JP2019535017A - ラージスケールエピゲノムのリプログラミングは、膵癌進行の進展中の同化グルコース代謝を遠位転移に結びつける - Google Patents
ラージスケールエピゲノムのリプログラミングは、膵癌進行の進展中の同化グルコース代謝を遠位転移に結びつける Download PDFInfo
- Publication number
- JP2019535017A JP2019535017A JP2019518463A JP2019518463A JP2019535017A JP 2019535017 A JP2019535017 A JP 2019535017A JP 2019518463 A JP2019518463 A JP 2019518463A JP 2019518463 A JP2019518463 A JP 2019518463A JP 2019535017 A JP2019535017 A JP 2019535017A
- Authority
- JP
- Japan
- Prior art keywords
- genes
- gene
- lock
- analysis
- data
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Granted
Links
- 230000008672 reprogramming Effects 0.000 title claims abstract description 75
- 230000004153 glucose metabolism Effects 0.000 title claims abstract description 14
- 206010027476 Metastases Diseases 0.000 title claims description 106
- 230000009401 metastasis Effects 0.000 title claims description 55
- 230000001195 anabolic effect Effects 0.000 title description 6
- 206010061902 Pancreatic neoplasm Diseases 0.000 title description 5
- 208000015486 malignant pancreatic neoplasm Diseases 0.000 title description 5
- 201000002528 pancreatic cancer Diseases 0.000 title description 5
- 208000008443 pancreatic carcinoma Diseases 0.000 title description 5
- 108090000623 proteins and genes Proteins 0.000 claims abstract description 170
- 206010028980 Neoplasm Diseases 0.000 claims abstract description 95
- 238000000034 method Methods 0.000 claims abstract description 94
- 206010061289 metastatic neoplasm Diseases 0.000 claims abstract description 50
- 230000001394 metastastic effect Effects 0.000 claims abstract description 43
- 108010034791 Heterochromatin Proteins 0.000 claims abstract description 40
- 210000004458 heterochromatin Anatomy 0.000 claims abstract description 40
- 230000001973 epigenetic effect Effects 0.000 claims abstract description 38
- 239000003795 chemical substances by application Substances 0.000 claims abstract description 21
- 201000011510 cancer Diseases 0.000 claims abstract description 17
- 230000000694 effects Effects 0.000 claims abstract description 17
- 150000001875 compounds Chemical class 0.000 claims abstract description 14
- 230000005764 inhibitory process Effects 0.000 claims abstract description 11
- 229920000371 poly(diallyldimethylammonium chloride) polymer Polymers 0.000 claims abstract description 11
- KDXKERNSBIXSRK-UHFFFAOYSA-N Lysine Natural products NCCCCC(N)C(O)=O KDXKERNSBIXSRK-UHFFFAOYSA-N 0.000 claims abstract description 9
- 239000004472 Lysine Substances 0.000 claims abstract description 9
- 230000033616 DNA repair Effects 0.000 claims abstract description 8
- 230000008995 epigenetic change Effects 0.000 claims abstract description 7
- 230000036542 oxidative stress Effects 0.000 claims abstract description 6
- 210000004027 cell Anatomy 0.000 claims description 134
- 238000004458 analytical method Methods 0.000 claims description 68
- 230000004048 modification Effects 0.000 claims description 54
- 238000012986 modification Methods 0.000 claims description 54
- 238000001262 western blot Methods 0.000 claims description 45
- 238000003556 assay Methods 0.000 claims description 35
- 230000014509 gene expression Effects 0.000 claims description 30
- 238000011282 treatment Methods 0.000 claims description 27
- 238000002487 chromatin immunoprecipitation Methods 0.000 claims description 18
- 108010022894 Euchromatin Proteins 0.000 claims description 16
- 210000000632 euchromatin Anatomy 0.000 claims description 16
- 238000012163 sequencing technique Methods 0.000 claims description 15
- 230000037437 driver mutation Effects 0.000 claims description 13
- 238000001514 detection method Methods 0.000 claims description 12
- 108010082117 matrigel Proteins 0.000 claims description 11
- 230000008859 change Effects 0.000 claims description 10
- 230000006429 DNA hypomethylation Effects 0.000 claims description 8
- 238000002512 chemotherapy Methods 0.000 claims description 7
- 238000001369 bisulfite sequencing Methods 0.000 claims description 4
- 230000028993 immune response Effects 0.000 claims description 3
- 101150067938 PGD gene Proteins 0.000 claims description 2
- 238000010195 expression analysis Methods 0.000 claims description 2
- 238000004393 prognosis Methods 0.000 claims 2
- 230000004043 responsiveness Effects 0.000 claims 2
- 238000001802 infusion Methods 0.000 claims 1
- 230000002265 prevention Effects 0.000 claims 1
- 238000001959 radiotherapy Methods 0.000 claims 1
- 238000011269 treatment regimen Methods 0.000 claims 1
- 230000004044 response Effects 0.000 abstract description 10
- 230000002068 genetic effect Effects 0.000 abstract description 6
- 108010077544 Chromatin Proteins 0.000 description 56
- 210000003483 chromatin Anatomy 0.000 description 56
- 201000008129 pancreatic ductal adenocarcinoma Diseases 0.000 description 56
- 230000011987 methylation Effects 0.000 description 51
- 238000007069 methylation reaction Methods 0.000 description 51
- 102000004567 6-phosphogluconate dehydrogenase Human genes 0.000 description 37
- 108020001657 6-phosphogluconate dehydrogenase Proteins 0.000 description 37
- 230000000153 supplemental effect Effects 0.000 description 37
- 108020004414 DNA Proteins 0.000 description 36
- WQZGKKKJIJFFOK-GASJEMHNSA-N Glucose Natural products OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O WQZGKKKJIJFFOK-GASJEMHNSA-N 0.000 description 34
- 239000008103 glucose Substances 0.000 description 34
- 210000001519 tissue Anatomy 0.000 description 29
- 230000001105 regulatory effect Effects 0.000 description 28
- 230000007067 DNA methylation Effects 0.000 description 25
- 238000002474 experimental method Methods 0.000 description 25
- 108010033040 Histones Proteins 0.000 description 24
- 239000000523 sample Substances 0.000 description 24
- 238000003559 RNA-seq method Methods 0.000 description 23
- 238000011161 development Methods 0.000 description 22
- 230000018109 developmental process Effects 0.000 description 22
- 230000003211 malignant effect Effects 0.000 description 21
- 239000002207 metabolite Substances 0.000 description 21
- 230000006870 function Effects 0.000 description 19
