
The (R)-enantiomer was synthesized from commercially available
starting materials (FIG. 3). This synthesized enantiomer had
similar activity to the more potent separated material and was
identical by chiral SCF chromatography, confirming stereochemistry
of the active enantiomer (FIGS. 4A-4C). Two (R)-des-nitro analogues
of DNMDP were synthesized, both of which tested similarly to
(R)-DNMDP (FIG. 3). FIGS. 4A-4C show super-critical fluid (SCF)
chromatographs of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) (top to bottom: ES+, diode array, ES- traces). FIG. 4A
shows Peak 1 (CRO separation); FIG. 4B shows Peak 2 (CRO
separation); and FIG. 4C shows synthesized (R)-DNMDP (5:95 ratio
peaks 1:2 by uv).
TABLE-US-00005 TABLE 1 Sensitivity data of 766 cancer cell lines
treated with DNMDP Cell line Lineage DNMDP AUC Robust Z-score
COV318 OVARY 0.095838 -6.863450362 IGR37 SKIN 0.41146 -6.532158389
JHUEM1 ENDOMETRIUM 0.53468 -6.402820773 HEL HAEMATOPOIETIC AND
0.57955 -6.355723071 LYMPHOID TISSUE CORL51 LUNG 0.59436
-6.340177786 HEL9217 HAEMATOPOIETIC AND 0.75005 -6.176758102
LYMPHOID TISSUE NCIH1563 LUNG 1.0887 -5.821294837 SKMEL3 SKIN
1.2215 -5.681901594 NCIH2122 LUNG 1.3105 -5.58848293 RVH421 SKIN
1.4556 -5.436179018 HUT78 HAEMATOPOIETIC AND 1.5307 -5.35735046
LYMPHOID TISSUE DKMG CENTRAL NERVOUS SYSTEM 1.7217 -5.156867709 GB1
CENTRAL NERVOUS SYSTEM 1.8269 -5.046444748 G292CLONEA141B1 BONE
1.9664 -4.900018865 HMCB SKIN 1.9762 -4.889732315 A2058 SKIN 2.0833
-4.777315024 NCIH1734 LUNG 2.2179 -4.636032415 NCIH196 LUNG 2.5263
-4.312320999 LI7 LIVER 2.5414 -4.296471315 JHOM1 OVARY 2.7006
-4.129367368 COLO741 COLON 2.7231 -4.10575029 HS578T BREAST 2.8012
-4.023772788 K029AX SKIN 2.9362 -3.88207032 MONOMAC1 HAEMATOPOIETIC
AND 2.9692 -3.847431939 LYMPHOID TISSUE HT1197 URINARY TRACT 3.0929
-3.717590492 NCIH520 LUNG 3.1351 -3.67329535 CAL78 BONE 3.1711
-3.635508025 NCIH647 LUNG 3.2187 -3.585544785 CGTHW1 THYROID 3.4296
-3.36417404 NCIH1666 LUNG 3.6097 -3.175132451 L33 PANCREAS 3.625
-3.159072838 UACC62 SKIN 3.9116 -2.858243747 CAS1 CENTRAL NERVOUS
SYSTEM 3.9993 -2.766189625 CAL51 BREAST 4.0017 -2.76367047 OSRC2
KIDNEY 4.326 -2.423269652 X8505C THYROID 4.3418 -2.406685215 SH4
SKIN 4.3672 -2.380024158 NCIH1395 LUNG 4.4473 -2.29594736 SNU503
LARGE INTESTINE 4.5692 -2.16799528 HS729 SOFT TISSUE 4.6518
-2.081294362 SW579 THYROID 4.697 -2.033850277 YH13 CENTRAL NERVOUS
SYSTEM 4.7007 -2.029966579 DBTRG05MG CENTRAL NERVOUS SYSTEM 4.7415
-1.987140944 SEM HAEMATOPOIETIC AND 4.7433 -1.985251578 LYMPHOID
TISSUE HS852T SKIN 4.7511 -1.977064324 SNU449 LIVER 4.752
-1.976119641 NCIH2286 LUNG 4.7782 -1.948618866 JHOS2 OVARY 4.8254
-1.899075485 BICR31 UPPER AERODIGESTIVE 4.8356 -1.888369076 TRACT
IGR1 SKIN 4.8613 -1.861393125 JHUEM3 ENDOMETRIUM 4.93 -1.789282313
SNU387 LIVER 4.9639 -1.753699249 UMUC1 URINARY TRACT 4.9933
-1.7228396 X8305C THYROID 5.0004 -1.7153871 NCIH1915 LUNG 5.0031
-1.712553051 P31FUJ HAEMATOPOIETIC AND 5.0106 -1.704680691 LYMPHOID
TISSUE COLO678 LARGE INTESTINE 5.0245 -1.690090585 EOL1
HAEMATOPOIETIC AND 5.0478 -1.665633789 LYMPHOID TISSUE KNS42
CENTRAL NERVOUS SYSTEM 5.0791 -1.632779809 SW1783 CENTRAL NERVOUS
SYSTEM 5.1161 -1.593942837 HS940T SKIN 5.1573 -1.550697343 SNU685
ENDOMETRIUM 5.206 -1.499579489 BCPAP THYROID 5.2336 -1.470609207
COLO829 SKIN 5.2432 -1.460532587 DM3 PLEURA 5.2635 -1.439224734
OCUM1 STOMACH 5.2843 -1.417392058 M059K CENTRAL NERVOUS SYSTEM
5.3059 -1.394719663 MG63 BONE 5.3943 -1.301930788 NCIH2172 LUNG
5.4245 -1.270231421 CAOV3 OVARY 5.4646 -1.228140539 PEER
HAEMATOPOIETIC AND 5.4754 -1.216804342 LYMPHOID TISSUE HS839T SKIN
5.5232 -1.166631172 CORL105 LUNG 5.5442 -1.144588566 SNU5 STOMACH
5.5498 -1.138710537 MFE296 ENDOMETRIUM 5.5618 -1.126114762 NCIH854
LUNG 5.576 -1.111209762 NCIH146 LUNG 5.5773 -1.10984522 NCIH2081
LUNG 5.5811 -1.105856558 COV644 OVARY 5.5849 -1.101867896 VCAP
PROSTATE 5.5863 -1.100398388 BICR18 UPPER AERODIGESTIVE 5.6
-1.086018212 TRACT RH18 SOFT TISSUE 5.6283 -1.056313176 KPNYN
AUTONOMIC GANGLIA 5.6717 -1.010758457 KPNSI9S AUTONOMIC GANGLIA
5.6827 -0.99921233 SKCO1 LARGE INTESTINE 5.688 -0.993649196 MV411
HAEMATOPOIETIC AND 5.6905 -0.991025076 LYMPHOID TISSUE COV362 OVARY
5.6913 -0.990185358 NCO2 HAEMATOPOIETIC AND 5.7088 -0.971816519
LYMPHOID TISSUE JHH4 LIVER 5.71 -0.970556942 NCIH2141 LUNG 5.7218
-0.958171096 LXF289 LUNG 5.734 -0.945365392 MEWO SKIN 5.738
-0.9411668 TE125T SOFT TISSUE 5.744 -0.934868913 SNU869 BILIARY
TRACT 5.7543 -0.924057539 LNCAPCLONEFGC PROSTATE 5.7557
-0.922588032 NCIH2009 LUNG 5.7594 -0.918704335 SKNBE2 AUTONOMIC
GANGLIA 5.7717 -0.905793666 IALM LUNG 5.775 -0.902329827 DU145
PROSTATE 5.7825 -0.894457468 HCC1419 BREAST 5.7835 -0.89340782
NALM6 HAEMATOPOIETIC AND 5.7872 -0.889524123 LYMPHOID TISSUE
PECAPJ15 UPPER AERODIGESTIVE 5.789 -0.887634757 TRACT LU99 LUNG
5.8016 -0.874409193 LAMA84 HAEMATOPOIETIC AND 5.8201 -0.854990707
LYMPHOID TISSUE ONCODG1 OVARY 5.8296 -0.845019051 HS888T BONE
5.8353 -0.839036058 SKNSH AUTONOMIC GANGLIA 5.8424 -0.831583558
TUHR14TKB KIDNEY 5.8451 -0.828749509 PF382 HAEMATOPOIETIC AND
5.8519 -0.821611903 LYMPHOID TISSUE ALLSIL HAEMATOPOIETIC AND
5.8724 -0.800094121 LYMPHOID TISSUE KMS34 HAEMATOPOIETIC AND 5.8799
-0.792221762 LYMPHOID TISSUE BICR6 UPPER AERODIGESTIVE 5.8837
-0.788233099 TRACT GRANTA519 HAEMATOPOIETIC AND 5.8937 -0.77773662
LYMPHOID TISSUE OCIAML2 HAEMATOPOIETIC AND 5.8945 -0.776896902
LYMPHOID TISSUE SUIT2 PANCREAS 5.8956 -0.775742289 BT549 BREAST
5.9226 -0.747401796 KMS28BM HAEMATOPOIETIC AND 5.9369 -0.732391831
LYMPHOID TISSUE HCC1428 BREAST 5.9402 -0.728927992 HCC1500 BREAST
5.9451 -0.723784718 A549 LUNG 5.9509 -0.71769676 KCL22
HAEMATOPOIETIC AND 5.9598 -0.708354893 LYMPHOID TISSUE COLO679 SKIN
5.9634 -0.704576161 SKMEL5 SKIN 5.9639 -0.704051337 HCC1395 BREAST
5.9716 -0.695969048 NCIH1435 LUNG 5.9756 -0.691770456 LOUNH91 LUNG
5.9793 -0.687886759 RPMI8402 HAEMATOPOIETIC AND 5.9827 -0.684317956
LYMPHOID TISSUE COLO668 LUNG 5.9969 -0.669412956 SKLU1 LUNG 6.0109
-0.654717885 KMS12BM HAEMATOPOIETIC AND 6.0135 -0.6519888 LYMPHOID
TISSUE SNU1272 KIDNEY 6.0226 -0.642437004 MOLM6 HAEMATOPOIETIC AND
6.0447 -0.619239786 LYMPHOID TISSUE EPLC272H LUNG 6.0469
-0.61693056 SCC4 UPPER AERODIGESTIVE 6.0502 -0.613466722 TRACT LMSU
STOMACH 6.0528 -0.610737638 KMS20 HAEMATOPOIETIC AND 6.0542
-0.60926813 LYMPHOID TISSUE G402 SOFT TISSUE 6.0606 -0.602550384
KYSE410 OESOPHAGUS 6.0741 -0.588380137 L540 HAEMATOPOIETIC AND
6.0807 -0.581452461 LYMPHOID TISSUE MOLT13 HAEMATOPOIETIC AND 6.084
-0.577988623 LYMPHOID TISSUE L1236 HAEMATOPOIETIC AND 6.0853
-0.57662408 LYMPHOID TISSUE LP1 HAEMATOPOIETIC AND 6.1029
-0.558150277 LYMPHOID TISSUE SNU620 STOMACH 6.1039 -0.557100629
MALME3M SKIN 6.112 -0.548598481 GSU STOMACH 6.1172 -0.543140312
MCF7 BREAST 6.1256 -0.53432327 COLO800 SKIN 6.1272 -0.532643833
MKN7 STOMACH 6.1453 -0.513645206 SNU119 OVARY 6.1473 -0.51154591
U118MG CENTRAL NERVOUS SYSTEM 6.1481 -0.510706192 OCILY19
HAEMATOPOIETIC AND 6.1512 -0.507452283 LYMPHOID TISSUE RKN SOFT
TISSUE 6.1579 -0.500419642 DV90 LUNG 6.1676 -0.490238057 NCIH1355
LUNG 6.171 -0.486669254 KMM1 HAEMATOPOIETIC AND 6.1723 -0.485304712
LYMPHOID TISSUE NCIH1184 LUNG 6.1776 -0.479741578 U937
HAEMATOPOIETIC AND 6.1777 -0.479636613 LYMPHOID TISSUE EJM
HAEMATOPOIETIC AND 6.1782 -0.479111789 LYMPHOID TISSUE C32 SKIN
6.1786 -0.47869193 NCIH23 LUNG 6.1854 -0.471554324 RERFLCAD1 LUNG
6.1862 -0.470714606 T3M10 LUNG 6.1867 -0.470189782 U266B1
HAEMATOPOIETIC AND 6.1906 -0.466096155 LYMPHOID TISSUE CAL54 KIDNEY
6.1949 -0.461582669 DND41 HAEMATOPOIETIC AND 6.1979 -0.458433726
LYMPHOID TISSUE PC14 LUNG 6.2003 -0.455914571 KMS11 HAEMATOPOIETIC
AND 6.2008 -0.455389747 LYMPHOID TISSUE DMS53 LUNG 6.2061
-0.449826613 SNU1214 UPPER AERODIGESTIVE 6.2071 -0.448776965 TRACT
GOS3 CENTRAL NERVOUS SYSTEM 6.2076 -0.448252141 TE8 OESOPHAGUS
6.2119 -0.443738655 ECGI10 OESOPHAGUS 6.2151 -0.440379781 KO52
HAEMATOPOIETIC AND 6.2174 -0.437965591 LYMPHOID TISSUE NCIH1793
LUNG 6.2189 -0.436391119 NB4 HAEMATOPOIETIC AND 6.219 -0.436286155
LYMPHOID TISSUE NCIH1105 LUNG 6.2191 -0.43618119 OCILY10
HAEMATOPOIETIC AND 6.222 -0.433137211 LYMPHOID TISSUE NCIH69 LUNG
6.2243 -0.430723021 A673 BONE 6.2304 -0.424320168 HCC4006 LUNG
6.2335 -0.42106626 SCC9 UPPER AERODIGESTIVE 6.2351 -0.419386823
TRACT OAW28 OVARY 6.2381 -0.416237879 BXPC3 PANCREAS 6.2387
-0.415608091 ISTMES1 PLEURA 6.2389 -0.415398161 SKMM2
HAEMATOPOIETIC AND 6.2396 -0.414663408 LYMPHOID TISSUE NCIN87
STOMACH 6.24 -0.414243548 T98G CENTRAL NERVOUS SYSTEM 6.2412
-0.412983971 GP2D LARGE INTESTINE 6.2536 -0.399968337 FTC238
THYROID 6.2564 -0.397029323 KMS27 HAEMATOPOIETIC AND 6.2607
-0.392515837 LYMPHOID TISSUE SNU201 CENTRAL NERVOUS SYSTEM 6.2618
-0.391361224 BC3C URINARY TRACT 6.266 -0.386952703 RS411
HAEMATOPOIETIC AND 6.2689 -0.383908724 LYMPHOID TISSUE TALL1
HAEMATOPOIETIC AND 6.2742 -0.37834559 LYMPHOID TISSUE RT4 URINARY
TRACT 6.2742 -0.37834559 SKOV3 OVARY 6.2773 -0.375091681 RERFLCAD2
LUNG 6.2783 -0.374042033
KHM1B HAEMATOPOIETIC AND 6.2859 -0.366064709 LYMPHOID TISSUE
KASUMI2 HAEMATOPOIETIC AND 6.2904 -0.361341294 LYMPHOID TISSUE
MOLT16 HAEMATOPOIETIC AND 6.2966 -0.354833477 LYMPHOID TISSUE
NUDUL1 HAEMATOPOIETIC AND 6.2966 -0.354833477 LYMPHOID TISSUE KMS18
HAEMATOPOIETIC AND 6.2973 -0.354098723 LYMPHOID TISSUE MDAMB175VII
BREAST 6.2981 -0.353259005 RMGI OVARY 6.3019 -0.349270343 KIJK
HAEMATOPOIETIC AND 6.305 -0.346016434 LYMPHOID TISSUE OCIAML5
HAEMATOPOIETIC AND 6.3062 -0.344756857 LYMPHOID TISSUE KMRC20
KIDNEY 6.3063 -0.344651892 LU65 LUNG 6.3082 -0.342657561 JIMT1
BREAST 6.3087 -0.342132737 SNU8 OVARY 6.3089 -0.341922807 KALS1
CENTRAL NERVOUS SYSTEM 6.3098 -0.340978124 SCABER URINARY TRACT
6.322 -0.32817242 OVMANA OVARY 6.3268 -0.32313411 TUHR10TKB KIDNEY
6.3302 -0.319565307 SUPM2 HAEMATOPOIETIC AND 6.3314 -0.318305729
LYMPHOID TISSUE JMSU1 URINARY TRACT 6.3317 -0.317990835 NCIH446
LUNG 6.3331 -0.316521328 COV434 OVARY 6.3341 -0.31547168 HCC38
BREAST 6.3361 -0.313372384 KMRC2 KIDNEY 6.3393 -0.310013511 SNU478
BILIARY TRACT 6.3432 -0.305919884 SUDHL1 HAEMATOPOIETIC AND 6.3444
-0.304660306 LYMPHOID TISSUE CMLT1 HAEMATOPOIETIC AND 6.3494
-0.299412067 LYMPHOID TISSUE UACC257 SKIN 6.3508 -0.29794256
NCIH1339 LUNG 6.3509 -0.297837595 M07E HAEMATOPOIETIC AND 6.3511
-0.297627665 LYMPHOID TISSUE KMRC3 KIDNEY 6.3514 -0.297312771
NCIH1693 LUNG 6.3603 -0.287970905 MM1S HAEMATOPOIETIC AND 6.3604
-0.28786594 LYMPHOID TISSUE HCC1143 BREAST 6.3611 -0.287131186
KATOIII STOMACH 6.3642 -0.283877278 MDAMB453 BREAST 6.3691
-0.278734003 J82 URINARY TRACT 6.3718 -0.275899954 CAL27 UPPER
AERODIGESTIVE 6.3725 -0.2751652 TRACT HS766T PANCREAS 6.3727
-0.274955271 HCT8 LARGE INTESTINE 6.3733 -0.274325482 NCIH1581 LUNG
6.3747 -0.272855975 REH HAEMATOPOIETIC AND 6.3759 -0.271596397
LYMPHOID TISSUE MPP89 PLEURA 6.3817 -0.265508439 SNU761 LIVER
6.3819 -0.26529851 RH30 SOFT TISSUE 6.3841 -0.262989284 KURAMOCHI
OVARY 6.3842 -0.26288432 HS936T SKIN 6.385 -0.262044601 HCC15 LUNG
6.3861 -0.260889989 F36P HAEMATOPOIETIC AND 6.388 -0.258895657
LYMPHOID TISSUE PANC0504 PANCREAS 6.3894 -0.25742615 NOMO1
HAEMATOPOIETIC AND 6.3925 -0.254172242 LYMPHOID TISSUE SKUT1 SOFT
TISSUE 6.3987 -0.247664425 CCK81 LARGE INTESTINE 6.4043
-0.241786397 NCIH211 LUNG 6.4058 -0.240211925 NH6 AUTONOMIC GANGLIA
6.4066 -0.239372206 BECKER CENTRAL NERVOUS SYSTEM 6.4161
-0.229400551 NCIH1869 LUNG 6.4177 -0.227721114 ASPC1 PANCREAS
6.4186 -0.226776431 VMCUB1 URINARY TRACT 6.4199 -0.225411889 SNU398
LIVER 6.4206 -0.224677136 THP1 HAEMATOPOIETIC AND 6.4214
-0.223837417 LYMPHOID TISSUE HS611T HAEMATOPOIETIC AND 6.4224
-0.222787769 LYMPHOID TISSUE ONS76 CENTRAL NERVOUS SYSTEM 6.4253