- 150000007523 nucleic acids Chemical group 0.000 description 18
- 210000001082 somatic cell Anatomy 0.000 description 17
- 108091030071 RNAI Proteins 0.000 description 16
- 230000009368 gene silencing by RNA Effects 0.000 description 16
- 239000002243 precursor Substances 0.000 description 16
- 239000000047 product Substances 0.000 description 16
- 230000005740 tumor formation Effects 0.000 description 16
- 102000000905 Cadherin Human genes 0.000 description 15
- 108050007957 Cadherin Proteins 0.000 description 15
- 206010051676 Metastases to peritoneum Diseases 0.000 description 15
- OKKJLVBELUTLKV-UHFFFAOYSA-N Methanol Chemical compound OC OKKJLVBELUTLKV-UHFFFAOYSA-N 0.000 description 15
- 238000010186 staining Methods 0.000 description 15
- LSNNMFCWUKXFEE-UHFFFAOYSA-M Bisulfite Chemical compound OS([O-])=O LSNNMFCWUKXFEE-UHFFFAOYSA-M 0.000 description 14
- 230000004069 differentiation Effects 0.000 description 14
- 208000010918 peritoneal neoplasm Diseases 0.000 description 14
- 239000006144 Dulbecco’s modified Eagle's medium Substances 0.000 description 13
- 201000010099 disease Diseases 0.000 description 13
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 13
- 102000039446 nucleic acids Human genes 0.000 description 13
- 108020004707 nucleic acids Proteins 0.000 description 13
- 238000003752 polymerase chain reaction Methods 0.000 description 13
- 238000012545 processing Methods 0.000 description 13
- 102100033589 DNA topoisomerase 2-beta Human genes 0.000 description 12
- WSFSSNUMVMOOMR-UHFFFAOYSA-N Formaldehyde Chemical compound O=C WSFSSNUMVMOOMR-UHFFFAOYSA-N 0.000 description 12
- 108050000637 N-cadherin Proteins 0.000 description 12
- 108010046308 Type II DNA Topoisomerases Proteins 0.000 description 12
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 11
- 210000004072 lung Anatomy 0.000 description 11
- 230000037361 pathway Effects 0.000 description 11
- 108090000765 processed proteins & peptides Proteins 0.000 description 11
- 102000004169 proteins and genes Human genes 0.000 description 11
- 238000012360 testing method Methods 0.000 description 11
- 206010027458 Metastases to lung Diseases 0.000 description 10
- 231100000504 carcinogenesis Toxicity 0.000 description 10
- 230000007423 decrease Effects 0.000 description 10
- 230000012010 growth Effects 0.000 description 10
- 125000003729 nucleotide group Chemical group 0.000 description 10
- 208000005623 Carcinogenesis Diseases 0.000 description 9
- 108091028043 Nucleic acid sequence Proteins 0.000 description 9
- 230000036952 cancer formation Effects 0.000 description 9
- 238000003364 immunohistochemistry Methods 0.000 description 9
- 239000002609 medium Substances 0.000 description 9
- 102000040430 polynucleotide Human genes 0.000 description 9
- 108091033319 polynucleotide Proteins 0.000 description 9
- 239000002157 polynucleotide Substances 0.000 description 9
- 102100030708 GTPase KRas Human genes 0.000 description 8
- 101000584612 Homo sapiens GTPase KRas Proteins 0.000 description 8
- JVTAAEKCZFNVCJ-UHFFFAOYSA-M Lactate Chemical compound CC(O)C([O-])=O JVTAAEKCZFNVCJ-UHFFFAOYSA-M 0.000 description 8
- 108091034117 Oligonucleotide Proteins 0.000 description 8
- 239000012091 fetal bovine serum Substances 0.000 description 8
- 230000002055 immunohistochemical effect Effects 0.000 description 8
- 238000005259 measurement Methods 0.000 description 8
- 230000002829 reductive effect Effects 0.000 description 8
- 230000000381 tumorigenic effect Effects 0.000 description 8
- 102000004190 Enzymes Human genes 0.000 description 7
- 108090000790 Enzymes Proteins 0.000 description 7
- 108700011259 MicroRNAs Proteins 0.000 description 7
- 102100024193 Mitogen-activated protein kinase 1 Human genes 0.000 description 7
- 230000021736 acetylation Effects 0.000 description 7
- 238000006640 acetylation reaction Methods 0.000 description 7
- 230000003321 amplification Effects 0.000 description 7
- 238000003745 diagnosis Methods 0.000 description 7
- 238000001727 in vivo Methods 0.000 description 7
- 238000013507 mapping Methods 0.000 description 7
- 238000003199 nucleic acid amplification method Methods 0.000 description 7
- 239000002773 nucleotide Substances 0.000 description 7
- 210000004303 peritoneum Anatomy 0.000 description 7
- 230000010076 replication Effects 0.000 description 7
- 230000028327 secretion Effects 0.000 description 7
- 239000012679 serum free medium Substances 0.000 description 7
- 230000008685 targeting Effects 0.000 description 7
- 231100000588 tumorigenic Toxicity 0.000 description 7
- WEVYAHXRMPXWCK-UHFFFAOYSA-N Acetonitrile Chemical compound CC#N WEVYAHXRMPXWCK-UHFFFAOYSA-N 0.000 description 6
- 102000004316 Oxidoreductases Human genes 0.000 description 6
- 108090000854 Oxidoreductases Proteins 0.000 description 6
- 108020004459 Small interfering RNA Proteins 0.000 description 6
- ISAKRJDGNUQOIC-UHFFFAOYSA-N Uracil Chemical compound O=C1C=CNC(=O)N1 ISAKRJDGNUQOIC-UHFFFAOYSA-N 0.000 description 6
- XJLXINKUBYWONI-DQQFMEOOSA-N [[(2r,3r,4r,5r)-5-(6-aminopurin-9-yl)-3-hydroxy-4-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2s,3r,4s,5s)-5-(3-carbamoylpyridin-1-ium-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphate Chemical compound NC(=O)C1=CC=C[N+]([C@@H]2[C@H]([C@@H](O)[C@H](COP([O-])(=O)OP(O)(=O)OC[C@@H]3[C@H]([C@@H](OP(O)(O)=O)[C@@H](O3)N3C4=NC=NC(N)=C4N=C3)O)O2)O)=C1 XJLXINKUBYWONI-DQQFMEOOSA-N 0.000 description 6
- WQZGKKKJIJFFOK-UKLRSMCWSA-N dextrose-2-13c Chemical compound OC[C@H]1OC(O)[13C@H](O)[C@@H](O)[C@@H]1O WQZGKKKJIJFFOK-UKLRSMCWSA-N 0.000 description 6
- 230000007705 epithelial mesenchymal transition Effects 0.000 description 6
- 238000009396 hybridization Methods 0.000 description 6
- 239000000463 material Substances 0.000 description 6
- 230000035772 mutation Effects 0.000 description 6
- 210000001778 pluripotent stem cell Anatomy 0.000 description 6
- 230000008569 process Effects 0.000 description 6
- 102000004196 processed proteins & peptides Human genes 0.000 description 6
- 230000008707 rearrangement Effects 0.000 description 6
- 230000000306 recurrent effect Effects 0.000 description 6
- 210000002966 serum Anatomy 0.000 description 6
- 101000782147 Homo sapiens WD repeat-containing protein 20 Proteins 0.000 description 5
- 241001465754 Metazoa Species 0.000 description 5
- 102100035423 POU domain, class 5, transcription factor 1 Human genes 0.000 description 5
- 238000011529 RT qPCR Methods 0.000 description 5
- 102100023345 Tyrosine-protein kinase ITK/TSK Human genes 0.000 description 5
- 102100036561 WD repeat-containing protein 20 Human genes 0.000 description 5
- 238000011888 autopsy Methods 0.000 description 5
- 230000033228 biological regulation Effects 0.000 description 5
- 238000006243 chemical reaction Methods 0.000 description 5
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical class NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 5
- 230000001419 dependent effect Effects 0.000 description 5
- 238000005516 engineering process Methods 0.000 description 5
- 210000002950 fibroblast Anatomy 0.000 description 5
- 229960005277 gemcitabine Drugs 0.000 description 5
- SDUQYLNIPVEERB-QPPQHZFASA-N gemcitabine Chemical compound O=C1N=C(N)C=CN1[C@H]1C(F)(F)[C@H](O)[C@@H](CO)O1 SDUQYLNIPVEERB-QPPQHZFASA-N 0.000 description 5
- 230000034659 glycolysis Effects 0.000 description 5
- 238000012744 immunostaining Methods 0.000 description 5
- 238000004519 manufacturing process Methods 0.000 description 5
- 239000003550 marker Substances 0.000 description 5
- 230000005012 migration Effects 0.000 description 5
- 238000013508 migration Methods 0.000 description 5
- 239000000203 mixture Substances 0.000 description 5
- 210000000056 organ Anatomy 0.000 description 5
- 230000003252 repetitive effect Effects 0.000 description 5
- 238000003860 storage Methods 0.000 description 5
- 239000000725 suspension Substances 0.000 description 5
- 230000004614 tumor growth Effects 0.000 description 5
- WHUUTDBJXJRKMK-VKHMYHEASA-N L-glutamic acid Chemical compound OC(=O)[C@@H](N)CCC(O)=O WHUUTDBJXJRKMK-VKHMYHEASA-N 0.000 description 4
- 238000000134 MTT assay Methods 0.000 description 4
- 231100000002 MTT assay Toxicity 0.000 description 4
- 206010027457 Metastases to liver Diseases 0.000 description 4
- -1 NANOG Proteins 0.000 description 4
- 206010061309 Neoplasm progression Diseases 0.000 description 4
- 210000004504 adult stem cell Anatomy 0.000 description 4
- 239000000090 biomarker Substances 0.000 description 4
- 230000002950 deficient Effects 0.000 description 4
- 238000009792 diffusion process Methods 0.000 description 4
- 230000004927 fusion Effects 0.000 description 4
- 108020001507 fusion proteins Proteins 0.000 description 4
- 102000037865 fusion proteins Human genes 0.000 description 4
- 230000004190 glucose uptake Effects 0.000 description 4
- 229930195712 glutamate Natural products 0.000 description 4
- 238000000338 in vitro Methods 0.000 description 4
- 238000004895 liquid chromatography mass spectrometry Methods 0.000 description 4
- 210000004185 liver Anatomy 0.000 description 4
- 230000001404 mediated effect Effects 0.000 description 4
- 230000004060 metabolic process Effects 0.000 description 4
- 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 description 4
- 229930027945 nicotinamide-adenine dinucleotide Natural products 0.000 description 4
- 235000015097 nutrients Nutrition 0.000 description 4
- 230000001590 oxidative effect Effects 0.000 description 4
- 238000007619 statistical method Methods 0.000 description 4
- 239000000126 substance Substances 0.000 description 4
- 239000000758 substrate Substances 0.000 description 4
- 239000013589 supplement Substances 0.000 description 4
- 230000005751 tumor progression Effects 0.000 description 4
- 102100037127 Developmental pluripotency-associated protein 3 Human genes 0.000 description 3
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 3
- 208000031448 Genomic Instability Diseases 0.000 description 3
- 101001050886 Homo sapiens Lysine-specific histone demethylase 1A Proteins 0.000 description 3
- 241000124008 Mammalia Species 0.000 description 3
- 108700020796 Oncogene Proteins 0.000 description 3
- 101710126211 POU domain, class 5, transcription factor 1 Proteins 0.000 description 3
- 239000012472 biological sample Substances 0.000 description 3
- 230000003833 cell viability Effects 0.000 description 3
- 238000004590 computer program Methods 0.000 description 3
- 229940079593 drug Drugs 0.000 description 3
- 239000003814 drug Substances 0.000 description 3
- 230000008482 dysregulation Effects 0.000 description 3
- ZDXPYRJPNDTMRX-UHFFFAOYSA-N glutamine Natural products OC(=O)C(N)CCC(N)=O ZDXPYRJPNDTMRX-UHFFFAOYSA-N 0.000 description 3
- 239000001963 growth medium Substances 0.000 description 3
- 230000006607 hypermethylation Effects 0.000 description 3
- 230000003834 intracellular effect Effects 0.000 description 3
- 210000002510 keratinocyte Anatomy 0.000 description 3
- 238000007726 management method Methods 0.000 description 3
- 230000007246 mechanism Effects 0.000 description 3
- 230000002503 metabolic effect Effects 0.000 description 3
- 238000002705 metabolomic analysis Methods 0.000 description 3
- 230000001431 metabolomic effect Effects 0.000 description 3
- 239000002679 microRNA Substances 0.000 description 3
- 238000002493 microarray Methods 0.000 description 3
- 238000012758 nuclear staining Methods 0.000 description 3
- 230000036961 partial effect Effects 0.000 description 3
- 239000013610 patient sample Substances 0.000 description 3
- 229920001184 polypeptide Polymers 0.000 description 3
- 230000000750 progressive effect Effects 0.000 description 3
- 230000002062 proliferating effect Effects 0.000 description 3
- 238000012175 pyrosequencing Methods 0.000 description 3
- 230000000717 retained effect Effects 0.000 description 3
- 238000010206 sensitivity analysis Methods 0.000 description 3
- 230000011664 signaling Effects 0.000 description 3
- 239000007787 solid Substances 0.000 description 3
- 238000011144 upstream manufacturing Methods 0.000 description 3
- 229940035893 uracil Drugs 0.000 description 3
- 102000002260 Alkaline Phosphatase Human genes 0.000 description 2
- 108020004774 Alkaline Phosphatase Proteins 0.000 description 2
- 206010063836 Atrioventricular septal defect Diseases 0.000 description 2