-0.21974379 LOVO LARGE INTESTINE 6.4266 -0.218379248 GMS10 CENTRAL
NERVOUS SYSTEM 6.4313 -0.213445903 RKO LARGE INTESTINE 6.4316
-0.213131009 ZR7530 BREAST 6.4339 -0.210716818 FU97 STOMACH 6.4421
-0.202109705 OCILY3 HAEMATOPOIETIC AND 6.4442 -0.199905445 LYMPHOID
TISSUE BV173 HAEMATOPOIETIC AND 6.4448 -0.199275656 LYMPHOID TISSUE
NCIH1568 LUNG 6.4489 -0.1949721 NCIH1155 LUNG 6.4497 -0.194132381
JURKAT HAEMATOPOIETIC AND 6.4524 -0.191298332 LYMPHOID TISSUE CW2
LARGE INTESTINE 6.4567 -0.186784846 RD SOFT TISSUE 6.4567
-0.186784846 RERFLCAI LUNG 6.4571 -0.186364987 YD10B UPPER
AERODIGESTIVE 6.4579 -0.185525268 TRACT SF295 CENTRAL NERVOUS
SYSTEM 6.4581 -0.185315339 JJN3 HAEMATOPOIETIC AND 6.4585
-0.18489548 LYMPHOID TISSUE EB1 HAEMATOPOIETIC AND 6.4633
-0.17985717 LYMPHOID TISSUE KNS60 CENTRAL NERVOUS SYSTEM 6.4642
-0.178912487 X697 HAEMATOPOIETIC AND 6.4674 -0.175553613 LYMPHOID
TISSUE TOV21G OVARY 6.4695 -0.173349353 JHH5 LIVER 6.4703
-0.172509634 OVTOKO OVARY 6.4718 -0.170935162 WM1799 SKIN 6.4744
-0.168206078 PL21 HAEMATOPOIETIC AND 6.4754 -0.16715643 LYMPHOID
TISSUE CA46 HAEMATOPOIETIC AND 6.4772 -0.165267064 LYMPHOID TISSUE
PATU8988S PANCREAS 6.479 -0.163377697 HCC44 LUNG 6.4794
-0.162957838 KARPAS299 HAEMATOPOIETIC AND 6.4827 -0.159494 LYMPHOID
TISSUE PANC0327 PANCREAS 6.4856 -0.156450021 YD8 UPPER
AERODIGESTIVE 6.4856 -0.156450021 TRACT GDM1 HAEMATOPOIETIC AND
6.4875 -0.15445569 LYMPHOID TISSUE IM95 STOMACH 6.4877 -0.154245761
HCT15 LARGE INTESTINE 6.4918 -0.149942204 WM793 SKIN 6.4939
-0.147737944 SHP77 LUNG 6.5008 -0.140495373 X8MGBA CENTRAL NERVOUS
SYSTEM 6.5012 -0.140075514 OUMS23 LARGE INTESTINE 6.5015
-0.139760619 SW1116 LARGE INTESTINE 6.5032 -0.137976218 NCIH1703
LUNG 6.5035 -0.137661324 HLF LIVER 6.5042 -0.13692657 REC1
HAEMATOPOIETIC AND 6.5051 -0.135981887 LYMPHOID TISSUE ML1 THYROID
6.5066 -0.134407415 HOS BONE 6.5069 -0.134092521 SW837 LARGE
INTESTINE 6.5072 -0.133777626 EHEB HAEMATOPOIETIC AND 6.5124
-0.128319457 LYMPHOID TISSUE HUH28 BILIARY TRACT 6.5145
-0.126115197 MDAMB157 BREAST 6.5173 -0.123176182 CHP212 AUTONOMIC
GANGLIA 6.5178 -0.122651359 RMUGS OVARY 6.52 -0.120342133 NCIH2106
LUNG 6.5249 -0.115198858 SKLMS1 SOFT TISSUE 6.5254 -0.114674034
X647V URINARY TRACT 6.5257 -0.11435914 HS294T SKIN 6.5258
-0.114254175 CHAGOK1 LUNG 6.5292 -0.110685372 NCIH2228 LUNG 6.5304
-0.109425795 MHHCALL3 HAEMATOPOIETIC AND 6.5324 -0.107326499
LYMPHOID TISSUE TE6 OESOPHAGUS 6.5328 -0.10690664 MHHES1 BONE
6.5353 -0.10428252 X42MGBA CENTRAL NERVOUS SYSTEM 6.5397
-0.099664069 SH10TC STOMACH 6.5448 -0.094310865 HCC202 BREAST
6.5484 -0.090532132 ACHN KIDNEY 6.5518 -0.08696333 SCC25 UPPER
AERODIGESTIVE 6.5527 -0.086018646 TRACT PANC0403 PANCREAS 6.5578
-0.080665442 A2780 OVARY 6.5613 -0.076991674 EBC1 LUNG 6.5617
-0.076571815 SW620 LARGE INTESTINE 6.5658 -0.072268259 SKMEL31 SKIN
6.5659 -0.072163294 PK45H PANCREAS 6.5666 -0.07142854 NCIH2030 LUNG
6.5688 -0.069119315 SKMES1 LUNG 6.5724 -0.065340583 NAMALWA
HAEMATOPOIETIC AND 6.5738 -0.063871075 LYMPHOID TISSUE CAL12T LUNG
6.5741 -0.063556181 HPBALL HAEMATOPOIETIC AND 6.5743 -0.063346251
LYMPHOID TISSUE HT1080 SOFT TISSUE 6.5745 -0.063136322 OE33
OESOPHAGUS 6.5749 -0.062716463 SR786 HAEMATOPOIETIC AND 6.5751
-0.062506533 LYMPHOID TISSUE NCIH929 HAEMATOPOIETIC AND 6.5755
-0.062086674 LYMPHOID TISSUE OVCAR4 OVARY 6.5755 -0.062086674 T47D
BREAST 6.5764 -0.061141991 HCC1937 BREAST 6.5773 -0.060197308
SKHEP1 LIVER 6.5773 -0.060197308 KMS26 HAEMATOPOIETIC AND 6.5778
-0.059672484 LYMPHOID TISSUE SNU1066 UPPER AERODIGESTIVE 6.5779
-0.059567519 TRACT SUPHD1 HAEMATOPOIETIC AND 6.5802 -0.057153329
LYMPHOID TISSUE L428 HAEMATOPOIETIC AND 6.5828 -0.054424244
LYMPHOID TISSUE PLCPRF5 LIVER 6.584 -0.053164667 MSTO211H PLEURA
6.5871 -0.049910758 GA10 HAEMATOPOIETIC AND 6.59 -0.046866779
LYMPHOID TISSUE HSC2 UPPER AERODIGESTIVE 6.59 -0.046866779 TRACT
MKN74 STOMACH 6.5911 -0.045712167 TOLEDO HAEMATOPOIETIC AND 6.5926
-0.044137695 LYMPHOID TISSUE KARPAS620 HAEMATOPOIETIC AND 6.5931
-0.043612871 LYMPHOID TISSUE CALU6 LUNG 6.5932 -0.043507906 SNU1196
BILIARY TRACT 6.5947 -0.041933434 HGC27 STOMACH 6.595 -0.04161854
NCIH716 LARGE INTESTINE 6.5964 -0.040149033 HDMYZ HAEMATOPOIETIC
AND 6.5974 -0.039099385 LYMPHOID TISSUE A3KAW HAEMATOPOIETIC AND
6.6031 -0.033116392 LYMPHOID TISSUE SNGM ENDOMETRIUM 6.6038
-0.032381638 CAL851 BREAST 6.6074 -0.028602906 JHUEM2 ENDOMETRIUM
6.608 -0.027973117 LN18 CENTRAL NERVOUS SYSTEM 6.6106 -0.025244032
VMRCRCZ KIDNEY 6.6107 -0.025139067 TE10 OESOPHAGUS 6.6127
-0.023039772 CAKI2 KIDNEY 6.614 -0.021675229 PK1 PANCREAS 6.6156
-0.019995793 TE1 OESOPHAGUS 6.6158 -0.019785863 IGR39 SKIN 6.6163
-0.019261039 NCIH1781 LUNG 6.6169 -0.01863125 A253 SALIVARY GLAND
6.6238 -0.01138868 NCIH727 LUNG 6.6253 -0.009814208 G361 SKIN
6.6284 -0.006560299 TYKNU OVARY 6.6296 -0.005300722 SNU1041 UPPER
AERODIGESTIVE 6.6307 -0.004146109 TRACT JL1 PLEURA 6.6309
-0.00393618 SNU283 LARGE INTESTINE 6.6315 -0.003306391 HCT116 LARGE
INTESTINE 6.632 -0.002781567 LS1034 LARGE INTESTINE 6.6323
-0.002466673 EFO21 OVARY 6.633 -0.001731919 DMS114 LUNG 6.6335
-0.001207095 SNU1077 ENDOMETRIUM 6.6342 -0.000472342 DAOY CENTRAL
NERVOUS SYSTEM 6.6343 -0.000367377 NCIH2342 LUNG 6.6346
-5.24824E-05 MOLP8 HAEMATOPOIETIC AND 6.6347 5.24824E-05 LYMPHOID
TISSUE BHT101 THYROID 6.6351 0.000472342 TE5 OESOPHAGUS 6.6355
0.000892201 PSN1 PANCREAS 6.6403 0.005930511 NCIH2170 LUNG 6.6424
0.008134771 RCHACV HAEMATOPOIETIC AND 6.6426 0.008344701 LYMPHOID
TISSUE HUH6 LIVER 6.6437 0.009499314 NCIH838 LUNG 6.6448
0.010653926 YAPC PANCREAS 6.6485 0.014537624 KYSE450 OESOPHAGUS
6.6505 0.016636919 RERFLCMS LUNG 6.6512 0.017371673 OVISE OVARY
6.6514 0.017581603 HT55 LARGE INTESTINE 6.6554 0.021780194 SNU899
UPPER AERODIGESTIVE 6.662 0.02870787
TRACT NCIH226 LUNG 6.6624 0.02912773 X639V URINARY TRACT 6.6635
0.030282342 TE14 OESOPHAGUS 6.6652 0.032066744 MKN45 STOMACH 6.6662
0.033116392 UMUC3 URINARY TRACT 6.6662 0.033116392 HEC6 ENDOMETRIUM
6.6667 0.033641216 X253JBV URINARY TRACT 6.6694 0.036475265 SKMEL24
SKIN 6.6712 0.038364631 VMRCLCD LUNG 6.6718 0.03899442 DLD1 LARGE
INTESTINE 6.6751 0.042458258 ECC12 STOMACH 6.6785 0.046027061
WSUDLCL2 HAEMATOPOIETIC AND 6.6801 0.047706498 LYMPHOID TISSUE
PFEIFFER HAEMATOPOIETIC AND 6.6804 0.048021392 LYMPHOID TISSUE
NCIH2087 LUNG 6.6806 0.048231322 NCIH2029 LUNG 6.6826 0.050330617
SJSA1 BONE 6.6844 0.052219984 A172 CENTRAL NERVOUS SYSTEM 6.6858
0.053689491 SNU1033 LARGE INTESTINE 6.6873 0.055263963 TM31 CENTRAL
NERVOUS SYSTEM 6.6885 0.05652354 X2313287 STOMACH 6.6886
0.056628505 SQ1 LUNG 6.6945 0.062821428 SUPT11 HAEMATOPOIETIC AND
6.695 0.063346251 LYMPHOID TISSUE NCIH2023 LUNG 6.6954 0.063766111
HCC1569 BREAST 6.6976 0.066075336 TT2609C02 THYROID 6.7014
0.070063998 SW1990 PANCREAS 6.7019 0.070588822 OVSAHO OVARY 6.7028
0.071533505 NCIH841 LUNG 6.7036 0.072373224 ME1 HAEMATOPOIETIC AND
6.7039 0.072688118 LYMPHOID TISSUE COLO205 LARGE INTESTINE 6.7052
0.07405266 TCCSUP URINARY TRACT 6.7056 0.074472519 TE11 OESOPHAGUS
6.7063 0.075207273 TE4 OESOPHAGUS 6.707 0.075942026 NCIH1694 LUNG
6.7095 0.078566146 KP4 PANCREAS 6.7102 0.0793009 CL11 LARGE
INTESTINE 6.711 0.080140618 NCIH596 LUNG 6.7123 0.08150516 OCIAML3
HAEMATOPOIETIC AND 6.7152 0.084549139 LYMPHOID TISSUE KMH2
HAEMATOPOIETIC AND 6.7155 0.084864034 LYMPHOID TISSUE PK59 PANCREAS
6.7163 0.085703752 HDLM2 HAEMATOPOIETIC AND 6.7172 0.086648435
LYMPHOID TISSUE ES2 OVARY 6.7183 0.087803048 SKNDZ AUTONOMIC
GANGLIA 6.7192 0.088747731 NCIH650 LUNG 6.7194 0.088957661 CAL62
THYROID 6.721 0.090637097 MDAMB231 BREAST 6.7222 0.091896675 HARA
LUNG 6.7238 0.093576111 MFE319 ENDOMETRIUM 6.7242 0.093995971
LCLC103H LUNG 6.7269 0.09683002 OE19 OESOPHAGUS 6.7273 0.097249879
HT144 SKIN 6.7297 0.099769034 HEC251 ENDOMETRIUM 6.7301 0.100188893
A4FUK HAEMATOPOIETIC AND 6.7317 0.10186833 LYMPHOID TISSUE K562
HAEMATOPOIETIC AND 6.7319 0.102078259 LYMPHOID TISSUE HEC59
ENDOMETRIUM 6.7321 0.102288189 NCIH1341 LUNG 6.7337 0.103967626
A204 SOFT TISSUE 6.7338 0.10407259 OV7 OVARY 6.7346 0.104912309
OV90 OVARY 6.7381 0.108586076 HCC827 LUNG 6.7384 0.108900971 DU4475
BREAST 6.742 0.112679703 SKMEL1 SKIN 6.742 0.112679703 KYSE70
OESOPHAGUS 6.7428 0.113519422 CHP126 AUTONOMIC GANGLIA 6.7459
0.11677333 DETROIT562 UPPER AERODIGESTIVE 6.7465 0.117403119 TRACT
CMK HAEMATOPOIETIC AND 6.7483 0.119292485 LYMPHOID TISSUE X769P
KIDNEY 6.7486 0.11960738 DEL HAEMATOPOIETIC AND 6.7494 0.120447098
LYMPHOID TISSUE PANC0813 PANCREAS 6.751 0.122126535 COLO201 LARGE
INTESTINE 6.752 0.123176182 SKNMC BONE 6.7533 0.124540725 CALU3
LUNG 6.7536 0.124855619 SNU1076 UPPER AERODIGESTIVE 6.7574
0.128844281 TRACT HCC78 LUNG 6.7625 0.134197486 ESS1 ENDOMETRIUM
6.7626 0.13430245 NCIH1755 LUNG 6.771 0.143119493 HPAFII PANCREAS
6.7751 0.147423049 CAKI1 KIDNEY 6.7755 0.147842908 COLO783 SKIN
6.778 0.150467028 NCIH2405 LUNG 6.7785 0.150991852 KNS81 CENTRAL
NERVOUS SYSTEM 6.7793 0.15183157 HCC95 LUNG 6.7794 0.151936535 HL60
HAEMATOPOIETIC AND 6.7796 0.152146465 LYMPHOID TISSUE FADU UPPER
AERODIGESTIVE 6.7809 0.153511007 TRACT TE617T SOFT TISSUE 6.782
0.15466562 KMBC2 URINARY TRACT 6.7837 0.156450021 HCC1171 LUNG
6.7838 0.156554986 CAPAN1 PANCREAS 6.786 0.158864211 CORL88 LUNG
6.7915 0.164637275 PECAPJ49 UPPER AERODIGESTIVE 6.7927 0.165896852
TRACT SF126 CENTRAL NERVOUS SYSTEM 6.7933 0.166526641 GSS STOMACH
6.794 0.167261395 U87MG CENTRAL NERVOUS SYSTEM 6.7949 0.168206078
HEYA8 OVARY 6.7972 0.170620268 HT1376 URINARY TRACT 6.7994
0.172929493 COLO792 SKIN 6.7997 0.173244388 SKMEL2 SKIN 6.8019
0.175553613 NCIH460 LUNG 6.8048 0.178597592 KU1919 URINARY TRACT
6.8061 0.179962134 SNU407 LARGE INTESTINE 6.8062 0.180067099 KU812
HAEMATOPOIETIC AND 6.8063 0.180172064 LYMPHOID TISSUE NCIH747 LARGE
INTESTINE 6.8075 0.181431642 A101D SKIN 6.8089 0.182901149
PATU8988T PANCREAS 6.8099 0.183950797 HS895T SKIN 6.8118
0.185945128 HMC18 BREAST 6.8147 0.188989107 X253J URINARY TRACT
6.8153 0.189618895 TE9 OESOPHAGUS 6.8154 0.18972386 LS123 LARGE
INTESTINE 6.8175 0.191928121 MCAS OVARY 6.8199 0.194447276 SW403
LARGE INTESTINE 6.8208 0.195391959 MDST8 LARGE INTESTINE 6.8209
0.195496924 RCM1 LARGE INTESTINE 6.8231 0.197806149 NCIH1650 LUNG
6.825 0.19980048 RPMI8226 HAEMATOPOIETIC AND 6.8256 0.200430269
LYMPHOID TISSUE SUDHL8 HAEMATOPOIETIC AND 6.8258 0.200640198
LYMPHOID TISSUE HEPG2 LIVER 6.8274 0.202319635 HT115 LARGE
INTESTINE 6.8303 0.205363614 KYSE520 OESOPHAGUS 6.8305 0.205573544
ISHIKAWAHERAKLIO02ER ENDOMETRIUM 6.8313 0.206413262 RT112 URINARY
TRACT 6.8313 0.206413262 SNU308 BILIARY TRACT 6.8314 0.206518227
HCC1806 BREAST 6.8314 0.206518227 NCIH2085 LUNG 6.8317 0.206833121
EFO27 OVARY 6.832 0.207148015 NCIH2052 PLEURA 6.8321 0.20725298
HSC4 UPPER AERODIGESTIVE 6.8327 0.207882769 TRACT KYSE140
OESOPHAGUS 6.836 0.211346607 LC1SQSF LUNG 6.8361 0.211451572 KMRC1
KIDNEY 6.8362 0.211556537 HUPT3 PANCREAS 6.837 0.212396255 NCIH1838
LUNG 6.8375 0.212921079 T24 URINARY TRACT 6.8383 0.213760797 WM115
SKIN 6.8396 0.21512534 KASUMI1 HAEMATOPOIETIC AND 6.8439
0.219638826 LYMPHOID TISSUE GAMG CENTRAL NERVOUS SYSTEM 6.8471
0.222997699 SBC5 LUNG 6.8494 0.225411889 WM2664 SKIN 6.8521
0.228245938 D283MED CENTRAL NERVOUS SYSTEM 6.857 0.233389213
MIAPACA2 PANCREAS 6.8607 0.23727291 BL70 HAEMATOPOIETIC AND 6.8619
0.238532488 LYMPHOID TISSUE NCIH1623 LUNG 6.862 0.238637453 BHY
UPPER AERODIGESTIVE 6.8627 0.239372206 TRACT OVCAR8 OVARY 6.8637
0.240421854 SNU840 OVARY 6.8651 0.241891361 CFPAC1 PANCREAS 6.8671
0.243990657 HS944T SKIN 6.8697 0.246719742 LK2 LUNG 6.8724
0.249553791 JHH1 LIVER 6.8737 0.250918333 OVKATE OVARY 6.8742
0.251443157 T84 LARGE INTESTINE 6.8791 0.256586432 SW1573 LUNG
6.8813 0.258895657 KYSE30 OESOPHAGUS 6.8825 0.260155235 DANG