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 description 2
- 108091029523 CpG island Proteins 0.000 description 2
- 108091029430 CpG site Proteins 0.000 description 2
- 102100037124 Developmental pluripotency-associated 5 protein Human genes 0.000 description 2
- 102100036949 Developmental pluripotency-associated protein 2 Human genes 0.000 description 2
- 108010043121 Green Fluorescent Proteins Proteins 0.000 description 2
- 102000004144 Green Fluorescent Proteins Human genes 0.000 description 2
- 102000006947 Histones Human genes 0.000 description 2
- 101000804948 Homo sapiens Developmental pluripotency-associated protein 2 Proteins 0.000 description 2
- 101000881866 Homo sapiens Developmental pluripotency-associated protein 3 Proteins 0.000 description 2
- 101001139134 Homo sapiens Krueppel-like factor 4 Proteins 0.000 description 2
- 101001094700 Homo sapiens POU domain, class 5, transcription factor 1 Proteins 0.000 description 2
- 101000740178 Homo sapiens Sal-like protein 4 Proteins 0.000 description 2
- 101000687905 Homo sapiens Transcription factor SOX-2 Proteins 0.000 description 2
- KFZMGEQAYNKOFK-UHFFFAOYSA-N Isopropanol Chemical compound CC(C)O KFZMGEQAYNKOFK-UHFFFAOYSA-N 0.000 description 2
- 102100020677 Krueppel-like factor 4 Human genes 0.000 description 2
- ZDXPYRJPNDTMRX-VKHMYHEASA-N L-glutamine Chemical compound OC(=O)[C@@H](N)CCC(N)=O ZDXPYRJPNDTMRX-VKHMYHEASA-N 0.000 description 2
- 102100024985 Lysine-specific histone demethylase 1A Human genes 0.000 description 2
- 241000699670 Mus sp. Species 0.000 description 2
- 238000011887 Necropsy Methods 0.000 description 2
- DFPAKSUCGFBDDF-UHFFFAOYSA-N Nicotinamide Chemical compound NC(=O)C1=CC=CN=C1 DFPAKSUCGFBDDF-UHFFFAOYSA-N 0.000 description 2
- 102000043276 Oncogene Human genes 0.000 description 2
- 108010043958 Peptoids Proteins 0.000 description 2
- 108700005075 Regulator Genes Proteins 0.000 description 2
- 102100037192 Sal-like protein 4 Human genes 0.000 description 2
- 241000862969 Stella Species 0.000 description 2
- 102100024270 Transcription factor SOX-2 Human genes 0.000 description 2
- 108050007918 Transcription factor STAT Proteins 0.000 description 2
- 102000013127 Vimentin Human genes 0.000 description 2
- 108010065472 Vimentin Proteins 0.000 description 2
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 2
- 230000004913 activation Effects 0.000 description 2
- 239000011543 agarose gel Substances 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- WQZGKKKJIJFFOK-VFUOTHLCSA-N beta-D-glucose Chemical compound OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O WQZGKKKJIJFFOK-VFUOTHLCSA-N 0.000 description 2
- 230000015572 biosynthetic process Effects 0.000 description 2
- 239000000872 buffer Substances 0.000 description 2
- 208000035269 cancer or benign tumor Diseases 0.000 description 2
- 229910052799 carbon Inorganic materials 0.000 description 2
- 230000021164 cell adhesion Effects 0.000 description 2
- 230000007960 cellular response to stress Effects 0.000 description 2
- 239000003153 chemical reaction reagent Substances 0.000 description 2
- 229940104302 cytosine Drugs 0.000 description 2
- 230000034994 death Effects 0.000 description 2
- 231100000517 death Toxicity 0.000 description 2
- 238000000326 densiometry Methods 0.000 description 2
- 238000013461 design Methods 0.000 description 2
- 238000001211 electron capture detection Methods 0.000 description 2
- 210000001671 embryonic stem cell Anatomy 0.000 description 2
- 210000001900 endoderm Anatomy 0.000 description 2
- 210000002919 epithelial cell Anatomy 0.000 description 2
- 239000000499 gel Substances 0.000 description 2
- 210000001654 germ layer Anatomy 0.000 description 2
- 230000002414 glycolytic effect Effects 0.000 description 2
- 239000005090 green fluorescent protein Substances 0.000 description 2
- 230000036541 health Effects 0.000 description 2
- 210000003958 hematopoietic stem cell Anatomy 0.000 description 2
- 210000005260 human cell Anatomy 0.000 description 2
- 238000010166 immunofluorescence Methods 0.000 description 2
- 238000011534 incubation Methods 0.000 description 2
- 238000002372 labelling Methods 0.000 description 2
- 230000003902 lesion Effects 0.000 description 2
- 238000004811 liquid chromatography Methods 0.000 description 2
- 210000003716 mesoderm Anatomy 0.000 description 2
- 238000007884 metabolite profiling Methods 0.000 description 2
- 239000013642 negative control Substances 0.000 description 2
- 210000004940 nucleus Anatomy 0.000 description 2
- 231100000590 oncogenic Toxicity 0.000 description 2
- 230000002246 oncogenic effect Effects 0.000 description 2
- 230000005959 oncogenic signaling Effects 0.000 description 2
- 230000033116 oxidation-reduction process Effects 0.000 description 2
- 210000000496 pancreas Anatomy 0.000 description 2
- 239000008188 pellet Substances 0.000 description 2
- 230000004108 pentose phosphate pathway Effects 0.000 description 2
- 230000004481 post-translational protein modification Effects 0.000 description 2
- 238000002360 preparation method Methods 0.000 description 2
- 238000000746 purification Methods 0.000 description 2
- 238000003762 quantitative reverse transcription PCR Methods 0.000 description 2
- 238000003753 real-time PCR Methods 0.000 description 2
- 230000008521 reorganization Effects 0.000 description 2
- 238000003757 reverse transcription PCR Methods 0.000 description 2
- 102200006531 rs121913529 Human genes 0.000 description 2
- 230000035945 sensitivity Effects 0.000 description 2
- 230000000392 somatic effect Effects 0.000 description 2
- 238000006467 substitution reaction Methods 0.000 description 2
- 230000004083 survival effect Effects 0.000 description 2
- 238000002626 targeted therapy Methods 0.000 description 2
- 230000001225 therapeutic effect Effects 0.000 description 2
- 238000001890 transfection Methods 0.000 description 2
- 108700026220 vif Genes Proteins 0.000 description 2
- 210000005048 vimentin Anatomy 0.000 description 2
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 2
- 102000040650 (ribonucleotides)n+m Human genes 0.000 description 1
- VOZDNCFKGOLECZ-BTVCFUMJSA-N 2-hydroxypropanoic acid;(2r,3s,4r,5r)-2,3,4,5,6-pentahydroxyhexanal Chemical compound CC(O)C(O)=O.OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C=O VOZDNCFKGOLECZ-BTVCFUMJSA-N 0.000 description 1
- HVCOBJNICQPDBP-UHFFFAOYSA-N 3-[3-[3,5-dihydroxy-6-methyl-4-(3,4,5-trihydroxy-6-methyloxan-2-yl)oxyoxan-2-yl]oxydecanoyloxy]decanoic acid;hydrate Chemical compound O.OC1C(OC(CC(=O)OC(CCCCCCC)CC(O)=O)CCCCCCC)OC(C)C(O)C1OC1C(O)C(O)C(O)C(C)O1 HVCOBJNICQPDBP-UHFFFAOYSA-N 0.000 description 1
- KJLPSBMDOIVXSN-UHFFFAOYSA-N 4-[4-[2-[4-(3,4-dicarboxyphenoxy)phenyl]propan-2-yl]phenoxy]phthalic acid Chemical compound C=1C=C(OC=2C=C(C(C(O)=O)=CC=2)C(O)=O)C=CC=1C(C)(C)C(C=C1)=CC=C1OC1=CC=C(C(O)=O)C(C(O)=O)=C1 KJLPSBMDOIVXSN-UHFFFAOYSA-N 0.000 description 1
- BIRSGZKFKXLSJQ-SQOUGZDYSA-N 6-Phospho-D-gluconate Chemical compound OP(=O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O BIRSGZKFKXLSJQ-SQOUGZDYSA-N 0.000 description 1
- ZLWYEPMDOUQDBW-UHFFFAOYSA-N 6-aminonicotinamide Chemical compound NC(=O)C1=CC=C(N)N=C1 ZLWYEPMDOUQDBW-UHFFFAOYSA-N 0.000 description 1
- 102000007469 Actins Human genes 0.000 description 1
- 108010085238 Actins Proteins 0.000 description 1
- 102100030379 Acyl-coenzyme A synthetase ACSM2A, mitochondrial Human genes 0.000 description 1
- 208000010507 Adenocarcinoma of Lung Diseases 0.000 description 1
- 206010001488 Aggression Diseases 0.000 description 1
- 101710145634 Antigen 1 Proteins 0.000 description 1
- 102100038108 Arylamine N-acetyltransferase 1 Human genes 0.000 description 1
- 206010003445 Ascites Diseases 0.000 description 1
- 241000283690 Bos taurus Species 0.000 description 1
- 101100010325 Bos taurus DPPA3 gene Proteins 0.000 description 1
- 108091003079 Bovine Serum Albumin Proteins 0.000 description 1
- 206010006187 Breast cancer Diseases 0.000 description 1
- 208000026310 Breast neoplasm Diseases 0.000 description 1
- 101150029001 CDH2 gene Proteins 0.000 description 1
- 102100025805 Cadherin-1 Human genes 0.000 description 1
- 201000009030 Carcinoma Diseases 0.000 description 1
- 108091007854 Cdh1/Fizzy-related Proteins 0.000 description 1
- 241000282693 Cercopithecidae Species 0.000 description 1
- 238000001353 Chip-sequencing Methods 0.000 description 1
- 208000037051 Chromosomal Instability Diseases 0.000 description 1
- 108010035532 Collagen Proteins 0.000 description 1
- 102000008186 Collagen Human genes 0.000 description 1
- 102000012422 Collagen Type I Human genes 0.000 description 1
- 108010022452 Collagen Type I Proteins 0.000 description 1
- 206010053138 Congenital aplastic anaemia Diseases 0.000 description 1
- 108090000695 Cytokines Proteins 0.000 description 1
- 102000004127 Cytokines Human genes 0.000 description 1
- HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical compound OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 1
- 102000053602 DNA Human genes 0.000 description 1
- 102100024812 DNA (cytosine-5)-methyltransferase 3A Human genes 0.000 description 1
- 108050002829 DNA (cytosine-5)-methyltransferase 3A Proteins 0.000 description 1
- 102100024810 DNA (cytosine-5)-methyltransferase 3B Human genes 0.000 description 1
- 101710123222 DNA (cytosine-5)-methyltransferase 3B Proteins 0.000 description 1
- 238000007400 DNA extraction Methods 0.000 description 1
- 238000000018 DNA microarray Methods 0.000 description 1
- 102100035619 DNA-(apurinic or apyrimidinic site) lyase Human genes 0.000 description 1
- 102100037126 Developmental pluripotency-associated protein 4 Human genes 0.000 description 1
- 206010061818 Disease progression Diseases 0.000 description 1
- 102000001301 EGF receptor Human genes 0.000 description 1
- 108060006698 EGF receptor Proteins 0.000 description 1
- 241000283086 Equidae Species 0.000 description 1
- 241000701959 Escherichia virus Lambda Species 0.000 description 1
- 101150099612 Esrrb gene Proteins 0.000 description 1
- 108010037362 Extracellular Matrix Proteins Proteins 0.000 description 1
- 102000010834 Extracellular Matrix Proteins Human genes 0.000 description 1
- 108010066805 F-Box Proteins Proteins 0.000 description 1
- 102000018700 F-Box Proteins Human genes 0.000 description 1
- 201000004939 Fanconi anemia Diseases 0.000 description 1
- 102000003969 Fibroblast growth factor 4 Human genes 0.000 description 1
- 108090000381 Fibroblast growth factor 4 Proteins 0.000 description 1
- GHASVSINZRGABV-UHFFFAOYSA-N Fluorouracil Chemical compound FC1=CNC(=O)NC1=O GHASVSINZRGABV-UHFFFAOYSA-N 0.000 description 1
- 102000017707 GABRB3 Human genes 0.000 description 1
- 101150112014 Gapdh gene Proteins 0.000 description 1
- 206010064571 Gene mutation Diseases 0.000 description 1
- 229930186217 Glycolipid Natural products 0.000 description 1
- 102000003886 Glycoproteins Human genes 0.000 description 1
- 108090000288 Glycoproteins Proteins 0.000 description 1
- 102100035364 Growth/differentiation factor 3 Human genes 0.000 description 1
- 102100034533 Histone H2AX Human genes 0.000 description 1
- 101710195517 Histone H2AX Proteins 0.000 description 1
- 102100033636 Histone H3.2 Human genes 0.000 description 1
- 102100028140 Homeobox protein NOBOX Human genes 0.000 description 1
- 102100028798 Homeodomain-only protein Human genes 0.000 description 1
- 241000282412 Homo Species 0.000 description 1
- 101100054737 Homo sapiens ACSM2A gene Proteins 0.000 description 1
- 101001137256 Homo sapiens DNA-(apurinic or apyrimidinic site) lyase Proteins 0.000 description 1
- 101000881848 Homo sapiens Developmental pluripotency-associated 5 protein Proteins 0.000 description 1
- 101000881868 Homo sapiens Developmental pluripotency-associated protein 4 Proteins 0.000 description 1
- 101001073597 Homo sapiens Gamma-aminobutyric acid receptor subunit beta-3 Proteins 0.000 description 1
- 101001023986 Homo sapiens Growth/differentiation factor 3 Proteins 0.000 description 1
- 101000632048 Homo sapiens Homeobox protein NOBOX Proteins 0.000 description 1
- 101000839095 Homo sapiens Homeodomain-only protein Proteins 0.000 description 1
- 101001046587 Homo sapiens Krueppel-like factor 1 Proteins 0.000 description 1
- 101001139146 Homo sapiens Krueppel-like factor 2 Proteins 0.000 description 1
- 101001139130 Homo sapiens Krueppel-like factor 5 Proteins 0.000 description 1