PANCREAS 6.8825 0.260155235 SU8686 PANCREAS 6.8851 0.26288432 YD15
SALIVARY GLAND 6.8858 0.263619073 COLO680N OESOPHAGUS 6.8864
0.264248862 SUDHL6 HAEMATOPOIETIC AND 6.887 0.264878651 LYMPHOID
TISSUE SNU626 CENTRAL NERVOUS SYSTEM 6.8886 0.266558087 SNU1105
CENTRAL NERVOUS SYSTEM 6.8918 0.269916961 BT20 BREAST 6.8931
0.271281503 FTC133 THYROID 6.8949 0.273170869 P12ICHIKAWA
HAEMATOPOIETIC AND 6.8951 0.273380799 LYMPHOID TISSUE NCIH292 LUNG
6.8954 0.273695693 JHH2 LIVER 6.9004 0.278943933 RCC10RGB KIDNEY
6.9009 0.279468757 JHOC5 OVARY 6.9036 0.282302806 X786O KIDNEY
6.9057 0.284507067 AN3CA ENDOMETRIUM 6.9081 0.287026222 KP3
PANCREAS 6.909 0.287970905 HEC151 ENDOMETRIUM 6.9099 0.288915588
KE39 STOMACH 6.9103 0.289335447 HS822T BONE 6.9115 0.290595024 A375
SKIN 6.9117 0.290804954 MORCPR LUNG 6.9126 0.291749637 C2BBE1 LARGE
INTESTINE 6.9144 0.293639003 NCIH2452 PLEURA 6.9169 0.296263123
TCCPAN2 PANCREAS 6.9184 0.297837595 VMRCRCW KIDNEY 6.9222
0.301826257 NCIH810 LUNG 6.9222 0.301826257 PC3 PROSTATE 6.9226
0.302246116 MDAMB435S SKIN 6.9227 0.302351081 NCIH322 LUNG 6.9254
0.30518513 MOLP2 HAEMATOPOIETIC AND 6.928 0.307914215 LYMPHOID
TISSUE HCC366 LUNG 6.9295 0.309488687 KELLY AUTONOMIC GANGLIA
6.9352 0.31547168 AGS STOMACH 6.9378 0.318200764 MDAMB468 BREAST
6.9388 0.319250412 SNUC5 LARGE INTESTINE 6.939 0.319460342 HCC1195
LUNG 6.941 0.321559638 NB1 AUTONOMIC GANGLIA 6.9466 0.327437666
NCIH2126 LUNG 6.9473 0.32817242 HT HAEMATOPOIETIC AND 6.9476
0.328487314 LYMPHOID TISSUE SW48 LARGE INTESTINE 6.9505 0.331531293
QGP1 PANCREAS 6.9517 0.33279087 NUGC3 STOMACH 6.9527 0.333840518
SNU719 STOMACH 6.9544 0.33562492 SKES1 BONE 6.9576 0.338983793
OVK18 OVARY 6.9579 0.339298688 HEC1B ENDOMETRIUM 6.9583 0.339718547
KLE ENDOMETRIUM 6.9584 0.339823511 HEC50B ENDOMETRIUM 6.9622
0.343812174 TF1 HAEMATOPOIETIC AND 6.9682 0.350110061 LYMPHOID
TISSUE AM38 CENTRAL NERVOUS SYSTEM 6.9715 0.353573899 HCC1954
BREAST 6.9728 0.354938441 MELHO SKIN 6.9769 0.359241998 EN
ENDOMETRIUM 6.9773 0.359661857 HCC2108 LUNG 6.9789 0.361341294
X22RV1 PROSTATE 6.9813 0.363860449 PATU8902 PANCREAS 6.9874
0.370263301 LN229 CENTRAL NERVOUS SYSTEM 6.9883 0.371207984 GI1
CENTRAL NERVOUS SYSTEM 6.9897 0.372677491 SNU213 PANCREAS 6.9923
0.375406576 COLO684 ENDOMETRIUM 6.993 0.376141329 SNU738 CENTRAL
NERVOUS SYSTEM 6.9945 0.377715801 JK1 HAEMATOPOIETIC AND 6.9966
0.379920062 LYMPHOID TISSUE KYSE510 OESOPHAGUS 6.9987 0.382124322
NCIH1299 LUNG 6.9991 0.382544181 IGROV1 OVARY 7.0026 0.386217949
ACCMESO1 PLEURA 7.0033 0.386952703 BICR16 UPPER AERODIGESTIVE
7.0071 0.390941365
TRACT HCC2279 LUNG 7.0072 0.39104633 PANC1 PANCREAS 7.0096
0.393565485 CCFSTTG1 CENTRAL NERVOUS SYSTEM 7.0119 0.395979675
SNU668 STOMACH 7.0126 0.396714428 SW1271 LUNG 7.0143 0.39849883
SUDHL4 HAEMATOPOIETIC AND 7.0162 0.400493161 LYMPHOID TISSUE GCT
SOFT TISSUE 7.0174 0.401752738 TT THYROID 7.0183 0.402697421 DMS454
LUNG 7.019 0.403432175 LS180 LARGE INTESTINE 7.0225 0.407105943
SNU182 LIVER 7.0252 0.409939992 KNS62 LUNG 7.0253 0.410044957 OC314
OVARY 7.0273 0.412144253 RH41 SOFT TISSUE 7.0285 0.41340383
NCIH1373 LUNG 7.0318 0.416867668 BEN LUNG 7.0341 0.419281858 MESSA
SOFT TISSUE 7.0401 0.425579746 HEC1A ENDOMETRIUM 7.0465 0.432297493
L363 HAEMATOPOIETIC AND 7.0473 0.433137211 LYMPHOID TISSUE CAL29
URINARY TRACT 7.0497 0.435656366 RAJI HAEMATOPOIETIC AND 7.0524
0.438490415 LYMPHOID TISSUE ZR751 BREAST 7.054 0.440169852 KYSE180
OESOPHAGUS 7.0541 0.440274817 LOXIMVI SKIN 7.058 0.444368444 YD38
UPPER AERODIGESTIVE 7.06 0.446467739 TRACT SNU410 PANCREAS 7.0646
0.45129612 NCIH2291 LUNG 7.0654 0.452135838 PANC0203 PANCREAS
7.0662 0.452975556 NCIH1792 LUNG 7.0701 0.457069183 SW1088 CENTRAL
NERVOUS SYSTEM 7.0786 0.46599119 SKMEL30 SKIN 7.079 0.46641105 KM12
LARGE INTESTINE 7.0792 0.466620979 HEC108 ENDOMETRIUM 7.0804
0.467880557 NCIH526 LUNG 7.0825 0.470084817 NCIH661 LUNG 7.0832
0.470819571 KYSE150 OESOPHAGUS 7.0859 0.47365362 TUHR4TKB KIDNEY
7.0861 0.47386355 U251MG CENTRAL NERVOUS SYSTEM 7.091 0.479006825
MKN1 STOMACH 7.0915 0.479531649 DMS273 LUNG 7.0958 0.484045135
HS683 CENTRAL NERVOUS SYSTEM 7.0975 0.485829536 HS746T STOMACH
7.1012 0.489713233 OAW42 OVARY 7.1038 0.492442318 KYO1
HAEMATOPOIETIC AND 7.1048 0.493491966 LYMPHOID TISSUE HS688AT SKIN
7.1049 0.493596931 SIGM5 HAEMATOPOIETIC AND 7.1077 0.496535945
LYMPHOID TISSUE HUCCT1 BILIARY TRACT 7.1094 0.498320346 HS819T BONE
7.1097 0.498635241 HCC1588 LUNG 7.1149 0.50409341 KPL1 BREAST
7.1178 0.507137389 KE97 HAEMATOPOIETIC AND 7.1187 0.508082072
LYMPHOID TISSUE HCC2218 BREAST 7.1208 0.510286332 OCIM1
HAEMATOPOIETIC AND 7.1253 0.515009748 LYMPHOID TISSUE NCIH441 LUNG
7.1284 0.518263657 NCIH1092 LUNG 7.139 0.529389924 SKMEL28 SKIN
7.1392 0.529599854 HPAC PANCREAS 7.1394 0.529809784 SAOS2 BONE
7.1406 0.531069361 RL952 ENDOMETRIUM 7.1432 0.533798446 SKNAS
AUTONOMIC GANGLIA 7.145 0.535687812 CAL148 BREAST 7.1477
0.538521861 DMS79 LUNG 7.1572 0.548493516 EFE184 ENDOMETRIUM 7.1614
0.552902038 SUPT1 HAEMATOPOIETIC AND 7.167 0.558780066 LYMPHOID
TISSUE NMCG1 CENTRAL NERVOUS SYSTEM 7.1746 0.56675739 NCIH358 LUNG
7.1753 0.567492144 TE441T SOFT TISSUE 7.1772 0.569486475 MELJUSO
SKIN 7.1877 0.580507778 IPC298 SKIN 7.1984 0.59173901 SW1353 BONE
7.1985 0.591843975 CAL33 UPPER AERODIGESTIVE 7.2038 0.597407109
TRACT SNU489 CENTRAL NERVOUS SYSTEM 7.2056 0.599296475 LCLC97TM1
LUNG 7.2086 0.602445419 BICR56 UPPER AERODIGESTIVE 7.2108
0.604754644 TRACT NCIH508 LARGE INTESTINE 7.2176 0.61189225 HSC3
UPPER AERODIGESTIVE 7.2237 0.618295103 TRACT SNU878 LIVER 7.2238
0.618400067 CAMA1 BREAST 7.2254 0.620079504 LS411N LARGE INTESTINE
7.2279 0.622703624 YKG1 CENTRAL NERVOUS SYSTEM 7.2376 0.632885208
JHH6 LIVER 7.2377 0.632990173 KG1C CENTRAL NERVOUS SYSTEM 7.238
0.633305068 BT474 BREAST 7.2422 0.637713589 SNU1079 BILIARY TRACT
7.2463 0.642017145 KARPAS422 HAEMATOPOIETIC AND 7.2487 0.6445363
LYMPHOID TISSUE HEC265 ENDOMETRIUM 7.2509 0.646845526 NCIH2444 LUNG
7.2606 0.65702711 NUDHL1 HAEMATOPOIETIC AND 7.2677 0.664479611
LYMPHOID TISSUE AMO1 HAEMATOPOIETIC AND 7.2764 0.673611547 LYMPHOID
TISSUE HCC1833 LUNG 7.2887 0.686522217 SNUC4 LARGE INTESTINE 7.2927
0.690720808 HDQP1 BREAST 7.2935 0.691560527 OV56 OVARY 7.2957
0.693869752 P3HR1 HAEMATOPOIETIC AND 7.2973 0.695549189 LYMPHOID
TISSUE NUGC4 STOMACH 7.2991 0.697438555 U2OS BONE 7.3013 0.69974778
SNU886 LIVER 7.3032 0.701742112 NCIH28 PLEURA 7.3081 0.706885386
SNU601 STOMACH 7.3091 0.707935034 ECC10 STOMACH 7.3182 0.71748683
LS513 LARGE INTESTINE 7.3199 0.719271232 CAL120 BREAST 7.32
0.719376196 SNU1040 LARGE INTESTINE 7.3288 0.728613098 NCIH2171
LUNG 7.3416 0.742048591 SUDHL5 HAEMATOPOIETIC AND 7.3508
0.751705352 LYMPHOID TISSUE BFTC905 URINARY TRACT 7.3514
0.752335141 HT29 LARGE INTESTINE 7.364 0.765560705 RPMI7951 SKIN
7.375 0.777106832 AML193 HAEMATOPOIETIC AND 7.3753 0.777421726
LYMPHOID TISSUE MEC1 HAEMATOPOIETIC AND 7.376 0.778156479 LYMPHOID
TISSUE HEP3B217 LIVER 7.4062 0.809855846 SNU475 LIVER 7.4091
0.812899825 HUH1 LIVER 7.4298 0.834627537 HUPT4 PANCREAS 7.4555
0.861603488 IMR32 AUTONOMIC GANGLIA 7.4593 0.865592151 NCIH889 LUNG
7.4952 0.903274511 HCC2935 LUNG 7.5084 0.917129863 MC116
HAEMATOPOIETIC AND 7.5146 0.92363768 LYMPHOID TISSUE X5637 URINARY
TRACT 7.5183 0.927521377 SKM1 HAEMATOPOIETIC AND 7.5234 0.932874582
LYMPHOID TISSUE SKBR3 BREAST 7.5494 0.960165427 EM2 HAEMATOPOIETIC
AND 7.5755 0.987561238 LYMPHOID TISSUE RI1 HAEMATOPOIETIC AND
7.5915 1.004355605 LYMPHOID TISSUE SIMA AUTONOMIC GANGLIA 7.6032
1.016636485 FUOV1 OVARY 7.6122 1.026083316 SNUC2A LARGE INTESTINE
7.6165 1.030596802 SNU61 LARGE INTESTINE 7.6228 1.037209584 CAPAN2
PANCREAS 7.6273 1.041933 SNU216 STOMACH 7.6319 1.04676138 MOLM13
HAEMATOPOIETIC AND 7.646 1.061561416 LYMPHOID TISSUE HUNS1
HAEMATOPOIETIC AND 7.6648 1.081294796 LYMPHOID TISSUE HCC1438 LUNG
7.7264 1.145953108 NCIH2196 LUNG 7.7386 1.158758812 SNU466 CENTRAL
NERVOUS SYSTEM 7.7589 1.180066665 SUDHL10 HAEMATOPOIETIC AND 7.7977
1.220793004 LYMPHOID TISSUE SNU46 UPPER AERODIGESTIVE 7.8035
1.226880962 TRACT CALU1 LUNG 7.8185 1.242625681 BFTC909 KIDNEY
7.9189 1.348010331 JVM3 HAEMATOPOIETIC AND 7.961 1.392200508
LYMPHOID TISSUE MHHCALL4 HAEMATOPOIETIC AND 8.031 1.465675862
LYMPHOID TISSUE JURLMK1 HAEMATOPOIETIC AND 8.1126 1.551327131
LYMPHOID TISSUE KE37 HAEMATOPOIETIC AND 8.1163 1.555210829 LYMPHOID
TISSUE S117 SOFT TISSUE 8.2668 1.713182839 KMS21BM HAEMATOPOIETIC
AND 8.3309 1.780465271 LYMPHOID TISSUE KYM1 SOFT TISSUE 8.4417
1.896766259 CORL95 LUNG 8.5762 2.037943903 MHHNB11 AUTONOMIC
GANGLIA 8.8255 2.299621128 MDAMB361 BREAST 9.2909 2.788127266
Example 2. Identification of PDE3A as a Putative Target of
DNMDP
[0128] Given the potent cell-selective growth inhibition by
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP), its mechanism of action was examined in more detail. To
determine the molecular target of DNMDP, chemogenomic analysis was
performed of the 766 tested cell lines, previously characterized
for mutations, copy number, and gene expression features as part of
the Cancer Cell Line Encyclopedia (CCLE, Barretina et al., 2012),
to look for correlation between these genomic features and DNMDP
sensitivity. Analysis of Pearson correlations between DNMDP
sensitivity and expression of individual genes across the cell line
set showed a strong correlation with expression of the PDE3A gene,
encoding phosphodiesterase 3A (FIG. 5A).
[0129] The correlation between DNMDP sensitivity and PDE3A
expression is not perfect (FIG. 8), and it is possible that some
errors are introduced due to the high-throughput nature of the cell
line sensitivity characterization, as manual validation for all 766
cell lines was not logistically feasible. Mutation and copy number
features, in contrast, did not correlate with DNMDP sensitivity.
Conversely, of 480 compounds tested, DNMDP sensitivity was the
closest correlate of PDE3A expression (FIG. 5B), indicating that
cancer cell lines with high PDE3A expression were more distinctly
sensitive to DNMDP than to any other tested compound. In contrast
to the motivation of the initial screen, there was no correlation
between TP53 mutation, or other measures of p53 function, and DNMDP
sensitivity.
[0130] Given these results and the clear structural similarity of
DNMDP to known PDE3 inhibitors, e.g., levosimendan and siguazodan
(FIGS. 6A-6C), biochemical analysis of DNMDP against 19
phosphodiesterases representing 11 PDE super families was
performed. At a concentration of 100 nM, DNMDP specifically
inhibited both PDE3A and PDE3B, weakly inhibited PDE10, and had
little or no detectable effect on other phosphodiesterases (Table
2).
[0131] Because of the cellular correlation between PDE3A expression
and DNMDP sensitivity, the in vitro inhibition of PDE3A and PDE3B
by DNMDP, and the structural similarity of DNMDP to known PDE3
inhibitors, it was analyzed whether all PDE3 inhibitors would
exhibit a similar cytotoxic profile to DNMDP. Surprisingly, there
was almost no correlation between IC.sub.50 for in vitro enzymatic
PDE3A inhibition and HeLa cell cytotoxicity across a series of
tested compounds (FIG. 5C and FIGS. 7A and 7B). Indeed, the potent
PDE3 inhibitor trequinsin (PDE3 IC.sub.50=0.25 nM, Ruppert et al.,
Life Sci. 31, 2037-2043, 1982) did not affect HeLa cell viability
in any detectable way. Despite their differential effects on HeLa
cell viability, the non-cytotoxic PDE3 inhibitor trequinsin and the
potent cytotoxic compound DNMDP had similar effects on
intracellular cAMP levels in forskolin-treated HeLa cells (FIGS. 8A
and 8B). This result indicates that inhibition of the cAMP and cGMP
hydrolysis functions of PDE3A was not sufficient for the cytotoxic
activity of DNMDP.