- 101000702559 Homo sapiens Probable global transcription activator SNF2L2 Proteins 0.000 description 1
- 101000652321 Homo sapiens Protein SOX-15 Proteins 0.000 description 1
- 101000984042 Homo sapiens Protein lin-28 homolog A Proteins 0.000 description 1
- 101000889749 Homo sapiens Putative ATP-dependent RNA helicase TDRD12 Proteins 0.000 description 1
- 101000825432 Homo sapiens SHC-transforming protein 4 Proteins 0.000 description 1
- 101000835745 Homo sapiens Teratocarcinoma-derived growth factor 1 Proteins 0.000 description 1
- 101000819088 Homo sapiens Transcription factor GATA-6 Proteins 0.000 description 1
- 101000652332 Homo sapiens Transcription factor SOX-1 Proteins 0.000 description 1
- 101000652326 Homo sapiens Transcription factor SOX-18 Proteins 0.000 description 1
- 101000687911 Homo sapiens Transcription factor SOX-3 Proteins 0.000 description 1
- 101000976622 Homo sapiens Zinc finger protein 42 homolog Proteins 0.000 description 1
- 206010020674 Hypermetabolism Diseases 0.000 description 1
- 206010061218 Inflammation Diseases 0.000 description 1
- 102100022248 Krueppel-like factor 1 Human genes 0.000 description 1
- 102100020675 Krueppel-like factor 2 Human genes 0.000 description 1
- 102100020680 Krueppel-like factor 5 Human genes 0.000 description 1
- 108700021430 Kruppel-Like Factor 4 Proteins 0.000 description 1
- 108090001030 Lipoproteins Proteins 0.000 description 1
- 102000004895 Lipoproteins Human genes 0.000 description 1
- 206010025538 Malignant ascites Diseases 0.000 description 1
- 102000013013 Member 2 Subfamily G ATP Binding Cassette Transporter Human genes 0.000 description 1
- 108010090306 Member 2 Subfamily G ATP Binding Cassette Transporter Proteins 0.000 description 1
- 241001430197 Mollicutes Species 0.000 description 1
- 241000699666 Mus <mouse, genus> Species 0.000 description 1
- 101000804949 Mus musculus Developmental pluripotency-associated protein 2 Proteins 0.000 description 1
- 101000881849 Mus musculus Developmental pluripotency-associated protein 4 Proteins 0.000 description 1
- 101100224389 Mus musculus Dppa5a gene Proteins 0.000 description 1
- 101100446513 Mus musculus Fgf4 gene Proteins 0.000 description 1
- 101100293261 Mus musculus Naa15 gene Proteins 0.000 description 1
- 101100404103 Mus musculus Nanog gene Proteins 0.000 description 1
- 101000976618 Mus musculus Zinc finger protein 42 Proteins 0.000 description 1
- 101100107167 Mus musculus Znf296 gene Proteins 0.000 description 1
- 108091057508 Myc family Proteins 0.000 description 1
- 108010064998 N-acetyltransferase 1 Proteins 0.000 description 1
- 101150082943 NAT1 gene Proteins 0.000 description 1
- 208000004072 Oncogene Addiction Diseases 0.000 description 1
- 241001494479 Pecora Species 0.000 description 1
- 102100031021 Probable global transcription activator SNF2L2 Human genes 0.000 description 1
- 102000001253 Protein Kinase Human genes 0.000 description 1
- 101710150336 Protein Rex Proteins 0.000 description 1
- 102100030244 Protein SOX-15 Human genes 0.000 description 1
- 102100025460 Protein lin-28 homolog A Human genes 0.000 description 1
- 102100040195 Putative ATP-dependent RNA helicase TDRD12 Human genes 0.000 description 1
- LCTONWCANYUPML-UHFFFAOYSA-M Pyruvate Chemical compound CC(=O)C([O-])=O LCTONWCANYUPML-UHFFFAOYSA-M 0.000 description 1
- 230000006819 RNA synthesis Effects 0.000 description 1
- 241000700159 Rattus Species 0.000 description 1
- 101100247004 Rattus norvegicus Qsox1 gene Proteins 0.000 description 1
- 108020004511 Recombinant DNA Proteins 0.000 description 1
- 108091028664 Ribonucleotide Proteins 0.000 description 1
- PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 1
- 238000011579 SCID mouse model Methods 0.000 description 1
- 101150086694 SLC22A3 gene Proteins 0.000 description 1
- 108010044012 STAT1 Transcription Factor Proteins 0.000 description 1
- 102000004265 STAT2 Transcription Factor Human genes 0.000 description 1
- 108010081691 STAT2 Transcription Factor Proteins 0.000 description 1
- 108010017324 STAT3 Transcription Factor Proteins 0.000 description 1
- 102000005886 STAT4 Transcription Factor Human genes 0.000 description 1
- 108010019992 STAT4 Transcription Factor Proteins 0.000 description 1
- 101150058731 STAT5A gene Proteins 0.000 description 1
- 101150063267 STAT5B gene Proteins 0.000 description 1
- 108010011005 STAT6 Transcription Factor Proteins 0.000 description 1
- 102100029904 Signal transducer and activator of transcription 1-alpha/beta Human genes 0.000 description 1
- 102100024040 Signal transducer and activator of transcription 3 Human genes 0.000 description 1
- 102100024481 Signal transducer and activator of transcription 5A Human genes 0.000 description 1
- 102100024474 Signal transducer and activator of transcription 5B Human genes 0.000 description 1
- 102100023980 Signal transducer and activator of transcription 6 Human genes 0.000 description 1
- 108091027967 Small hairpin RNA Proteins 0.000 description 1
- 108091060271 Small temporal RNA Proteins 0.000 description 1
- 238000002105 Southern blotting Methods 0.000 description 1
- 238000000692 Student's t-test Methods 0.000 description 1
- LSNNMFCWUKXFEE-UHFFFAOYSA-N Sulfurous acid Chemical group OS(O)=O LSNNMFCWUKXFEE-UHFFFAOYSA-N 0.000 description 1
- 206010042971 T-cell lymphoma Diseases 0.000 description 1
- 208000027585 T-cell non-Hodgkin lymphoma Diseases 0.000 description 1
- 210000001744 T-lymphocyte Anatomy 0.000 description 1
- 108010017842 Telomerase Proteins 0.000 description 1
- 102100026404 Teratocarcinoma-derived growth factor 1 Human genes 0.000 description 1
- 101710183280 Topoisomerase Proteins 0.000 description 1
- 108091023040 Transcription factor Proteins 0.000 description 1
- 102000040945 Transcription factor Human genes 0.000 description 1
- 102100030248 Transcription factor SOX-1 Human genes 0.000 description 1
- 102100030249 Transcription factor SOX-18 Human genes 0.000 description 1
- 102100024276 Transcription factor SOX-3 Human genes 0.000 description 1
- 102000000887 Transcription factor STAT Human genes 0.000 description 1