TABLE-US-00006 TABLE 2 Results of phosphodiesterase inhibition
reactions PDE % inh. #1 % inh. #2 % inhibition PDE1A1 3 7 5 PDE1B
-5 0 -2 PDE1C 2 9 5 PDE2A 6 10 8 PDE3A 95 95 95 PDE3B 98 97 97
PDE4A1A 14 18 16 PDE4B1 21 20 21 PDE4C1 10 14 12 PDE4D3 14 16 15
PDE4D7 19 20 20 PDE5A1 16 16 16 PDE7A 24 20 22 PDE7B 5 11 8 PDE8A1
10 12 11 PDE9A2 0 5 2 PDE10A1 61 65 63 PDE10A2 67 70 68 PDE11A 14
18 16
Example 3. Target Validation of PDE3A
[0132] The complex relationship between phosphodiesterase 3A
(PDE3A) inhibition and cell killing, g in which
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) and some PDE3 inhibitors kill HeLa and other
DNMDP-sensitive cells, whereas others PDE3 g inhibitors do not
affect cell viability, indicated several possible interpretations
including: 1) the cytotoxic activity might be PDE3-independent and
due to action on a different protein though screening 234 kinases
found no kinase inhibition by 10 .mu.M DNMDP; 2) cytotoxic and
non-cytotoxic g PDE3 inhibitors might bind to different sites
within the protein and exert distinct activities; or 3) the
cytotoxic and non-cytotoxic PDE3 inhibitors might bind to the PDE3
active sites but have different effects on the conformation and
activity of the protein. This third possibility might be
unexpected, but allosteric modulators of PDE4 have been shown to
bind the PDE4 active site and interact with upstream (UCR2), and
downstream (CR3) regulatory domains and thereby stabilize specific
inactive conformations (Burgin et al., Nat Biotechnol 28, 63-70,
2010). Most importantly, PDE4 competitive inhibitors and PDE4
allosteric modulators with similar IC.sub.50s for cAMP hydrolysis
in vitro had different cellular activities and safety profiles in
animal studies (Burgin et al., Nat Biotechnol 28, 63-70, 2010). To
evaluate whether PDE inhibitors or other small molecules compete
with DNMDP, the PHARMAKON 1600 collection of 1600 bioactive
compounds (PHARMAKON 1600 is a unique collection of 1600 known
drugs from US and International Pharmacopeia) was screened to
identify compounds that were able to rescue cell death induced by
DNMDP. HeLa cells were co-treated with nM DNMDP (the EC.sub.70
concentration) and 20 .mu.M of each bioactive compound. Cell
viability after 48-hour treatment was assessed by ATP consumption
as described earlier. The five most potent compounds that rescued
cell death induced by DNMDP were all PDE inhibitors, and the three
most potent compounds, levosimendan, milrinone, and cilostazol,
were all selective PDE3 inhibitors (FIG. 9A).
[0133] In follow-up experiments, it was confirmed that cilostamide,
levosimendan, milrinone, and several other non-cytotoxic selective
PDE3 inhibitors were able to rescue DNMDP cytotoxicity in a
dose-dependent manner (FIG. 9B). The most potent DNMDP competitor
was trequinsin, with an "RC.sub.50" (the concentration at which it
achieved 50% rescue) of <1 nM; in contrast, PDE5 inhibitors such
as sildenafil and vardenafil, as well as the pan-PDE inhibitors
idubulast and dipyridamole, were not effective competitors up to 10
.mu.M concentrations in this assay (FIG. 9B). This indicated that
non-cytotoxic PDE3 inhibitors and DNMDP compete for binding to the
same molecular target that is mediating the cytotoxic
phenotype.
[0134] To identify the molecular target of DNMDP, an affinity
purification was performed using an (R)-des-nitro-DNMDP solid-phase
tethered linker analogue (FIG. 10A) incubated with HeLa cell
lysate. This linker analogue had the same DNMDP cytotoxicity rescue
phenotype as non-cytotoxic PDE3 inhibitors described above (FIG.
10B), indicating that it too bound to the same molecular target. It
was competed for the molecular target by adding either an excess of
trequinsin or separate enantiomers of DNMDP, where only the
(R)-enantiomer was cytotoxic. Immunoblotting for PDE3A of the
affinity purified material showed that PDE3A indeed binds to the
linker analogue. Binding of PDE3A to the linker analogue was
blocked by both trequinsin and (R)-DNMDP, but not by the
non-cytotoxic enantiomer (5)-DNMDP (FIG. 9C). Thus both trequinsin
and (if)-DNMDP prevented the binding of PDE3A to the tethered DNMDP
analogue, and it was concluded that both molecules bind PDE3A
directly.
[0135] Based on the observations that DNMDP-sensitive cells
expressed high levels of PDE3A, and that DNMDP competed with
non-cytotoxic inhibitors for PDE3A binding, it was hypothesized
that DNMDP mediated its cytotoxic phenotype through the interaction
with PDE3A and that PDE3A abundance was a direct cellular
determinant of DNMDP sensitivity. To validate this hypothesis, the
effect of reducing levels of PDE3A on the response to DNMDP was
tested. A clustered regularly interspaced short palindromic
(CRISPR)-associated CAS9 enzyme that was targeted with three guide
RNAs (sgRNA) targeting three different sites in the PDE3A locus led
to complete loss of PDE3A expression (Cong et al., Science 339,
819-823, 2013) sgRNA2 and sgRNA3 almost completely reduced PDE3A
protein levels, whereas sgRNA1 had a moderate effect on PDE3A
expression (FIG. 11A). Importantly, both sgRNA2 and sgRNA3 led to
significant rescue of toxicity by an active cytotoxic DNMDP analog,
3 (FIGS. 11A and 11B and FIGS. 5A-5C). Both sgRNA2 and sgRNA3 led
to significant rescue of toxicity by DNMDP (FIG. 11C). Changes in
proliferation rate or morphology in HeLa cells with reduced PDE3A
expression were not observed, indicating that PDE3A was not
required for cell survival. In an independent approach using an
siRNA smart-pool containing four different siRNAs targeting PDE3A,
PDE3A expression was reduced in HeLa cell line with a maximum
efficiency of 70% between 24 and 72 hours after transfection. HeLa
cells treated with siPDE3A had a higher EC.sub.50 to a DNMDP analog
compared to the control siRNA condition (FIGS. 12A and 12B).
Without being bound by theory it was concluded that DNMDP
cytotoxicity requires PDE3A, and that DNMDP likely modulates the
function of PDE3A.
Example 4. Determining the Mechanism of Action of DNMDP
[0136] The dependence of
6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-on-
e (DNMDP) cytotoxicity on phosphodiesterase 3A (PDE3A) protein
abundance indicated a possible mechanism similar to that recently
observed for lenalidomide, which acts by a neomorphic or
hypermorphic mechanism by stabilizing an interaction between
cereblon and IKAROS Family Zinc Finger 1 (IKZF1) and IKZF3 (Kronke
et al., Science 343, 301-305, 2014; Lu et al., Science 343,
305-309, 2014). In addition, PDE4 allosteric modulators, but not
competitive inhibitors, have been shown to bind and stabilize a
"closed" protein conformation that has independently been shown to
uniquely bind the PDE4-partner protein DISC1 (Millar et al.,
Science 310, 1187-1191, 2005). The protein complexes in which PDE3A
resides were characterized under normal conditions, and it was
examined how these complexes change when PDE3A is bound to DNMDP or
the non-cytotoxic PDE3 inhibitor trequinsin. PDE3A and interacting
proteins from Hela cells were immunoprecipitated in the presence of
DNMDP and trequinsin followed by labeling with isobaric stable
isotope tags for relative abundance and quantitation by mass
spectrometry (iTRAQ/MS, FIG. 13A). PDE3A immunoprecipitates from
HeLa cells were enriched for multiple protein phosphatase subunits
including protein phosphatase 2 subunits (PPP2CA, PPP2R1A, PPP2R1B,
PPP2R2A, PPP2R2D), calcineurin (PPP3R1, PPP3CA, Beca et al., Circ.
Res. 112, 289-297, 2013), 14-3-3 (YWHAB, YWHAQ, YWHAG, YWHAZ,
Pozuelo Rubio et al., Biochem. J. 392, 163-172, 2005), and tubulin
(TUBA1C, TUBA1B) family members (FIG. 13B and FIG. 14A). In
addition, it was found that PDE3A and PDE3B reside in the same
protein complex, which has been previously reported (Malovannaya et
ah, Cell 145,787-799,2011).
[0137] Binding of DNMDP altered the composition of interacting
proteins that were co-immunoprecipitated with PDE3A. Proteins that
were specifically enriched in PDE3A immunoprecipitates after
treatment with DNMDP included Sirtuin 7 (SIRT7) and Schlafen 12
(SLFN12) (FIG. 13C and FIG. 14B). These proteins specifically
interacted with PDE3A in the presence of DNMDP, and were not
observed in the trequinsin treated control, whereas a known PDE3B
interactor, abhydrolase domain-containing protein 15 (ABHD15,
Chavez et al., Biochem. Biophys. Res. Commun. 342, 1218-1222,
2006), was enriched in the immunoprecipitate from
trequinsin-treated cells (FIG. 13C and FIG. 14C). The interaction
promoted by DNMDP between PDE3A and both SIRT7 and SLFN12 was
validated with affinity reagents. Immunoprecipitation of endogenous
PDE3A in HeLa cells treated with DNMDP, but not DMSO or trequinsin,
enhanced complex formation of ectopically expressed V5-tagged SIRT7
and SLFN12 with PDE3A, as evidenced by coimmunoprecipitation (FIG.
19). FIG. 20 further shows that DNMDP and (weakly) anagrelide, but
not trequinsin, induced PDE3A and SFLN12 complex formation.
[0138] Similar to PDE3A, overexpression of SLFN12 appears to have a
cytotoxic effect in DNMDP sensitive cell lines, contributing to the
difficulty of detecting SLFN12 in whole cell lysates.
[0139] The enhanced interaction of PDE3A with SIRT7 and SLFN12
indicated the possibility that one or more of these interacting
proteins might contribute to DNMDP sensitivity. SIRT7 mRNA
expression was relatively constant among all cells tested, but the
co-expression of SLFN12 and PDE3A mRNA showed a strong correlation
with DNMDP sensitivity; almost all DNMDP-sensitive cell lines
expressed high levels of SLFN12 (FIG. 15A-15C). Importantly, almost
half of sensitive cell lines expressing high levels of SLFN12 and
PDE3A were found to be melanoma cell lines (FIG. 15B). SLFN12
expression alone was also one of the top genes correlating with
sensitivity to DNMDP, corroborating the hypothesis that SLFN12
could be functionally involved in DNMDP-induced cytotoxicity (FIG.
16A). Moreover, when correcting for PDE3A expression, SLFN12
expression was the top correlating gene with DNMDP sensitivity
(FIG. 16B). To assess whether SLFN12 is required for the cytotoxic
phenotype of DMNDP, we reduced SLFN12 mRNA expression by 60% by
knockdown with two shRNAs in HeLa cells (FIG. 15D). Similar to
reduction in PDE3A expression, reduction of SLFN12 expression did
not result in cytotoxicity, and in fact decreased sensitivity to
DNMDP (FIG. 15E). These results show that SLFN12, like PDE3A, is
required for the cytotoxic phenotype of DMNDP. Characterization of
normal expression of SLFN12 and PDE3A by the GTEX consortium
(Pierson, E. et al. PLoS Comput. Biol. 11, e1004220 (2015)) shows
low expression of SLFN12 in normal tissues, while high
co-expression of both PDE3A and SLFN12 is rarely observed (Table
3). This could suggest that on-target toxicity of DNMDP and related
compounds may be potentially limited.
TABLE-US-00007 TABLE 3 RPKM values of SLFN12 and PDE3A expression
in multiple healthy tissue types SLFN12 (RPKM) PDE3A (RPKM) Mean SD
Mean SD n Adipose - Subcutaneous 2.14 0.70 4.76 2.03 128 Adipose -
Visceral 2.43 1.03 4.26 1.94 31 (Omentum) Adrenal Gland 3.01 0.83
0.34 0.21 52 Artery - Aorta 2.10 0.71 16.15 5.12 82 Artery -
Coronary 1.80 0.80 17.73 6.52 44 Artery - Tibial 1.09 0.49 22.97
6.35 137 Bladder 1.38 0.57 1.33 0.40 11 Brain - Amygdala 0.37 0.23
0.96 0.34 26 Brain - Anterior cingulate 0.28 0.16 0.77 0.45 22
cortex (BA24) Brain - Caudate (basal 0.40 0.23 1.27 0.37 36
ganglia) Brain - Cerebellar 0.11 0.07 2.73 1.49 29 Hemisphere Brain
- Cerebellum 0.19 0.10 2.40 0.98 31 Brain - Cortex 0.25 0.12 0.56
0.59 25 Brain - Frontal Cortex 0.26 0.15 0.54 0.33 28 (BA9) Brain -
Hippocampus 0.39 0.31 0.82 0.38 28 Brain - Hypothalamus 0.46 0.29
0.93 0.48 30 Brain - Nucleus accumbens 0.28 0.16 1.11 0.41 32
(basal ganglia) Brain - Putamen (basal 0.29 0.18 0.91 0.33 24
ganglia) Brain - Spinal cord 0.50 0.32 0.65 0.55 19 (cervical c-1)
Brain - Substantia nigra 0.62 0.50 0.82 0.47 27 Breast - Mammary
Tissue 2.48 0.74 3.19 2.35 66 Cells - EBV-transformed 4.70 1.57
0.02 0.01 54 lymphocytes Cells - Transformed 5.34 2.27 0.58 0.60
155 fibroblasts Colon - Sigmoid 1.58 0.50 10.27 3.45 13 Colon -
Transverse 0.99 0.47 11.24 4.32 45 Esophagus - 1.14 0.31 16.87 5.53
22 Gastroesophageal Junction Esophagus - Mucosa 1.01 0.45 0.82 1.32
106 Esophagus - Muscularis 1.29 0.35 15.71 6.02 99 Fallopian Tube
2.32 0.86 3.80 1.86 6 Heart - Atrial Appendage 1.05 0.38 15.65 6.31
38 Heart - Left Ventricle 0.81 0.38 26.55 13.43 95 Kidney - Cortex
1.21 1.07 1.40 0.84 8 Liver 0.29 0.16 0.49 0.28 34 Lung 2.83 1.12
2.78 1.48 133 Minor Salivary Gland 1.75 0.61 0.62 0.44 5 Muscle -
Skeletal 0.25 0.18 0.84 0.42 157 Nerve - Tibial 2.82 0.87 3.39 1.71
114 Ovary 1.92 0.57 2.17 1.13 35 Pancreas 0.52 0.27 2.65 0.86 65
Pituitary 0.47 0.23 1.04 0.47 22 Prostate 1.41 0.57 4.04 3.74 42
Skin - Not Sun Exposed 0.76 0.37 0.66 0.34 41 (Suprapubic) Skin -
Sun Exposed (Lower 0.63 0.31 1.00 0.69 126 leg) Small Intestine -
Terminal 1.61 0.72 7.34 4.83 17 Ileum Spleen 3.46 0.92 1.18 0.46 34
Stomach 1.10 0.40 3.93 5.35 81 Testis 0.49 0.19 0.43 0.20 60
Thyroid 3.19 0.96 2.59 1.34 120 Uterus 1.99 0.56 3.29 1.55 32
Vagina 1.39 1.39 2.49 2.49 34 Whole Blood 1.40 1.10 0.06 0.05
191
[0140] FIG. 21 shows that SLFN12 is lost in cells that have
acquired resistance to DNMDP. Cell lines initially sensitive to
DNMDP were made resistant by persistent exposure to DNMDP and
subsequently analyzed by RNA-seq. One gene was downregulated in
both HeLa and H2122: SLFN 12. Accordingly, a reduction in levels of
SLFN 12 indicates that cells have become resistant to DNMDP and
other PDE3A modulators.
[0141] FIG. 22 shows sensitization of a DNMDP-resistant cell line
by expression of SLFN12 or expression of SFLN12 and PDE3A.
Expression of SLFN12 was sufficient to confer DNMDP sensitivity to
A549 cells. Adding PDE3A expression led to further
sensitization.
[0142] Leiomyosarcomas are malignant smooth muscle tumors. Patient
tumor samples from leiomyosarcomas were analyzed for PDE3A and
SLFN12 expression to characterize sensitivity of leiomyosarcomas
(LMS) to DNMDP. Leiomyosarcomas are thought to be sensitive to
DNMDP due to prevalence among high purity TCGA samples expressing
elevated levels of PDE3A and SLFN12 (FIG. 23, Table 4). P value for
association of biomarker expression with leiomyosarcoma lineage:
0.0001.
TABLE-US-00008 TABLE 4 Leiomyosarcomas Characterization Marker
Marker Expression Expression Indicates Indicates DNMDP DNMDP
sensitive not sensitive LMS 17 31 Not LMS 38 1516
[0143] Differential scanning fluorimetry (DSF) was used to
demonstrate binding of DNMDP to purified PDE3A catalytic domain,
PDE3A(677-1141). In this experiment, 5 .mu.M hsPDE3A(640-1141) was
incubated in the absence or presence of 100 .mu.M compounds, as
indicated in Table 5. Binding buffer: 20 mM Hepes pH 7.4, 100 .mu.M
TCEP, 1 mM MgCl.sub.2, 150 mM NaCl.
TABLE-US-00009 TABLE 5 Binding of DNMDP to PDE3A(677-1141) T.sub.m
(.degree. C.) .DELTA.T.sub.m (.degree. C.) PDE3A.sub.677-1141 52.4
.+-. 0.0 PDE3A.sub.677-1141 + DNMDP 58.4 .+-. 0.0 6.0
PDE3A.sub.677-1141 + Anagrelide 56.6 .+-. 0.0 4.2
PDE3A.sub.677-1141 + Trequinsin 66.2 .+-. 0.0 14.2
[0144] Using chemogenomics, a class of compounds was discovered,
exemplified by DNMDP, that targeted a novel cancer dependency by
small-molecule modulation of PDE3A. These compounds bound PDE3A in
a mutually exclusive manner with non-cytotoxic PDE3 inhibitors and
exerted a neomorphic or hypermorphic effect on the function of
PDE3A, leading to a change in its protein-protein interactions. One
unique protein-interaction partner, SLFN12, was highly expressed in
DNMDP-sensitive cell lines, indicating a functional role in the
pathway through which the cytotoxic signal was relayed. As a
result, DNMDP was both selective and potent across a large panel of
cancer cell lines.
[0145] Here, a novel cytotoxic compound was identified with great
selectivity and low-nM potency against cancer cell lines across
multiple lineages. Using gene-expression correlates for
chemogenomics, PDE3A was identified as the putative target of this
small molecule, DNMDP. Interestingly, loss of PDE3A expression
resulted in resistance to DNMDP. Moreover, PDE3A
immunoprecipitation followed by isobaric stable isotope tags for
relative abundance and quantitation by mass spectrometry (iTRAQ/MS)
identified SLFN12 and SIRT7 as novel protein-protein interaction
partners of PDE3A upon DNMDP binding, possibly due to allosteric
modulation of the function of PDE3A. Importantly, SLFN12 expression
was the top correlating gene with DNMDP sensitivity when corrected
for PDE3A expression. Single gene or multi-gene expression
correlations have shown to help elucidate the mechanism of action
and relevant signaling pathways of small molecules. A novel
biochemical target for cancer treatment was identified that is
unlikely to have been found by target identification approaches
such as loss-of-function screens or genomic analysis.
[0146] PDE3A belongs to the superfamily of phosphodiesterases and
together with PDE3B forms the PDE3 family. The PDE3 family has dual
substrate affinity and hydrolyses both cAMP and cGMP. Expression of
PDE3A is highest in the cardiovascular system, platelets, kidney,
and oocytes (Ahmad et al., Horm Metab Res 44, 776-785, 2012). The
clinical PDE3 inhibitor cilostazol has been developed to treat
intermittent claudication, as PDE3A inhibition in platelets impairs
activation and platelet coagulation (Bedenis et al., Cochrane
Database Syst Rev 10, CD003748, 2014). Other PDE3 inhibitors, such
as milrinone, amrinone, and levosimendan, are indicated to treat
congestive heart failure, where the combination of vasodilation and
elevated cardiac cAMP levels increases cardiac contractility
(Movsesian et al., Curr Op in Pharmacol 11, 707-713, 2011). None of
these clinical inhibitors were able to replicate the cytotoxic
phenotype of DNMDP, indicating that cyclic nucleotide hydrolysis
was not sufficient to induce cell death in DNMDP-sensitive cell
lines.
[0147] Interestingly however, other PDE3 inhibitors such as
zardaverine, anagrelide, and quazinone have been reported
previously to have cell cytotoxic characteristics in a select
number of cancer cell lines (Sun et al., PLoS ONE 9, e90627, 2014;
Fryknas et al., J Biomol Screen 11,457-468, 2006). In concordance
with the present findings, other PDE3 and PDE4 inhibitors were
found not to replicate the cytotoxic phenotype of zardaverine where
retinoblastoma protein retinoblastoma 1 (RB1) expression was
reported to separate zardaverine sensitive cell lines from
non-sensitive cell lines (Sun et al., PLoS ONE 9, e90627, 2014).
This finding was in contrast to the present data where a
correlation between cytotoxic activities of DNMDP and copy-number
or mRNA expression of RB1 was not identified. Another PDE3
inhibitor, anagrelide, uniquely inhibited megakaryocyte
differentiation, resulting in apoptosis. Other PDE3 inhibitors
tested did not have this activity (Wang et al., Br. J. Pharmacol.
146, 324 332, 2005; Espasandin, Y. et al., J. Thromb. Haemost. n/a
n/a, 2015, doi: 10.1111/jth.12850). It was hypothesized that the
reported effects of zardaverine on cell viability and anagrelide on
megakaryocyte differentiation are mediated through the same PDE3A
modulation as described in this study.
[0148] Multiple PDE3 inhibitors were competitive inhibitors and
have been shown to occupy the catalytic binding site of cAMP and
cGMP (Card et al., Structure 12, 2233-2247, 2004; Zhan et al., Mol.
Pharmacol. 62, 514-520, 2002). In addition, zardaverine has been
co-crystalized in a complex with PDE4D, where it occupies the
cAMP-binding site, and has been modeled to bind PDE3B in a similar
manner (Lee et al., FEBS Lett. 530, 53-58, 2002). Given the
structural similarity of DNMDP to zardaverine and that DNMDP
inhibited both PDE3A and PDE3B, it was hypothesized that the
binding mode of DNMDP is very similar to that of zardaverine. This
indicated that in addition to acting as a cAMP/cGMP-competitive
inhibitor, DNMDP allosterically induces a conformation that is
responsible for its cytotoxic phenotype. Allosteric modulation of
phosphodiesterases has been described previously for PDE4, where
small molecules bound in the active site and simultaneously
interacted with regulatory domains that came across the PDE4 active
site. As a result, allosteric modulators stabilized a protein
conformation that has been shown to differentially bind different
PDE4 partner proteins (Burgin et al., Nat Biotechnol 28, 63-70,
2010).
[0149] The study of proteins associated with PDE3A might illuminate
both its normal function and the way in which PDE3A modulators such
as DNMDP kill cancer cells. PDE3A interacted with protein
phosphatase 2 subunits, which are implicated in oncogenic viral
transformation and are mutated in human cancers (Nagao et al., Int.
Symp. Princess Takamatsu Cancer Res. Fund 20, 177-184, 1989;
Imielinski et al., Cell 150, 1107-1120, 2012; Lawrence et al.,
Nature 499, 214-218, 2013), indicating a role for PDE3A in cancer
cell signaling. Even though these interactions were not induced by
DNMDP binding, the importance of the protein phosphatases in cancer
biology would warrant further research.
[0150] The enhanced interaction between PDF3A and SLFN12,
facilitated by DNMDP binding to PDE3A, and the correlation between
sensitivity to DNMDP with SLFN12 expression strongly indicated that
it is necessary to understand the functional impact of the
PDE3A-SLFN12 interaction. However, lithe is known at this time
about the functional role of SLFN12 in human physiology and cancer
biology. SLFN12 is part of the schlafen gene family that diverges
largely between humans and rodents. The large difference is due to
rapid gene evolution and positive selection (Bustos et al., Gene
447, 1-11, 2009). Therefore, SLFN12 has no murine orthologue,
preventing the study of SLFN12 in a well-understood model organism.
The single publication on SLFN12 showed modulation of prostate
cancer cell lines after ectopic expression of SLFN12 (Kovalenko et
al., J. Surg. Res. 190, 177-184, 2014). Additional studies into the
function of SLFN12 and its interaction with PDE3A could elucidate
the mechanism of DNMDP cytotoxicity. Two observations indicated
that DNMDP acted as a neomorph or hypermorph on PDE3A function: 1)
DNMDP-sensitive cancer cell lines did not depend on PDE3A
expression for survival, but rather PDE3A knock-down led to DNMDP
resistance; and 2) DNMDP induced or enhanced protein-protein
interactions upon binding to PDE3A. Lenalidomide was an example of
a small molecule that acted as a neomorph or hypermorph rather than
as an enzymatic inhibitor. Lenalidomide modulated a specific
protein-protein interaction between the cereblon ubiquitin ligase
and Ikaros transcription factors, which were then subsequently
targeted for degradation (Kronke et al., Science 343, 301-305,
2014; Lu et al., Science 343, 305-309, 2014). By analogy, DNMDP
might directly stabilize a PDE3A-SLFN12 interaction, or DNMDP could
allosterically stabilize a PDE3 conformation that binds SLFN12.
Either of these mechanisms could result in a neo- or hypermorphic
phenotype. Further characterization of the neomorphic phenotype
induced by DNMDP might facilitate synthesis of small molecules that
will not inhibit cyclic nucleotide hydrolysis by PDE3A. Toxicity
profiles of such small molecules should differ from PDE3 inhibitors
prescribed for cardiovascular indications.
[0151] This study has uncovered a previously unknown role for PDE3A
in cancer maintenance, in which its function can be modified by a
subset of PDE3 inhibitors, resulting in toxicity to a subset of
cancer cell lines. These data indicated that DNMDP and its analogs
had a hyper- or neomorphic effect on PDE3A, leading to cellular
toxicity, which was corroborated by cells becoming less sensitive
to DNMDP with decreasing levels of cellular PDE3A. These
observations are comparable with other reports of allosteric
modulation of phosphodiesterases (Burgin et al., Nat Biotechnol 28,
63-70, 2010), indicating that DNMDP and analogues may have similar
effects on PDE3A. The exact mechanism of cell-selective
cytotoxicity remains unknown for now; however, further studies into
the novel interactions with SLFN12, and perhaps SIRT7, might be
informative.
[0152] In summary, the study herein used differential cytotoxicity
screening to discover a cancer cell cytotoxic small molecule,
DNMDP. Profiling of DNMDP in 766 genomically-characterized cancer
cell lines revealed stereospecific nanomolar efficacy in about 3%
of cell lines tested. A search for genomic features that indicated
sensitivity revealed that elevated PDE3A expression strongly
correlated with DNMDP response. DNMDP inhibited PDE3A and PDE3B,
with little or no activity towards other PDEs. However,
unexpectedly, most other PDE3A inhibitors tested did not phenocopy
DNMDP, including the potent and selective PDE3A inhibitor,
trequinsin. Co-treatment of DNMDP-sensitive cells with trequinsin
competed away the cancer cell cytotoxic activity of DNMDP, and
knockout of PDE3A rescued the otherwise sensitive cells from
DNMDP-induced cytotoxicity, leading us to hypothesize that PDE3A is
required for cancer cell killing by DNMDP, which induces a
neomorphic alteration of PDE3A. Mass spectrometric analysis of
PDE3A immunoprecipitates alone or in the presence of DNMDP or
trequinsin revealed differential binding of SLFN12 and SIRT7 only
in the presence of DNMDP. Similar to PDE3A, SLFN 12 expression
levels were elevated in DNMDP-sensitive cell lines, and knock down
of SLFN12 with shRNA decreased sensitivity of cells to DNMDP,
indicating that DNMDP-induced complex formation of PDE3A with
SLFN12 is critical to the cancer cell cytotoxic phenotype. Results
herein therefore implicate PDE3A modulators as candidate cancer
therapeutic agents and demonstrate the power of chemogenomics in
small molecule s discovery.
[0153] The experiments above were performed with the following
methods and materials.
Compound Library Screening in NCI-II1734 and A549 Cell Lines
[0154] 1500 NCI-II1734 or 1000 A549 cells were plated in a 384-well
plate in 40 .mu.l of RPMI supplemented with 10% Fetal Bovine Serum
and 1% Pen/Strep. 24 hours after plating, a compound-library of
1924 small molecules was added at a concentration of 10 .mu.M.
Staurosporine was used a positive control for cytotoxicity at a
concentration of 10 .mu.M, and DMSO was used a negative control at
a concentration of 1%. All compounds were incubated for 48 hours
with indicated small molecules. After 48 hours, 384-well plates
were removed from the incubator and allowed to cool to room
temperature for 20 minutes. Cell viability was assessed by adding
40 .mu.l of a 25% CELLTITERGLO.RTM. (Promega) in PBS with a THERMO
COMBI.TM. or multichannel-pipette and incubated for 10 minutes. The
luminescence signal was read using a Perkin-Elmer EnVision.
Viability percentage was calculated by normalizing to DMSO
controls.
Compound Sensitivity Testing in Cell Lines
[0155] 1000 HeLa (DMEM), 1000 A549 (RPMI), 500 MCF-7 (DMEM), 4000
PC3 (F12-K), 1000 NCI-H2122 (RPMI) or 1500 NCI-H1563 (RPMI) cells
were plated in a 384-well plate in 40 .mu.l of corresponding growth
media supplemented with 10% Fetal Bovine Serum. 24 hours after
plating, indicated compounds were added at indicated concentrations
and incubated for 48 hours. Cell viability was assessed as
described in Compound library screening in NCI-H1734 and A549 cell
lines.
Caspase Activity in HeLa Cells
[0156] 1000 HeLa cells were plated in 384-well plate in 40 .mu.l of
corresponding growth media supplemented with 10% Fetal Bovine
Scrum. 24 hours after plating, indicated compounds were added at
indicated concentrations and incubated for 48 hours. Caspase-Glo
from Promega was added according to the manufacturers
recommendations and luminescence was determined as described in
Compound library screening in NCI-H1734 and A549 cell lines.
Large-Scale Cell-Line Viability Measurements
[0157] The sensitivity of 777 cancer cell lines (CCLs) was measured
drawn from 23 different lineages to DNMDP. Each cell line was
plated in its preferred media in white opaque 1536-plates at a
density of 500 cells/well. After incubating overnight, DNMDP was
added by acoustic transfer at 16 concentrations ranging from 66.4
.mu.M-2 nM in 2-fold steps in duplicate (Labcyte Echo 555, Labcyte
Inc., Sunnyvale, Calif.). After 72 hours treatment, cellular ATP
levels were measured as a surrogate for viability
(CELLTITERGLO.RTM., Promega Corporation, Madison, Wis.) according
to manufacturer's protocols using a ViewLux Microplate Imager
(PerkinElmer, Waltham, Mass.) and normalized to background
(media-only) and vehicle (DMS 0)-treated control wells.
[0158] Concentration response curves were fit using nonlinear fits
to 2- or 3-parameter sigmoid functions through all 16
concentrations with the low-concentration asymptote set to the
DMSO-normalized value, and an optimal 8-point dose curve spanning
the range of compound-sensitivity was identified. The area under
the 8-point dose curve (AUC) was computed by numeric integration as
a metric for sensitivity for further analysis. Similar sensitivity
measurements have been obtained for a collection of 480 other
compounds, enabling analyses that identify cell lines responding
uniquely to DNMDP (see Broad Institute Cancer Therapeutics Response
Portal, a dataset ter identify comprehensively relationships
between genetic and lineage features of human cancer cell lines and
small-molecule sensitivities for complete list of compounds).
Correlation of Sensitivity Measurements with Basal Gene
Expression
[0159] Gene-centric robust multichip average (RMA)-normalized basal
mRNA gene expression data measured on the Affymetrix GeneChip Human
Genome U133 Plus 2.0 Array were downloaded from the Cancer Cell
Line Encyclopedia (CCLE, a detailed genetic characterization of a
large panel of human cancer cell lines; Barretina et al., Nature
483, 603-607, 2012). Pearson correlation coefficients were
calculated between gene expression (18,988 transcripts) and areas
under the curve (AUCs) across 760 overlapping CCLs. For comparisons
across small molecules exposed to differing numbers of CCLs,
correlation coefficients were transformed using Fisher's
transformation.
Chemistry Experimental Methods
General Details
[0160] All reactions were carried out under nitrogen (N2)
atmosphere. All reagents and solvents were purchased from
commercial vendors and used as received. Nuclear magnetic resonance
(NMR) spectra were recorded on a Bruker (300 or 400 MHz .sup.1H, 75
or 101 MHz .sup.13C) spectrometer. Proton and carbon chemical
shifts are reported in ppm (.delta.) referenced to the NMR solvent.
Data are reported as follows: chemical shifts, multiplicity
(br=broad, s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet;
coupling constant(s) in Hz). Flash chromatography was performed
using 40-60 .mu.m Silica Gel (60 .ANG. mesh) on a Teledyne Isco
Combiflash Rf. Tandem Liquid Chromatography/Mass Spectrometry
(LC/MS) was performed on a Waters 2795 separations module and 3100
mass detector with a Waters Symmetry C18 column (3.5 .mu.m,
4.6.times.100 mm) with a gradient of 0-100% CH3CN in water over 2.5
min with constant 0.1% formic acid. Analytical thin layer
chromatography (TLC) was performed on EM Reagent 0.25 mm silica gel
60-F plates. Elemental analysis was performed by Robertson Microlit
Laboratories, Ledgewood N.J.
Synthesis of (R)-DNMDP
##STR00014##
[0162] In 5 mL of acetic anhydride, 2.00 g (9.84 mmol) of
(R)-6-(4-aminophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one (A,
Toronto Research Chemicals) was stirred 1 hour before addition of
30 mL water, filtration, rinsing the solids with water and drying
to yield 2.20 g of product B (91%). .sup.1H NMR (300 MHz,
DMSO-d.sub.6) .delta. 10.92 (s, 1H), 10.13 (s, 1H), 7.74 (d, J=8.9,
2H), 7.65 (d, J=8.8, 2H), 3.41-3.33 (m, 1H), 2.68 (dd, J=6.8, 16.8,
1H), 2.23 (d, J=16.7, 1H), 2.08 (s, 3H), 1.07 (d, J=7.3, 3H).
.sup.13C NMR (75 MHz, DMSO-d.sub.6) .delta. 168.50, 166.27, 152.25,
140.27, 129.24, 126.24, 118.70, 33.47, 26.91, 24.02, 15.87. HPLC:
R.sub.t 0.72 min, purity>95%. MS: 246 (M+1).
[0163] To 3.09 g of B (15.3 mmol) dissolved in 30 mL of sulfuric
acid and cooled in an ice bath was added 0.72 mL of 90% nitric acid
(15 mmol) in 8 mL sulfuric acid via an addition funnel over 10
minutes. After stirring 1 hour the mixture was poured onto ice. The
yellow solid was filtered off and the water was rinsed several
times with EtOAc before drying and combining with the yellow solid.
Chromatography with 40-60% EtOAc in hexane yielded 1.12 g (25%) of
product as a yellow solid which was recrystallized from EtOAc.
.sup.1H NMR (300 MHz, DMSO-d.sub.6) .delta. 11.13 (s, 1H), 10.41
(s, 1H), 8.25 (d, J=1.8, 1H), 8.07 (dd, J=1.8, 8.6, 1H), 7.71 (d,
J=8.6, 1H), 3.55-3.40 (m, 1H), 2.74 (dd, J=6.9, 16.8, 1H), 2.27 (d,
J=16.8, 1H), 2.09 (s, 3H), 1.08 (d, J=7.2, 3H). .sup.13C NMR (75
MHz, DMSO-d6) .delta. 168.57, 166.31, 150.37, 142.19, 131.69,
131.32, 130.60, 125.07, 121.70, 33.30, 26.81, 23.44, 15.64. TLC: Rf
0.25 (1:1 EtOAc:hexane). HPLC: R.sub.t 0.87 min, purity>95%. MS:
291 (M+1). HRMS Exact Mass (M+1): 291.1088. Found: 291.1091.
[0164] To 58 mg of C (0.20 mmol) dissolved in 10 mL of MeOH was
added a solution of 48 mg NaOH (1.2 mmol) in 0.5 mL water. After 1
hour the reaction was concentrated, water was added and rinsed with
EtOAc, the EtOAc was dried and concentrated to give 48 mg (93%) of
product D. .sup.1H NMR (300 MHz, DMSO-d6) .delta. 10.92 (s, 1H),
8.28 (d, J=2.0, 1H), 7.87 (dd, J=2.1, 9.0, 1H), 7.76 (s, 2H), 7.06
(d, J=9.0, 1H), 3.33 (s, 1H), 2.67 (dd, J=6.8, 16.8, 1H), 2.22 (d,
J=16.6, 1H), 1.06 (d, J=7.3, 3H). .sup.13C NMR (75 MHz,
DMSO-d.sub.6) .delta. 166.25, 151.12, 146.69, 132.72, 129.80,
122.57, 122.19, 119.80, 33.43, 26.70, 15.77. MS: 249 (M+1).
[0165] To 35 mg of amine D (0.14 mmol) dissolved in 0.5 mL
Dimethylformamide (DMF) was added 70 mg of acetaldehyde (1.6 mmol)
and 170 mg of NaBH(OAc).sub.3 (0.80 mmol) and 10 .mu.L, (0.2 mmol)
of HOAc. After stirring 3 hours, water and EtOAc were added, the
EtOAc separated, dried, concentrated and chromatographed with
30-50% EtOAc in hexane to isolate 3 mg of the (R)-DNMDP (7%). The
synthesized material was identical to purchased racemic material by
TLC, HPLC and .sup.1H NMR. .sup.1H NMR (300 MHz, CDCl.sub.3)
.delta. 8.58 (s, 1H), 8.04 (d, J=2.3, 1H), 7.84 (dd, J=2.3, 9.0,
1H), 7.11 (d, J=9.0, 1H), 3.30-3.36 (m, 1H), 3.26 (q, 7=7.1, 4H),
2.71 (dd, J=6.8, 16.9, 1H), 2.48 (d, J=17.0, 1H), 1.25 (d, J=7.4,
3H), 1.16 (t, J=7.1, 6H). TLC: Rf0.25 (1:1 EtOAc:hexane). HPLC:
R.sub.t 1.27 min, purity>95%. MS: 305 (M+1). Exact Mass (M+1):
305.1608 Found: 305.1616. .sup.13C NMR (75 MHz, CDCl.sub.3,
purchased material) .delta. 166.28, 152.02, 145.24, 141.21, 129.77,
124.94, 123.94, 121.00, 46.10, 33.80, 27.81, 16.24, 12.56.
[0166] The optical purity of (R)-DNMDP was determined using chiral
SCF chromatography and comparison to commercially available racemic
material: Column: ChiralPak AS-H, 250.times.4.6 mm, 5 .mu.m, Mobile
Phase Modifier: 100% Methanol, Gradient: 5 to 50% Methanol over 10
minutes, Flow Rate: 4 mL/min, Back Pressure: 100 bar, Column
Temperature: 40 C. UV detection was from 200-400 nm. Retention
times of separated isomers: 5.36, 6.64 minutes; retention time of
(R)-DNMDP, 6.60 minutes, 1:19 ratio of enantiomers detected.