- 102100022012 Transcription intermediary factor 1-beta Human genes 0.000 description 1
- 101710177718 Transcription intermediary factor 1-beta Proteins 0.000 description 1
- 101710101305 Transducin-like enhancer protein 1 Proteins 0.000 description 1
- 241001105097 Trox Species 0.000 description 1
- 206010064390 Tumour invasion Diseases 0.000 description 1
- 230000006682 Warburg effect Effects 0.000 description 1
- 108700029631 X-Linked Genes Proteins 0.000 description 1
- 101001029301 Xenopus tropicalis Forkhead box protein D3 Proteins 0.000 description 1
- 102100028430 Zinc finger protein 296 Human genes 0.000 description 1
- 101710147072 Zinc finger protein 296 Proteins 0.000 description 1
- 102100023550 Zinc finger protein 42 homolog Human genes 0.000 description 1
- 238000002679 ablation Methods 0.000 description 1
- 239000002253 acid Substances 0.000 description 1
- 230000009471 action Effects 0.000 description 1
- 230000006978 adaptation Effects 0.000 description 1
- 230000002776 aggregation Effects 0.000 description 1
- 238000004220 aggregation Methods 0.000 description 1
- 230000016571 aggressive behavior Effects 0.000 description 1
- 208000012761 aggressive behavior Diseases 0.000 description 1
- HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 1
- 150000001413 amino acids Chemical group 0.000 description 1
- 230000000340 anti-metabolite Effects 0.000 description 1
- 230000000692 anti-sense effect Effects 0.000 description 1
- 229940100197 antimetabolite Drugs 0.000 description 1
- 239000002256 antimetabolite Substances 0.000 description 1
- 239000000074 antisense oligonucleotide Substances 0.000 description 1
- 238000012230 antisense oligonucleotides Methods 0.000 description 1
- 230000006907 apoptotic process Effects 0.000 description 1
- 238000013459 approach Methods 0.000 description 1
- QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 description 1
- 210000003719 b-lymphocyte Anatomy 0.000 description 1
- 229960000397 bevacizumab Drugs 0.000 description 1
- 230000000975 bioactive effect Effects 0.000 description 1
- 238000003766 bioinformatics method Methods 0.000 description 1
- 230000001851 biosynthetic effect Effects 0.000 description 1
- 230000000903 blocking effect Effects 0.000 description 1
- 210000000601 blood cell Anatomy 0.000 description 1
- 210000004556 brain Anatomy 0.000 description 1
- 230000009400 cancer invasion Effects 0.000 description 1
- 150000001720 carbohydrates Chemical class 0.000 description 1
- 210000004413 cardiac myocyte Anatomy 0.000 description 1
- 230000022131 cell cycle Effects 0.000 description 1
- 230000030833 cell death Effects 0.000 description 1
- 230000007348 cell dedifferentiation Effects 0.000 description 1
- 230000024245 cell differentiation Effects 0.000 description 1
- 230000010261 cell growth Effects 0.000 description 1
- 210000000170 cell membrane Anatomy 0.000 description 1
- 230000009087 cell motility Effects 0.000 description 1
- 210000003855 cell nucleus Anatomy 0.000 description 1
- 230000004663 cell proliferation Effects 0.000 description 1
- 230000019522 cellular metabolic process Effects 0.000 description 1
- 238000005119 centrifugation Methods 0.000 description 1
- 210000001612 chondrocyte Anatomy 0.000 description 1
- 230000004186 co-expression Effects 0.000 description 1
- 229920001436 collagen Polymers 0.000 description 1
- 238000004891 communication Methods 0.000 description 1
- 230000000052 comparative effect Effects 0.000 description 1
- 230000008602 contraction Effects 0.000 description 1
- 239000012228 culture supernatant Substances 0.000 description 1
- 230000001351 cycling effect Effects 0.000 description 1
- 238000004163 cytometry Methods 0.000 description 1
- SUYVUBYJARFZHO-RRKCRQDMSA-N dATP Chemical compound C1=NC=2C(N)=NC=NC=2N1[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 SUYVUBYJARFZHO-RRKCRQDMSA-N 0.000 description 1
- SUYVUBYJARFZHO-UHFFFAOYSA-N dATP Natural products C1=NC=2C(N)=NC=NC=2N1C1CC(O)C(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 SUYVUBYJARFZHO-UHFFFAOYSA-N 0.000 description 1
- 238000007405 data analysis Methods 0.000 description 1
- 238000013480 data collection Methods 0.000 description 1
- 238000013500 data storage Methods 0.000 description 1
- 230000002498 deadly effect Effects 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 230000032459 dedifferentiation Effects 0.000 description 1
- 238000012350 deep sequencing Methods 0.000 description 1
- 230000007812 deficiency Effects 0.000 description 1
- 238000012217 deletion Methods 0.000 description 1
- 230000037430 deletion Effects 0.000 description 1
- 239000005547 deoxyribonucleotide Substances 0.000 description 1
- 125000002637 deoxyribonucleotide group Chemical group 0.000 description 1
- 238000010586 diagram Methods 0.000 description 1
- 235000014113 dietary fatty acids Nutrition 0.000 description 1
- 230000005750 disease progression Effects 0.000 description 1
- 230000003828 downregulation Effects 0.000 description 1
- 210000003981 ectoderm Anatomy 0.000 description 1
- 210000002242 embryoid body Anatomy 0.000 description 1
- 210000002889 endothelial cell Anatomy 0.000 description 1
- 230000007613 environmental effect Effects 0.000 description 1
- 238000006911 enzymatic reaction Methods 0.000 description 1
- 210000001339 epidermal cell Anatomy 0.000 description 1
- 230000004049 epigenetic modification Effects 0.000 description 1
- 230000006565 epigenetic process Effects 0.000 description 1
- 230000006718 epigenetic regulation Effects 0.000 description 1
- 210000003743 erythrocyte Anatomy 0.000 description 1
- 230000001747 exhibiting effect Effects 0.000 description 1
- 210000002744 extracellular matrix Anatomy 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 229930195729 fatty acid Natural products 0.000 description 1
- 239000000194 fatty acid Substances 0.000 description 1
- 150000004665 fatty acids Chemical class 0.000 description 1
- 108091006047 fluorescent proteins Proteins 0.000 description 1
- 102000034287 fluorescent proteins Human genes 0.000 description 1
- 229960002949 fluorouracil Drugs 0.000 description 1
- 239000012634 fragment Substances 0.000 description 1