##STR00015##
[0167] 2. To 200 mg (0.98 mmol) of A dissolved in 5 mL of MeOH was
added 87 mg of acetaldehyde (2.0 mmol), 113 uL of HOAc (2.0 mmol)
and 124 mg (2.0 mmol) of NaBH.sub.3CN and the reaction was stirred
overnight at room temperature. The next day the same quantity of
reagents were added and the reaction stirred another 24 hours. The
mixture was concentrated and partitioned between CH.sub.2Cl.sub.2
and water, the CH.sub.2Cl.sub.2 was separated, dried, and
concentrated before chromatography with 20-40% EtOAc in hexane
isolated 210 mg of product as a white solid (82%). .sup.1H NMR (300
MHz, CDCl.sub.3) .delta. 8.95 (s, 1H), 7.64 (d, J=8.7, 2H), 6.66
(d, J=8.7, 2H), 3.37 (dd, J=9.6, 16.4, 5H), 2.67 (dd, J=6.5, 16.8,
1H), 2.43 (d, J=16.8, 1H), 1.41-1.02 (m, 10H). .sup.13C NMR (75
MHz, CDCl.sub.3) 1 .delta. .delta. 166.82, 154.55, 148.79, 127.32,
120.81, 111.08, 44.32, 33.92, 27.74, 16.37, 12.50. TLC: Rf0.25 (1:1
EtOAc:hexane). HPLC: R.sub.t 1.05 min, purity>95%. MS: 260
(M+1). HRMS Exact Mass (M+1): 260.1757. Found: 260.1764
##STR00016##
[0168] 3. To 200 mg (0.984 mmol) of A dissolved in 1 mL of
Dimethylformamide (DMF) was: added 250 .mu.L (2.00 mmol) of bis
(2-bromoethyl) ether and 400 mg of K2CO3 and the mixture was
stirred overnight at 60.degree. C. The next day another 250 .mu.L
of bis (2-bromoethyl) ether and 170 mg of K2CO3 were added. After 3
hours, EtOAc and water were added, the water was rinsed with EtOAc,
the combined EtOAc washes were dried and concentrated.
Chromatography with 0-4% MeOH in CH2Cl2 yielded 125 mg of product
(46%). .sup.1H NMR (300 MHz, CDCl.sub.3) .delta. 8.61 (s, 1H), 7.68
(d, J=8.8, 2H), 6.92 (d, J=8.8, 2H), 3.99-3.76 (m, 4H), 3.44-3.31
(m, 1H), 3.29-3.22 (m, 4H), 2.70 (dd, J=6.7, 16.8, 1H), 2.46 (d,
0.1=16.7, 1H), 1.24 (d, J=7.3, 3H). .sup.13C NMR (75 MHz,
CDCl.sub.3) .delta. 166.64, 154.05, 152.18, 127.10, 125.33, 114.73,
66.69, 48.33, 33.93, 27.94, 16.36. TLC: R.sub.f0.1 (1:50
MeOH:CH.sub.2Cl.sub.2). HPLC: R.sub.t 1.05 min, purity>95%. MS:
274 (M+1). HRMS: calcd. 274.1556 (M+1); found 274.1552. Anal.
Calcd. for C.sub.15H.sub.19N.sub.3O.sub.2: C, 65.91; H, 7.01; N,
15.37; Found. 65.81, H, 6.66, N, 15.26.
##STR00017##
[0169] DNMDP-2L. To 130 mg of A (0.64 mmol) dissolved in 0.4 mL of
Dimethylformamide (DMF) was added 100 mg of tert-butyl
2-(2-(2-bromoethoxy)ethoxy)-ethylcarbamate (Toronto Research
Chemical, 0.32 mmol) and 90 mg of K.sub.2CO.sup.3 (64 mmol) and the
mixture was stirred at 60.degree. C. overnight. After cooling,
water was added and rinsed several times with EtOAc. The combined
EtOAc layers were dried, concentrated, and chromatographed with
50-70% EtOAc to yield 81 mg of product (58%). .sup.1H NMR (300 MHz,
CDCl.sub.3) .delta. 9.06 (s, 1H), 7.59 (d, J=8.8 Hz, 2H), 6.62 (d,
J=8.8 Hz, 2H), 5.15 (s, 1H), 4.53 (s, 1H), 3.72 (t, J=5.2 Hz, 2H),
3.65 (s, 4H), 3.55 (t, J=5.2 Hz, 2H), 3.32 (m, 5H), 2.67 (dd,
J=16.8, 6.7 Hz, 1H), 2.42 (d, J=16.4 Hz, 1H), 1.44 (s, 9H), 1.22
(d, J=7.4 Hz, 3H). .sup.13C NMR (75 MHz, CDCl.sub.3) .delta.
166.83, 155.99, 154.45, 149.64, 127.33, 123.24, 112.58, 79.28,
70.30, 70.26, 70.22, 69.45, 43.14, 40.39, 33.96, 28.43, 27.89,
16.40; HPLC: R, 2.50 min (7.5 min run), purity>95%. MS: 435
(M+1). This product (0.19 mmol) was dissolved in 1 mL MeOH and to
the solution was added acetaldehyde (50 uL, 0.89 mmol), 10 uL HOAc
(0.2 mmol) and 12 mg NaBH.sub.3CN (0.19 mmol). After 1 hour,
NaHCO.sub.3(aq) and CH.sub.2Cl.sub.2 were added, the
CH.sub.2Cl.sub.2 was separated and the water washed twice with
CH.sub.2Cl.sub.2. The combined CH.sub.2Cl.sub.2 was dried,
concentrated, and chromatography with 60-70% EtOAc in hexane
yielded 71 mg of product as a clear oil (82%). .sup.1H NMR (400
MHz, CDCl.sub.3) .delta. 8.91 (s, 1H), 7.63 (d, J=8.9 Hz, 2H), 6.69
(d, J=8.9 Hz, 2H), 5.07 (s, 1H), 3.65 (t, J=6.0 Hz, 2H), 3.61 (s,
4H), 3.55 (dt, J=9.9, 5.5 Hz, 4H), 3.46 (q, J=7.0 Hz, 2H),
3.38-3.22 (m, 3H), 2.67 (dd, J=16.8, 6.7 Hz, 1H), 2.43 (d, J=16.7
Hz, 1H), 1.45 (s, 10H), 1.23 (d, J=7.3 Hz, 3H), 1.18 (t, J=7.0 Hz,
3H). .sup.13C NMR (101 MHz, CDCl.sub.3) .delta. 166.84, 155.96,
154.46, 148.89, 127.35, 121.38, 111.28, 79.22, 70.68, 70.27, 70.24,
68.74, 49.95, 45.49, 40.32, 33.97, 28.43, 27.80, 16.43, 12.14.
R.sub.t 2.99 min (7.5 min run), purity>95%. MS: 463 (M+1).
Attachment to Resin
[0170] To a solution of 18 mg of DNMDP-2L (0.04 mmol) in 0.8 mL of
CH.sub.2Cl.sub.2 was added 0.2 mL of trifluoroacetic acid (TFA) and
the solution was stirred 2 h before concentration and dissolution
in 0.5 mL DMSO. To this was added 10 uL of Et.sub.3N (0.07 mmol)
and 12 mg of N,N'-disuccinimidyl carbonate (DSC) (0.05 mmol) and
the solution was stirred overnight. LC analysis indicated the
reaction was not complete, another 25 mg of N,N'-disuccinimidyl
carbonate (0.1 mmol) was added. LC analysis after 2 hours showed
ca. 5:1 ratio of DSC product:amine. A 1 mL sample of Affi-Gel 102
resin was rinsed five times with DMSO with a centrifuge, then
suspended in 0.5 mL DMSO. To the resin was added 30 uL of the DSC
product solution and 25 uL Et3N and the mixture was swirled. After
2 days, LC analysis of the DMSO solution showed complete
disappearance of the DCS adduct the underivatized amine was still
present. The DMSO was removed by centrifuge and decanted and the
resin was rinsed several times with DMSO and stored in PBS
buffer.
Bioactives Screen to Rescue DNMDP Induced Cytotoxicity
[0171] 1000 HeLa cells were plated in a 384-well plate in 40 .mu.l
of DMEM supplemented with 10% Fetal Bovine Serum and 1% Pen/Strep.
24 hours after plating, a compound-library of 1600 bioactive
molecules (Pharmacon) was added at a concentration of 20 .mu.M. In
parallel to bioactive compound incubation, DNMDP was added to a
final concentration of 30 nM and incubated for 48 hours. Cell
viability was assessed as described in Compound library screening
in NCI-H1734 and A549 cell lines.
Linker-Affinity Purification of Molecular Target of DNMDP and
Immunoblotting
[0172] HeLa cells were washed with ice-cold PBS before lysed with
NP-40 lysis buffer (150 mM NaCl, 10% glycerol, 50 mM Tris-Cl pH
8.0, 50 mM MgCl.sub.2, 1% NP-40) supplemented with EDTA-free
protease inhibitors (Roche) and phosphatase inhibitor mixtures I
and II (Calbiochem). Cell lysates were incubated on ice for at
least 2 minutes and subsequently centrifuged for 10 minutes at
4.degree. C. at 15,700.times.g after which the supernatant was
quantified using BCA protein assay kit (Pierce). 200 .mu.g total
HeLa cell lysate was incubated with 3 .mu.l Affi-Gel 102 resin
(BioRad) coupled to affinity linker DNMDP-2L in a total volume of
400 .mu.l for four hours. Prior to incubation, indicated compounds
were added to affinity purifications at a final concentration of 10
.mu.M. Samples were washed three times with lysis buffer containing
corresponding compound concentrations of 10 .mu.M. Proteins bound
to Affi-Gel 102 resin were reduced, denatured, and separated using
Tris-Glycine gels (Novex) and transferred to nitrocellulose
membranes using the iBlot transfer system (Novex). Membranes were
incubated overnight at 4.degree. C. with primary antibodies against
PDE3A (1:1000, Bethyl). Incubation with secondary antibodies
(1:20,000, LI-COR Biosciences) for two hours at room temperature
and subsequent detection (Odyssey Imaging System, LI-COR
Biosciences) were performed according to manufacturer's
recommendations.
PARP-Cleavage Immunoblotting
[0173] HeLa cells were treated with indicated concentration of
DNMDP and staurosporine for 36 hours. HeLa cells were lysed and
processed as described in Linker-affinity purification of molecular
target of DNMDP and immunoblotting. Membranes were incubated with
an antibody against PARP (1:1000, Cell Signaling #9532) and actin
and subsequently imaged as described in Linker-affinity
purification of molecular target of DNMDP and immunoblotting.
Targeting PDE3A Locus Using CRISPR
[0174] CRISPR target sites were identified using the MIT CRISPR
Design Tool (online MIT CRISPR design portal). For cloning of
sgRNAs, forward and reverse oligos were annealed, phosphorylated
and ligated into BsmBI-digested pXPR_BRD001. Oligo sequences are as
follows:
TABLE-US-00010 sRNA Forward oligo Reverse oligo PDE3A_sg1
CACCGTTTTCACTGA AAACTCACTTCGCTC GCGAAGTGA AGTGAAAAC (SEQ ID NO.: 7)
(SEQ ID NO.: 8) PDE3A_sg2 CACCGAGACAAGCTT AAACTTGGAATAGCAA
GCTATTCCAA GCTTGTCTC (SEQ ID NO.: 9) (SEQ ID NO.: 10) PDE3A_sg3
CACCGGCACTCTGAG AAACTAACTTACACTC TGTAAGTTA AGAGTGCC (SEQ ID NO.:
11) (SEQ ID NO.: 12)
To produce lentivirus, 293T cells were co-transfected with pXPR
BRD001, psPAX2 and pMD2.G using calcium phosphate. Infected HeLa
cells were selected with 2 ug/ml of puromycin. Reduction of PDE3A
expression using siRNA HeLa cells were plated in 96-well plates and
transfected after 24 hours with PDE3A and Non-Targeting siRNA
smartpools (On Target Plus, Thermo Scientific) according to the
manufacturers recommendations. HeLa cell lysate was obtained 24
hours and 72 hours after transfection and immunoblotted for PDE3A
and Actin (1:20,000, Cell Signaling) as described in
Linker-affinity purification of molecular target of DNMDP and
immunoblotting. HeLa cells were treated for 48 hours with indicated
concentrations of Compound 3. Cell viability was assessed as
described in Compound library screening in NCI-H1734 and A549 cell
lines. Measuring Cellular cAMP Concentrations in HeLa Cells
[0175] 5000 HeLa cells were plated in 96-well plates. 24 hours
after plating, HeLa cells were incubated for one hour with
indicated compounds at indicated concentrations. cAMP levels were
determined with the CAMP-GLO.TM. assay (Promega) according to the
manufacturers recommendations. Cellular concentrations of cAMP were
determined by normalizing to a standard curve generated according
to the manufacturers recommendations.
Extended Proteomics Methods for PDE3A-Protein Interaction
Studies
Immunoprecipitation of PDE3A in HeLa Cells
[0176] HeLa cells were treated for four hours prior to lysis with
10 .mu.M of indicated compounds: DMSO, DNMDP and trequinsin. HeLa
cells were lysed with ModRipa lysis buffer (1% NP-40:50 25 mM
Tris-HCl, pH 7.8, 150 mM NaCl, 0.1% sodium deoxycholate, 1 mM EDTA)
supplemented with protease and phosphatase inhibitors as described
in Linker-affinity purification of molecular target of DNMDP and
immunoblotting, and indicated compounds as described above to a
final concentration of 10 .mu.M. 13 mg of HeLa total cell lysate
was incubated with 0.5% PDE3A antibody (Bethyl) and incubated
overnight. Blocking peptide (Bethyl) against the PDE3A antibody was
added simultaneously with the PDE3A antibody in the corresponding
condition. Total cell lysate and antibody mixture was then
incubated with 10 .mu.l Protein A Plus Agarose (Fisher Scientific)
for 30 minutes at 4.degree. C. Protein A Plus Agarose was then
washed two times with lysis buffer containing indicated compounds
at a concentration of 10 .mu.M. Finally, Protein A Plus Agarose was
washed once with lysis buffer containing no NP-40 and indicated
compounds at a concentration of 10 .mu.M.
On-Bead Digest
[0177] The beads from immunopurification were washed once with IP
lysis buffer, then three times with PBS, the three different
lysates of each replicate were resuspended in 90 uL digestion
buffer (2M Urea, 50 mM Tris HCl), 2 ug of sequencing grade trypsin
added, 1 hour shaking at 700 rpm. The supernatant was removed and
placed in a fresh tube. The beads were then washed twice with 50 uL
digestion buffer and combined with the supernatant. The combined
supernatants were reduced (2 uL 500 mM DTT, 30 minutes, room
temperature), alkylated (4 uL 500 mM 1AA, 45 minutes, dark) and a
longer overnight digestion performed: 2 ug (4 uL) trypsin, shake
overnight. The samples were then quenched with 20 uL 10% folic acid
(FA) and desalted on 10 mg SEP-PAK.RTM. columns.
iTRAQ Labeling of Peptides and Strong Cation Exchange (Sex)
Fractionation
[0178] Desalted peptides were labeled with isobaric tags for
relative and absolute quantification (iTRAQ)-reagents according to
the manufacturer's instructions (AB Sciex, Foster City, Calif.).
Peptides were dissolved in 30 .mu.l of 0.5 M TEAB pH 8.5 solution
and labeling reagent was added in 70 ul of ethanol. After 1 hour
incubation the reaction was stopped with 50 mM Tris/HCl pH 7.5.
Differentially labeled peptides were mixed and subsequently
desalted on 10 mg SEP-PAK.RTM. columns.
TABLE-US-00011 iTRAQ labeling 114 115 116 117 Rep1 Blocking peptide
No addition DNMDP trequinsin Rep2 Blocking peptide No addition
DNMDP trequinsin
SCX fractionation of the differentially labelled and combined
peptides was done as described in Rappsilber et al. (Rappsilber et
ah, Nat Protoc 2, 1896-1906, 2007), with 6 pH steps (buffers--all
contain 25% acetonitrile) as below: [0179] 1: ammonium acetate 50
mM pH 4.5, [0180] 2: ammonium acetate 50 mM pH 5.5, [0181] 3:
ammonium acetate 50 mM pH 6.5, [0182] 4: ammonium bicarbonate 50 mM
pH 8, [0183] 5: ammonium hydroxide 0.1% pH 9, [0184] 6: ammonium
hydroxide 0.1% pH 11. Empore SCX disk used to make
stop-and-go-extraction-tips (StageTips) as described in the
paper.
MS Analysis
[0185] Reconstituted peptides were separated on an online nanoflow
EASY-NLC.TM. 1000 UHPLC system (Thermo Fisher Scientific) and
analyzed on a benchtop Orbitrap Q EXACTIVE.TM. mass spectrometer
(Thermo Fisher Scientific). The peptide samples were injected onto
a capillary column (PICOFRIT.RTM. with 10 .mu.m tip opening/75
.mu.m diameter, New Objective, PF360-75-10-N-5) packed in-house
with 20 cm C18 silica material (1.9 .mu.m REPROSIL-PUR.RTM. C18-AQ
medium, Dr. Maisch f GmbH, rI 19.aq). The UHPLC setup was connected
with a custom-fit microadapting tee (360 .mu.m, IDEX Health &
Science, UH-753), and capillary columns were heated to 50.degree.
C. in column heater sleeves (Phoenix-ST) to reduce backpressure
during UHPLC separation. Injected peptides were separated at a flow
rate of 200 nL/min with a linear 80 min gradient from 100% solvent
A (3% acetonitrile, 0.1% formic acid) to 30% solvent B (90%
acetonitrile, 0.1% formic acid), followed by a linear 6 min
gradient from 30% solvent B to 90% solvent B. Each sample was run
for 120 minutes, including sample loading and column equilibration
times. The Q EXACTIVE.TM. instrument was operated in the
data-dependent mode acquiring high-energy collisional dissociation
(HCD) MS/MS scans (R=17,500) after each MS1 scan (R=70,000) on the
12 top most abundant ions using an MS1 ion target of 3.times.106
ions and an MS2 target of 5.times.104 ions. The maximum ion time
utilized for the MS/MS scans was 120 ms; the HCD-normalized
collision energy was set to 27; the dynamic exclusion time was set
to 20s, and the peptide match and isotope exclusion functions were
enabled.
Quantification and Identification of Peptides and Proteins
[0186] All mass spectra were processed using the Spectrum Mill
software package v4.1 beta (Agilent Technologies) which includes
modules developed by Applicants for isobaric tags for relative and
absolute quantification (iTRAQ)-based quantification. Precursor ion
quantification was done using extracted ion chromatograms (XIC's)
for each precursor ion. The peak area for the XIC of each precursor
ion subjected to MS/MS was calculated automatically by the Spectrum
Mill software in the intervening high-resolution MS1 scans of the
liquid chromatography (LC)-MS/MS runs using narrow windows around
each individual member of the isotope cluster. Peak widths in both
the time and m/z domains were dynamically determined based on MS
scan resolution, precursor charge and m/z, subject to quality
metrics on the relative distribution of the peaks in the isotope
cluster vs theoretical. Similar MS/MS spectra acquired on the same
precursor m/z in the same dissociation mode within +/-60 seconds
were merged. MS/MS spectra with precursor charge>7 and poor
quality MS/MS spectra, which failed the quality filter by not
having a sequence tag length>1 (i.e., minimum of 3 masses
separated by the in-chain mass of an amino acid) were excluded from
searching.
[0187] For peptide identification MS/MS spectra were searched
against human Universal Protein Resource (Uniprot) database to
which a set of common laboratory contaminant proteins was appended.
Search parameters included: ESI-Q EXACTIVE.TM.-HCD scoring
parameters, trypsin enzyme specificity with a maximum of two missed
cleavages, 40% minimum matched peak intensity, +/-20 ppm precursor
mass tolerance, +/-20 ppm product mass tolerance, and
carbamidomethylation of cysteines and iTRAQ labeling of lysines and
peptide n-termini as fixed modifications. Allowed s variable
modifications were oxidation of methionine, N-terminal acetylation,
Pyroglutamic acid (N-termQ), Deamidated (N), Pyro Carbamidomethyl
Cys (N-termC), with a precursor MH+shift range of -18 to 64 Da.
identities interpreted for individual spectra were automatically
designated as valid by optimizing score and delta rank1-rank2 score
thresholds separately for each precursor charge state in each
liquid chromatography (LC)-MS/MS while allowing a maximum
target-decoy-based false-discovery rate (FDR) of 1.0% at the
spectrum level.
[0188] In calculating scores at the protein level and reporting the
identified proteins, redundancy is addressed in the following
manner: the protein score is the sum of the scores of distinct
peptides. A distinct peptide is the single highest scoring instance
of a peptide detected through an MS/MS spectrum. MS/MS spectra for
a particular peptide may have been recorded multiple times, (i.e.
as different precursor charge states, isolated from adjacent SCX
fractions, modified by oxidation of Met) but are still counted as a
single distinct peptide. When a peptide sequence>8 residues long
is contained in multiple protein entries in the sequence database,
the proteins are grouped together and the highest scoring one and
its accession number are reported. In some cases when the protein
sequences are grouped in this manner there are distinct peptides
which uniquely represent a lower scoring member of the group
(isoforms or family members). Each of these instances spawns a
subgroup and multiple subgroups are reported and counted towards
the total number of proteins. iTRAQ ratios were obtained from the
protein-comparisons export table in Spectrum Mill. To obtain iTRAQ
protein ratios the median was calculated over all distinct peptides
assigned to a protein subgroup in each replicate. To assign
interacting proteins the Limma package in the R environment was
used to calculate moderated t-test p, as described previously and
added Blandt-Altman testing to filter out proteins for which the Cl
for reproducibility was below 95% (Udeshi et al., Mol Cell
Proteomics 11, 148-159, 2012).
Validation of DNMDP-Induced PDE3A Protein Interactions Using
Immunoprecipitation and Immunoblotting
[0189] HeLa cells were transfected with ORF overexpression
constructs expressing V5-tagged SIRT7, V5-tagged SLFN12, or
V5-tagged GFP. ORF expression constructs were obtained from the TRC
(clone IDs: TRCN0000468231, TRCN000476272, cesbBroad304_99997). At
72 hours post transfection, cells were treated with 10 .mu.M DNMDP
or trequinsin for 4 hours followed by lysis using the ModRipa lysis
buffer and immunoprecipitation of PDE3A. For each condition, 2 mg
total protein lysate was incubated with 1 .mu.g of anti-PDE3A
antibody at 4.degree. C. overnight, after which 7.5 .mu.l each of
Protein A- and Protein G-Dynabeads (Life Technologies 10001D and
10003D) were added and incubated for another 1 hour. Beads were
washed and bound proteins were eluted with 30 .mu.l of LDS PAGE gel
loading buffer. Input (.about.60 .mu.g total protein lysate) and IP
products were resolved on 4-12% Tris-Glycine PAGE gels and
immunoblotted with an anti-V5 antibody (Life Technologies R96205,
1:5000), the Bethyl anti-PDE3A antibody (1:1000), and secondary
antibodies from LiCOR Biosciences (Cat. #926-32210 and 926068021,
each at 1:10,000). Blots were washed and imaged using a LiCOR
Odyssey infrared imager.
Knockdown of SLFN12 Expression Using shRNA and Testing for Drug
Sensitivity
[0190] Constructs expressing shRNAs targeting SLFN12, or the
control vector, were packaged into lentiviruses and delivered into
HeLa cells by viral transduction. Three SLFN12-targeting shRNAs
were used, all of which were obtained from the TRC (CloneIDs:
TRCN0000152141 and TRCN0000153520). Infected cells were selected
using 1 .mu.g/ml puromycin for 3 days and then grown in
non-selective media for 3 more days. Cells were then plated into
384-well assay plates and tested for drug sensitivity as described
above. Knockdown of SLFN12 was validated by qPCR. Total RNA was
extracted using kit reagents (RNeasy Mini Kit (Qiagen #74104) and
QIAschredder (Qiagen #79656)). cDNA was generated using kit
reagents (Superscript III First-Strand Synthesis System (Life
Technologies #18080-051)). qPCR was performed for GAPDH and SLFN12
(Life Technologies Hs00430118_m1) according to the manufacturer's
recommendations. SLFN12 expression was normalized to corresponding
samples GAPDH ct-values.
Other Embodiments
[0191] From the foregoing description, it will be apparent that
variations and modifications may be made to the invention described
herein to adopt it to various usages and conditions. Such
embodiments are also within the scope of the following claims.
[0192] The recitation of a listing of elements in any definition of
a variable herein includes definitions of that variable as any
single element or combination (or subcombination) of listed
elements. The recitation of an embodiment herein includes that
embodiment as any single embodiment or in combination with any
other embodiments or portions thereof.
INCORPORATION BY REFERENCE
[0193] The ASCII text file submitted herewith via EFS-Web, entitled
"167741_011205US.txt" created on Sep. 13, 2016, having a size of
29,587 bytes, is hereby incorporated by reference in its
entirety.
[0194] All patents and publications mentioned in this specification
are herein incorporated by reference to the same extent as if each
independent patent and publication was specifically and
individually indicated to be incorporated by reference. In
particular, Lewis et al., "Compounds and Compositions for the
Treatment of Cancer," PCT/US2014/023263 (WO 2014/164704) is
incorporated by reference in its entirety.
Sequence CWU 1
1
1011141PRTHomo sapiens 1Met Ala Val Pro Gly Asp Ala Ala Arg Val Arg
Asp Lys Pro Val His1 5 10 15Ser Gly Val Ser Gln Ala Pro Thr Ala Gly
Arg Asp Cys His His Arg 20 25 30Ala Asp Pro Ala Ser Pro Arg Asp Ser
Gly Cys Arg Gly Cys Trp Gly 35 40 45Asp Leu Val Leu Gln Pro Leu Arg
Ser Ser Arg Lys Leu Ser Ser Ala 50 55 60Leu Cys Ala Gly Ser Leu Ser
Phe Leu Leu Ala Leu Leu Val Arg Leu65 70 75 80Val Arg Gly Glu Val
Gly Cys Asp Leu Glu Gln Cys Lys Glu Ala Ala 85 90 95Ala Ala Glu Glu
Glu Glu Ala Ala Pro Gly Ala Glu Gly Gly Val Phe 100 105 110Pro Gly
Pro Arg Gly Gly Ala Pro Gly Gly Gly Ala Arg Leu Ser Pro 115 120
125Trp Leu Gln Pro Ser Ala Leu Leu Phe Ser Leu Leu Cys Ala Phe Phe
130 135 140Trp Met Gly Leu Tyr Leu Leu Arg Ala Gly Val Arg Leu Pro
Leu Ala145 150 155 160Val Ala Leu Leu Ala Ala Cys Cys Gly Gly Glu
Ala Leu Val Gln Ile 165 170 175Gly Leu Gly Val Gly Glu Asp His Leu
Leu Ser Leu Pro Ala Ala Gly 180 185 190Val Val Leu Ser Cys Leu Ala
Ala Ala Thr Trp Leu Val Leu Arg Leu 195 200 205Arg Leu Gly Val Leu
Met Ile Ala Leu Thr Ser Ala Val Arg Thr Val 210 215 220Ser Leu Ile
Ser Leu Glu Arg Phe Lys Val Ala Trp Arg Pro Tyr Leu225 230 235
240Ala Tyr Leu Ala Gly Val Leu Gly Ile Leu Leu Ala Arg Tyr Val Glu
245 250 255Gln Ile Leu Pro Gln Ser Ala Glu Ala Ala Pro Arg Glu His
Leu Gly 260 265 270Ser Gln Leu Ile Ala Gly Thr Lys Glu Asp Ile Pro
Val Phe Lys Arg 275 280 285Arg Arg Arg Ser Ser Ser Val Val Ser Ala
Glu Met Ser Gly Cys Ser 290 295 300Ser Lys Ser His Arg Arg Thr Ser
Leu Pro Cys Ile Pro Arg Glu Gln305 310 315 320Leu Met Gly His Ser
Glu Trp Asp His Lys Arg Gly Pro Arg Gly Ser 325 330 335Gln Ser Ser
Gly Thr Ser Ile Thr Val Asp Ile Ala Val Met Gly Glu 340 345 350Ala
His Gly Leu Ile Thr Asp Leu Leu Ala Asp Pro Ser Leu Pro Pro 355 360
365Asn Val Cys Thr Ser Leu Arg Ala Val Ser Asn Leu Leu Ser Thr Gln
370 375 380Leu Thr Phe Gln Ala Ile His Lys Pro Arg Val Asn Pro Val
Thr Ser385 390 395 400Leu Ser Glu Asn Tyr Thr Cys Ser Asp Ser Glu
Glu Ser Ser Glu Lys 405 410 415Asp Lys Leu Ala Ile Pro Lys Arg Leu
Arg Arg Ser Leu Pro Pro Gly 420 425 430Leu Leu Arg Arg Val Ser Ser
Thr Trp Thr Thr Thr Thr Ser Ala Thr 435 440 445Gly Leu Pro Thr Leu
Glu Pro Ala Pro Val Arg Arg Asp Arg Ser Thr 450 455 460Ser Ile Lys
Leu Gln Glu Ala Pro Ser Ser Ser Pro Asp Ser Trp Asn465 470 475
480Asn Pro Val Met Met Thr Leu Thr Lys Ser Arg Ser Phe Thr Ser Ser
485 490 495Tyr Ala Ile Ser Ala Ala Asn His Val Lys Ala Lys Lys Gln
Ser Arg 500 505 510Pro Gly Ala Leu Ala Lys Ile Ser Pro Leu Ser Ser
Pro Cys Ser Ser 515 520 525Pro Leu Gln Gly Thr Pro Ala Ser Ser Leu
Val Ser Lys Ile Ser Ala 530 535 540Val Gln Phe Pro Glu Ser Ala Asp
Thr Thr Ala Lys Gln Ser Leu Gly545 550 555 560Ser His Arg Ala Leu
Thr Tyr Thr Gln Ser Ala Pro Asp Leu Ser Pro 565 570 575Gln Ile Leu
Thr Pro Pro Val Ile Cys Ser Ser Cys Gly Arg Pro Tyr 580 585 590Ser
Gln Gly Asn Pro Ala Asp Glu Pro Leu Glu Arg Ser Gly Val Ala 595 600
605Thr Arg Thr Pro Ser Arg Thr Asp Asp Thr Ala Gln Val Thr Ser Asp
610 615 620Tyr Glu Thr Asn Asn Asn Ser Asp Ser Ser Asp Ile Val Gln
Asn Glu625 630 635 640Asp Glu Thr Glu Cys Leu Arg Glu Pro Leu Arg
Lys Ala Ser Ala Cys 645 650 655Ser Thr Tyr Ala Pro Glu Thr Met Met
Phe Leu Asp Lys Pro Ile Leu 660 665 670Ala Pro Glu Pro Leu Val Met
Asp Asn Leu Asp Ser Ile Met Glu Gln 675 680 685Leu Asn Thr Trp Asn
Phe Pro Ile Phe Asp Leu Val Glu Asn Ile Gly 690 695 700Arg Lys Cys
Gly Arg Ile Leu Ser Gln Val Ser Tyr Arg Leu Phe Glu705 710 715
720Asp Met Gly Leu Phe Glu Ala Phe Lys Ile Pro Ile Arg Glu Phe Met
725 730 735Asn Tyr Phe His Ala Leu Glu Ile Gly Tyr Arg Asp Ile Pro
Tyr His 740 745 750Asn Arg Ile His Ala Thr Asp Val Leu His Ala Val
Trp Tyr Leu Thr 755 760 765Thr Gln Pro Ile Pro Gly Leu Ser Thr Val
Ile Asn Asp His Gly Ser 770 775 780Thr Ser Asp Ser Asp Ser Asp Ser
Gly Phe Thr His Gly His Met Gly785 790 795 800Tyr Val Phe Ser Lys
Thr Tyr Asn Val Thr Asp Asp Lys Tyr Gly Cys 805 810 815Leu Ser Gly
Asn Ile Pro Ala Leu Glu Leu Met Ala Leu Tyr Val Ala 820 825 830Ala
Ala Met His Asp Tyr Asp His Pro Gly Arg Thr Asn Ala Phe Leu 835 840
845Val Ala Thr Ser Ala Pro Gln Ala Val Leu Tyr Asn Asp Arg Ser Val
850 855 860Leu Glu Asn His His Ala Ala Ala Ala Trp Asn Leu Phe Met
Ser Arg865 870 875 880Pro Glu Tyr Asn Phe Leu Ile Asn Leu Asp His
Val Glu Phe Lys His 885 890 895Phe Arg Phe Leu Val Ile Glu Ala Ile
Leu Ala Thr Asp Leu Lys Lys 900 905 910His Phe Asp Phe Val Ala Lys
Phe Asn Gly Lys Val Asn Asp Asp Val 915 920 925Gly Ile Asp Trp Thr
Asn Glu Asn Asp Arg Leu Leu Val Cys Gln Met 930 935 940Cys Ile Lys
Leu Ala Asp Ile Asn Gly Pro Ala Lys Cys Lys Glu Leu945 950 955
960His Leu Gln Trp Thr Asp Gly Ile Val Asn Glu Phe Tyr Glu Gln Gly
965 970 975Asp Glu Glu Ala Ser Leu Gly Leu Pro Ile Ser Pro Phe Met
Asp Arg 980 985 990Ser Ala Pro Gln Leu Ala Asn Leu Gln Glu Ser Phe
Ile Ser His Ile 995 1000 1005Val Gly Pro Leu Cys Asn Ser Tyr Asp
Ser Ala Gly Leu Met Pro 1010 1015 1020Gly Lys Trp Val Glu Asp Ser
Asp Glu Ser Gly Asp Thr Asp Asp 1025 1030 1035Pro Glu Glu Glu Glu
Glu Glu Ala Pro Ala Pro Asn Glu Glu Glu 1040 1045 1050Thr Cys Glu
Asn Asn Glu Ser Pro Lys Lys Lys Thr Phe Lys Arg 1055 1060 1065Arg
Lys Ile Tyr Cys Gln Ile Thr Gln His Leu Leu Gln Asn His 1070 1075
1080Lys Met Trp Lys Lys Val Ile Glu Glu Glu Gln Arg Leu Ala Gly
1085 1090 1095Ile Glu Asn Gln Ser Leu Asp Gln Thr Pro Gln Ser His
Ser Ser 1100 1105 1110Glu Gln Ile Gln Ala Ile Lys Glu Glu Glu Glu
Glu Lys Gly Lys 1115 1120 1125Pro Arg Gly Glu Glu Ile Pro Thr Gln
Lys Pro Asp Gln 1130 1135 114027319DNAHomo sapiens 2gggggccact
gggaattcag tgaagagggc accctatacc atggcagtgc ccggcgacgc 60tgcacgagtc
agggacaagc ccgtccacag tggggtgagt caagccccca cggcgggccg
120ggactgccac catcgtgcgg accccgcatc gccgcgggac tcgggctgcc
gtggctgctg 180gggagacctg gtgctgcagc cgctccggag ctctcggaaa
ctttcctccg cgctgtgcgc 240gggctccctg tcctttctgc tggcgctgct
ggtgaggctg gtccgcgggg aggtcggctg 300tgacctggag cagtgtaagg
aggcggcggc ggcggaggag gaggaagcag ccccgggagc 360agaagggggc
gtcttcccgg ggcctcgggg aggtgctccc gggggcggtg cgcggctcag
420cccctggctg cagccctcgg cgctgctctt cagtctcctg tgtgccttct
tctggatggg 480cttgtacctc ctgcgcgccg gggtgcgcct gcctctggct
gtcgcgctgc tggccgcctg 540ctgcgggggg gaagcgctcg tccagattgg
gctgggcgtc ggggaggatc acttactctc 600actccccgcc gcgggggtgg
tgctcagctg cttggccgcc gcgacatggc tggtgctgag 660gctgaggctg
ggcgtcctca tgatcgcctt gactagcgcg gtcaggaccg tgtccctcat
720ttccttagag aggttcaagg tcgcctggag accttacctg gcgtacctgg
ccggcgtgct 780ggggatcctc ttggccaggt acgtggaaca aatcttgccg
cagtccgcgg aggcggctcc 840aagggagcat ttggggtccc agctgattgc
tgggaccaag gaagatatcc cggtgtttaa 900gaggaggagg cggtccagct
ccgtcgtgtc cgccgagatg tccggctgca gcagcaagtc 960ccatcggagg
acctccctgc cctgtatacc gagggaacag ctcatggggc attcagaatg
1020ggaccacaaa cgagggccaa gaggatcaca gtcttcagga accagtatta
ctgtggacat 1080cgccgtcatg ggcgaggccc acggcctcat taccgacctc
ctggcagacc cttctcttcc 1140accaaacgtg tgcacatcct tgagagccgt
gagcaacttg ctcagcacac agctcacctt 1200ccaggccatt cacaagccca
gagtgaatcc cgtcacttcg ctcagtgaaa actatacctg 1260ttctgactct
gaagagagct ctgaaaaaga caagcttgct attccaaagc gcctgagaag
1320gagtttgcct cctggcttgt tgagacgagt ttcttccact tggaccacca
ccacctcggc 1380cacaggtcta cccaccttgg agcctgcacc agtacggaga
gaccgcagca ccagcatcaa 1440actgcaggaa gcaccttcat ccagtcctga
ttcttggaat aatccagtga tgatgaccct 1500caccaaaagc agatccttta
cttcatccta tgctatttct gcagctaacc atgtaaaggc 1560taaaaagcaa
agtcgaccag gtgccctcgc taaaatttca cctctttcat cgccctgctc
1620ctcacctctc caagggactc ctgccagcag cctggtcagc aaaatttctg
cagtgcagtt 1680tccagaatct gctgacacaa ctgccaaaca aagcctaggt
tctcacaggg ccttaactta 1740cactcagagt gccccagacc tatcccctca
aatcctgact ccacctgtta tatgtagcag 1800ctgtggcaga ccatattccc
aagggaatcc tgctgatgag cccctggaga gaagtggggt 1860agccactcgg
acaccaagta gaacagatga cactgctcaa gttacctctg attatgaaac
1920caataacaac agtgacagca gtgacattgt acagaatgaa gatgaaacag
agtgcctgag 1980agagcctctg aggaaagcat cggcttgcag cacctatgct
cctgagacca tgatgtttct 2040ggacaaacca attcttgctc ccgaacctct
tgtcatggat aacctggact caattatgga 2100gcagctaaat acttggaatt
ttccaatttt tgatttagtg gaaaatatag gaagaaaatg 2160tggccgtatt
cttagtcagg tatcttacag actttttgaa gacatgggcc tctttgaagc
2220ttttaaaatt ccaattaggg aatttatgaa ttattttcat gctttggaga
ttggatatag 2280ggatattcct tatcataaca gaatccatgc cactgatgtt
ttacatgctg tttggtatct 2340tactacacag cctattccag gcctctcaac
tgtgattaat gatcatggtt caaccagtga 2400ttcagattct gacagtggat
ttacacatgg acatatggga tatgtattct caaaaacgta 2460taatgtgaca
gatgataaat acggatgtct gtctgggaat atccctgcct tggagttgat
2520ggcgctgtat gtggctgcag ccatgcacga ttatgatcat ccaggaagga
ctaatgcttt 2580cctggttgca actagtgctc ctcaggcggt gctatataac
gatcgttcag ttttggagaa 2640tcatcacgca gctgctgcat ggaatctttt
catgtcccgg ccagagtata acttcttaat 2700taaccttgac catgtggaat
ttaagcattt ccgtttcctt gtcattgaag caattttggc 2760cactgacctg
aagaaacact ttgacttcgt agccaaattt aatggcaagg taaatgatga
2820tgttggaata gattggacca atgaaaatga tcgtctactg gtttgtcaaa
tgtgtataaa 2880gttggctgat atcaatggtc cagctaaatg taaagaactc
catcttcagt ggacagatgg 2940tattgtcaat gaattttatg aacagggtga
tgaagaggcc agccttggat tacccataag 3000ccccttcatg gatcgttctg
ctcctcagct ggccaacctt caggaatcct tcatctctca 3060cattgtgggg
cctctgtgca actcctatga ttcagcagga ctaatgcctg gaaaatgggt
3120ggaagacagc gatgagtcag gagatactga tgacccagaa gaagaggagg
aagaagcacc 3180agcaccaaat gaagaggaaa cctgtgaaaa taatgaatct
ccaaaaaaga agactttcaa 3240aaggagaaaa atctactgcc aaataactca
gcacctctta cagaaccaca agatgtggaa 3300gaaagtcatt gaagaggagc
aacggttggc aggcatagaa aatcaatccc tggaccagac 3360ccctcagtcg
cactcttcag aacagatcca ggctatcaag gaagaagaag aagagaaagg
3420gaaaccaaga ggcgaggaga taccaaccca aaagccagac cagtgacaat
ggatagaatg 3480ggctgtgttt ccaaacagat tgacttgtca aagactctct
tcaagccagc acaacattta 3540gacacaacac tgtagaaatt tgagatgggc
aaatggctat tgcattttgg gattcttcgc 3600attttgtgtg tatattttta
cagtgaggta cattgttaaa aactttttgc tcaaagaagc 3660tttcacattg
caacaccagc ttctaaggat tttttaagga gggaatatat atgtgtgtgt
3720gtatataagc tcccacatag atacatgtaa aacatattca cacccatgca
cgcacacaca 3780tacacactga aggccacgat tgctggctcc acaatttagt
aacatttata ttaagatata 3840tatatagtgg tcactgtgat ataataaatc
ataaaggaaa ccaaatcaca aaggagatgg 3900tgtggcttag caaggaaaca
gtgcaggaaa tgtaggttac caactaagca gcttttgctc 3960ttagtactga
gggatgaaag ttccagagca ttatttgaat tctgatacat cctgccaaca
4020ctgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgaaaga
gagacagaag 4080ggaatggttt gagagggtgc ttgtgtgcat gtgtgtgcat
atgtaaagag atttttgtgg 4140tttaagtaac tcagaatagc tgtagcaaat
gactgaatac atgtgaacaa acagaaggaa 4200gttcactctg gagtgtcttt
gggaggcagc cattccaaat gccctcctcc atttagcttc 4260aataaagggc
cttttgctga tggagggcac tcaagggctg ggtgagaggg ccacgtgttt
4320ggtattacat tactgctatg caccacttga aggagctcta tcaccagcct
caaacccgaa 4380agactgaggc attttccagt ctacttgcct aatgaatgta
taggaactgt ctatgagtat 4440ggatgtcact caactaagat caaatcacca
tttaagggga tggcattctt tatacctaaa 4500cacctaagag ctgaagtcag
gtcttttaat caggttagaa ttctaaatga tgccagagaa 4560ggcttgggaa
attgtacttc agcgtgatag cctgtgtctt cttaatttgc tgcaaaatat
4620gtggtagaga aagaaaagga aacagaaaaa tcactctggg ttatatagca
agagatgaag 4680gagaatattt caacacaggg tttttgtgtt gacataggaa
aagcctgatt cttggcaact 4740gttgtagttt gtctttcagg ggtgaaggtc
ccactgacaa cccctgttgt ggtgttccac 4800acgctgtttg ttggggtagc
ttccatcggc agtctggccc attgtcagtc atgcttcttc 4860tggccgggga
gattatagag agattgtttg aagattgggt tattattgaa agtctttttt
4920tttgtttgtt ttgttttggt ttgtttgttt atctacactt gtttatgctg
tgagccaaac 4980ctctatttaa aaagttgata ctcactttca atattttatt
tcatattatt atatatgtca 5040tgatagttat cttgatgtaa atatgaagat
ttttttgttt ctgtagatag taaactcttt 5100ttttaaaaaa ggaaaaggga
aacattttta taaagttata ttttaatcac catttttata 5160cattgtagtt
ctctccaagc ccagtaagag aatgatgatt catttgcatg gaggtcgatg
5220gacaaccaat catctacctt ttctaattta aatgataatc tgatatagtt
ttattgccag 5280ttaaatgagg atgctgcaaa gcatgttttt tcactagtaa
cttttgctaa ctgaatgaat 5340tctgggtcca tatctcccag atgaaaaact
gttaaccaat accatatttt atagttggtg 5400tccatttctt tccaacactg
tttgttatga ttcttccttg agtacttata tacagacctg 5460ctcattatct
aaacaatctt accttctaag taaaccttga ttgtgatttc cagtttttat
5520tttctctgac gtagtagaaa ggaatgttta cattaaaaat acttttgttt
ctcataaatg 5580gatattgtac tccccccttt caaagcatta ttttacaata
attcatggca ttttaaaaaa 5640taaggcaaag ataatacgac aaaaaatata
catggtttca aggcaaattc tccaataagt 5700tggaaaatgt aaaaaggatc
aagtggatgc agcctctacc taaataatta aaatatattt 5760cagtatattt
ctgaattaac accaggtctt cattatttag aacttactaa attgttttca
5820ttttcttagt tttacctgtg tatctccatg tttgcaaaaa ttactataag
tcaaattttg 5880ccagtgaatt taactatttt tctttccttg caattaaggg
gaaaaaagca tttatcttat 5940cttctcatac cccttgcatc taagtactta
gcaaagtcaa tattttccca ttttccaaat 6000gcgtccatct ctaacataaa
tattaattga acatagagct atgtttggag tgagtggact 6060ggcaggacag
ttggaagtcc atcacagtct attgacagtt tcatcaaagc tgtatagtcc
6120aactagtggg gcagcttggc tactatggtg gaagtctcag caaactgcct
ggttttgttt 6180gtttgttttg ttttaaggta caggaaataa gaggaataat
agtggccaaa gcaattagaa 6240catcttcatt ccagaactgt gttcagcaat
ccaggcagat tgatacattt ttctttaaaa 6300ataaattgct attacagcta
gacgtcaatt gggataaata aagggatgaa gatccactaa 6360gtttgtgact
ttcatacaca cccagtacat ctcaaaggat gctaagggac attttctgcc
6420agtagagttc tccccctttt tggtgacagc aatattatta tgttcacatc
taactccaga 6480gcttacttcc tgtggtgcca atgtatttgt tgcaatttac
tacattttta tatgagccta 6540tttataggtg ccattaaact caggtctttc
aaatgaaaga gtttctagcc cacttaggga 6600aaaagataat tgtttagaaa
accataaaat caatggtagg aaaagttgga actggttacc 6660tggatgccat
ggttctctgt taaataaagt aagagaccag gtgtattctg agtgtcatca
6720gtgttatttt cagcatgcta ataaatgtct ttccggttat atatctatct
aaattaacct 6780ttaaaatatt ggtttccttg ataaaagcac cacttttgct
tttgttagct gtaatatttt 6840ttgtcattta gataagacct ggtttggctc
tcaataaaag atgaagacag tagctctgta 6900cagggatata tctatattag
tcttcatctg atgaatgaag aaattttctc atattatgtt 6960caagaaagta
tttacttcct aaaaatagaa ttcccgattc tgtctatttt ggttgaatac
7020cagaacaaat ctttccgttg caatcccagt aaaacgaaag aaaaggaata
tcttacagac 7080tgttcatatt agatgtatgt agactgttaa tttgcaattt
ccccatattt cctgcctatc 7140ttacccagat aactttcttt gaaggtaaaa
gctgtgcaaa aggcatgaga ctcaggccta 7200ctctttgttt aaatgatgga
aaaatataaa ttattttcta agtaataaaa gtataaaaat 7260tatcattata
aataaagtct aaagtttgaa attattaatt taaaaaaaaa aaaaaaaaa
73193578PRTHomo sapiens 3Met Asn Ile Ser Val Asp Leu Glu Thr Asn
Tyr Ala Glu Leu Val Leu1 5 10 15Asp Val Gly Arg Val Thr Leu Gly Glu
Asn Ser Arg Lys Lys Met Lys 20 25 30Asp Cys Lys Leu Arg Lys Lys Gln
Asn Glu Ser Val Ser Arg Ala Met 35 40 45Cys Ala Leu Leu Asn Ser Gly
Gly Gly Val Ile Lys Ala Glu Ile Glu 50 55 60Asn Glu Asp Tyr Ser Tyr
Thr Lys Asp Gly Ile Gly Leu Asp Leu Glu65 70 75 80Asn Ser Phe Ser
Asn Ile Leu Leu Phe Val Pro Glu Tyr Leu Asp Phe 85 90 95Met Gln Asn
Gly Asn Tyr Phe Leu Ile Phe Val Lys Ser Trp Ser Leu 100 105 110Asn
Thr Ser Gly Leu Arg Ile Thr Thr Leu Ser Ser
Asn Leu Tyr Lys 115 120 125Arg Asp Ile Thr Ser Ala Lys Val Met Asn
Ala Thr Ala Ala Leu Glu 130 135 140Phe Leu Lys Asp Met Lys Lys Thr
Arg Gly Arg Leu Tyr Leu Arg Pro145 150 155 160Glu Leu Leu Ala Lys
Arg Pro Cys Val Asp Ile Gln Glu Glu Asn Asn 165 170 175Met Lys Ala
Leu Ala Gly Val Phe Phe Asp Arg Thr Glu Leu Asp Arg 180 185 190Lys
Glu Lys Leu Thr Phe Thr Glu Ser Thr His Val Glu Ile Lys Asn 195 200
205Phe Ser Thr Glu Lys Leu Leu Gln Arg Ile Lys Glu Ile Leu Pro Gln
210 215 220Tyr Val Ser Ala Phe Ala Asn Thr Asp Gly Gly Tyr Leu Phe
Ile Gly225 230 235 240Leu Asn Glu Asp Lys Glu Ile Ile Gly Phe Lys
Ala Glu Met Ser Asp 245 250 255Leu Asp Asp Leu Glu Arg Glu Ile Glu
Lys Ser Ile Arg Lys Met Pro 260 265 270Val His His Phe Cys Met Glu
Lys Lys Lys Ile Asn Tyr Ser Cys Lys 275 280 285Phe Leu Gly Val Tyr
Asp Lys Gly Ser Leu Cys Gly Tyr Val Cys Ala 290 295 300Leu Arg Val
Glu Arg Phe Cys Cys Ala Val Phe Ala Lys Glu Pro Asp305 310 315
320Ser Trp His Val Lys Asp Asn Arg Val Met Gln Leu Thr Arg Lys Glu
325 330 335Trp Ile Gln Phe Met Val Glu Ala Glu Pro Lys Phe Ser Ser
Ser Tyr 340 345 350Glu Glu Val Ile Ser Gln Ile Asn Thr Ser Leu Pro
Ala Pro His Ser 355 360 365Trp Pro Leu Leu Glu Trp Gln Arg Gln Arg
His His Cys Pro Gly Leu 370 375 380Ser Gly Arg Ile Thr Tyr Thr Pro
Glu Asn Leu Cys Arg Lys Leu Phe385 390 395 400Leu Gln His Glu Gly
Leu Lys Gln Leu Ile Cys Glu Glu Met Asp Ser 405 410 415Val Arg Lys
Gly Ser Leu Ile Phe Ser Arg Ser Trp Ser Val Asp Leu 420 425 430Gly
Leu Gln Glu Asn His Lys Val Leu Cys Asp Ala Leu Leu Ile Ser 435 440
445Gln Asp Ser Pro Pro Val Leu Tyr Thr Phe His Met Val Gln Asp Glu
450 455 460Glu Phe Lys Gly Tyr Ser Thr Gln Thr Ala Leu Thr Leu Lys
Gln Lys465 470 475 480Leu Ala Lys Ile Gly Gly Tyr Thr Lys Lys Val
Cys Val Met Thr Lys 485 490 495Ile Phe Tyr Leu Ser Pro Glu Gly Met
Thr Ser Cys Gln Tyr Asp Leu 500 505 510Arg Ser Gln Val Ile Tyr Pro
Glu Ser Tyr Tyr Phe Thr Arg Arg Lys 515 520 525Tyr Leu Leu Lys Ala
Leu Phe Lys Ala Leu Lys Arg Leu Lys Ser Leu 530 535 540Arg Asp Gln
Phe Ser Phe Ala Glu Asn Leu Tyr Gln Ile Ile Gly Ile545 550 555
560Asp Cys Phe Gln Lys Asn Asp Lys Lys Met Phe Lys Ser Cys Arg Arg
565 570 575Leu Thr42530DNAHomo sapiens 4tttgtaactt cacttcagcc
tcccattgat cgctttctgc aaccattcag actgatctcg 60ggctcctatt tcatttacat
tgtgtgcaca ccaagtaacc agtgggaaaa ctttagaggg 120tacttaaacc
ccagaaaatt ctgaaaccgg gctcttgagc cgctatcctc gggcctgctc
180ccaccctgtg gagtgcactt tcgttttcaa taaatctctg cttttgttgc
ttcattcttt 240ccttgctttg tttgtgtgtt tgtccagttc tttgttcaac
acgccaagaa cctggacact 300cttcactggt aacatatttt ggcaagccaa
ccaggagaaa agaatttctg cttggacact 360gcatagctgc tgggaaaatg
aacatcagtg ttgatttgga aacgaattat gccgagttgg 420ttctagatgt
gggaagagtc actcttggag agaacagtag gaaaaaaatg aaggattgta
480aactgagaaa aaagcagaat gaaagtgtct cacgagctat gtgtgctctg
ctcaattctg 540gagggggagt gatcaaggct gaaattgaga atgaagacta
tagttataca aaagatggaa 600taggactaga tttggaaaat tcttttagta
acattctgtt atttgttcct gagtacttag 660acttcatgca gaatggtaac
tactttctga tttttgtgaa gtcatggagc ttgaacacct 720ctggtctgcg
gattaccacc ttgagctcca atttgtacaa aagagatata acatctgcaa
780aagtcatgaa tgccactgct gcactggagt tcctcaaaga catgaaaaag
actagaggga 840gattgtattt aagaccagaa ttgctggcaa agaggccctg
tgttgatata caagaagaaa 900ataacatgaa ggccttggcc ggggtttttt
ttgatagaac agaacttgat cggaaagaaa 960aattgacctt tactgaatcc
acacatgttg aaattaaaaa cttctcgaca gaaaagttgt 1020tacaacgaat
taaagagatt ctccctcaat atgtttctgc atttgcaaat actgatggag
1080gatatttgtt cattggttta aatgaagata aagaaataat tggctttaaa
gcagagatga 1140gtgacctcga tgacttagaa agagaaatcg aaaagtccat
taggaagatg cctgtgcatc 1200acttctgtat ggagaagaag aagataaatt
attcatgcaa attccttgga gtatatgata 1260aaggaagtct ttgtggatat
gtctgtgcac tcagagtgga gcgcttctgc tgtgcagtgt 1320ttgctaaaga
gcctgattcc tggcatgtga aagataaccg tgtgatgcag ttgaccagga
1380aggaatggat ccagttcatg gtggaggctg aaccaaaatt ttccagttca
tatgaagagg 1440tgatctctca aataaatacg tcattacctg ctccccacag
ttggcctctt ttggaatggc 1500aacggcagag acatcactgt ccagggctat
caggaaggat aacgtatact ccagaaaacc 1560tttgcagaaa actgttctta
caacatgaag gacttaagca attaatatgt gaagaaatgg 1620actctgtcag
aaagggctca ctgatcttct ctaggagctg gtctgtggat ctgggcttgc
1680aagagaacca caaagtcctc tgtgatgctc ttctgatttc ccaggacagt
cctccagtcc 1740tatacacctt ccacatggta caggatgagg agtttaaagg
ctattctaca caaactgccc 1800taaccttaaa gcagaagctg gcaaaaattg
gtggttacac taaaaaagtg tgtgtcatga 1860caaagatctt ctacttgagc
cctgaaggca tgacaagctg ccagtatgat ttaaggtcgc 1920aagtaattta
ccctgaatcc tactatttta caagaaggaa atacttgctg aaagcccttt
1980ttaaagcctt aaagagactc aagtctctga gagaccagtt ttcctttgca
gaaaatctat 2040accagataat cggtatagat tgctttcaga agaatgataa
aaagatgttt aaatcttgtc 2100gaaggctcac ctgatggaaa atggactggg
ctactgagat atttttcatt atatatttga 2160taacattctc taattctgtg
aaaatatttc tttgaaaact ttgcaagtta agcaacttaa 2220tgtgatgttg
gataattggg ttttgtctat tttcacttct ccctaaataa tcttcacaga
2280tattgtttga gggatattag gaaaattaat ttgttaactc gtctgtgcac
agtattattt 2340actctgtctg tagttcctga ataaattttc ttccatgctt
gaactgggaa aattgcaaca 2400cttttattct taatgacaac agtgaaaatc
tcccagcata tacctagaaa acaattataa 2460cttacaaaag attatccttg
atgaaactca gaatttccac agtgggaatg aataagaagg 2520caaaactcat
2530524DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 5caccgttttc actgagcgaa gtga
24624DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 6aaactcactt cgctcagtga aaac
24725DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 7caccgagaca agcttgctat tccaa
25825DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 8aaacttggaa tagcaagctt gtctc
25924DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 9caccggcact ctgagtgtaa gtta
241024DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 10aaactaactt acactcagag tgcc 24
* * * * *