- 239000012737 fresh medium Substances 0.000 description 1
- 239000000446 fuel Substances 0.000 description 1
- 238000012252 genetic analysis Methods 0.000 description 1
- 238000003205 genotyping method Methods 0.000 description 1
- 239000006481 glucose medium Substances 0.000 description 1
- 210000000442 hair follicle cell Anatomy 0.000 description 1
- 210000002216 heart Anatomy 0.000 description 1
- 210000003494 hepatocyte Anatomy 0.000 description 1
- 238000004896 high resolution mass spectrometry Methods 0.000 description 1
- 238000012165 high-throughput sequencing Methods 0.000 description 1
- HNDVDQJCIGZPNO-UHFFFAOYSA-N histidine Natural products OC(=O)C(N)CC1=CN=CN1 HNDVDQJCIGZPNO-UHFFFAOYSA-N 0.000 description 1
- 230000006951 hyperphosphorylation Effects 0.000 description 1
- 230000003832 immune regulation Effects 0.000 description 1
- 238000003018 immunoassay Methods 0.000 description 1
- 239000012133 immunoprecipitate Substances 0.000 description 1
- 238000009169 immunotherapy Methods 0.000 description 1
- 238000012606 in vitro cell culture Methods 0.000 description 1
- 238000010348 incorporation Methods 0.000 description 1
- 230000006698 induction Effects 0.000 description 1
- 230000001939 inductive effect Effects 0.000 description 1
- 230000004054 inflammatory process Effects 0.000 description 1
- 238000013101 initial test Methods 0.000 description 1
- 238000003780 insertion Methods 0.000 description 1
- 230000037431 insertion Effects 0.000 description 1
- 230000010354 integration Effects 0.000 description 1
- 210000000936 intestine Anatomy 0.000 description 1
- 210000004153 islets of langerhan Anatomy 0.000 description 1
- 210000003734 kidney Anatomy 0.000 description 1
- 230000000670 limiting effect Effects 0.000 description 1
- 150000002632 lipids Chemical class 0.000 description 1
- 238000011068 loading method Methods 0.000 description 1
- 230000033001 locomotion Effects 0.000 description 1
- 230000007774 longterm Effects 0.000 description 1
- 201000005249 lung adenocarcinoma Diseases 0.000 description 1
- 210000004698 lymphocyte Anatomy 0.000 description 1
- 210000002540 macrophage Anatomy 0.000 description 1
- 230000014759 maintenance of location Effects 0.000 description 1
- 230000036210 malignancy Effects 0.000 description 1
- 210000004962 mammalian cell Anatomy 0.000 description 1
- 210000001161 mammalian embryo Anatomy 0.000 description 1
- 210000002752 melanocyte Anatomy 0.000 description 1
- 210000002901 mesenchymal stem cell Anatomy 0.000 description 1
- 230000037353 metabolic pathway Effects 0.000 description 1
- 230000006510 metastatic growth Effects 0.000 description 1
- 238000012164 methylation sequencing Methods 0.000 description 1
- 238000007855 methylation-specific PCR Methods 0.000 description 1
- 238000012775 microarray technology Methods 0.000 description 1
- 238000001000 micrograph Methods 0.000 description 1
- 230000003278 mimic effect Effects 0.000 description 1
- 210000001616 monocyte Anatomy 0.000 description 1
- 210000005087 mononuclear cell Anatomy 0.000 description 1
- 238000010172 mouse model Methods 0.000 description 1
- 210000002894 multi-fate stem cell Anatomy 0.000 description 1
- 210000003205 muscle Anatomy 0.000 description 1
- 210000000663 muscle cell Anatomy 0.000 description 1
- 210000005170 neoplastic cell Anatomy 0.000 description 1
- 230000009826 neoplastic cell growth Effects 0.000 description 1
- 210000001178 neural stem cell Anatomy 0.000 description 1
- 210000002569 neuron Anatomy 0.000 description 1
- 238000007481 next generation sequencing Methods 0.000 description 1
- 229960003966 nicotinamide Drugs 0.000 description 1
- 235000005152 nicotinamide Nutrition 0.000 description 1
- 239000011570 nicotinamide Substances 0.000 description 1
- 238000010606 normalization Methods 0.000 description 1
- 238000007899 nucleic acid hybridization Methods 0.000 description 1
- 235000021232 nutrient availability Nutrition 0.000 description 1
- 235000003715 nutritional status Nutrition 0.000 description 1
- 230000002018 overexpression Effects 0.000 description 1
- 229910052760 oxygen Inorganic materials 0.000 description 1
- 239000001301 oxygen Substances 0.000 description 1
- 239000012188 paraffin wax Substances 0.000 description 1
- 230000001776 parthenogenetic effect Effects 0.000 description 1
- 239000000816 peptidomimetic Substances 0.000 description 1
- 230000002093 peripheral effect Effects 0.000 description 1
- 230000002688 persistence Effects 0.000 description 1
- 150000004713 phosphodiesters Chemical class 0.000 description 1
- 230000004962 physiological condition Effects 0.000 description 1
- 238000007747 plating Methods 0.000 description 1
- 230000001124 posttranscriptional effect Effects 0.000 description 1
- 230000003389 potentiating effect Effects 0.000 description 1
- 229940002612 prodrug Drugs 0.000 description 1
- 239000000651 prodrug Substances 0.000 description 1
- 230000035755 proliferation Effects 0.000 description 1
- 108060006633 protein kinase Proteins 0.000 description 1
- 230000004850 protein–protein interaction Effects 0.000 description 1
- 238000011002 quantification Methods 0.000 description 1
- 238000004445 quantitative analysis Methods 0.000 description 1
- 238000011158 quantitative evaluation Methods 0.000 description 1
- 238000010791 quenching Methods 0.000 description 1
- 102000016914 ras Proteins Human genes 0.000 description 1
- 108010014186 ras Proteins Proteins 0.000 description 1
- 239000011535 reaction buffer Substances 0.000 description 1
- 238000011897 real-time detection Methods 0.000 description 1
- 230000009467 reduction Effects 0.000 description 1
- 238000000611 regression analysis Methods 0.000 description 1
- 230000022983 regulation of cell cycle Effects 0.000 description 1
- 230000014493 regulation of gene expression Effects 0.000 description 1
- 230000029588 regulation of mitotic cell cycle Effects 0.000 description 1
- 230000001850 reproductive effect Effects 0.000 description 1
- 230000003938 response to stress Effects 0.000 description 1
- 239000002336 ribonucleotide Substances 0.000 description 1
- 125000002652 ribonucleotide group Chemical group 0.000 description 1
- 238000007480 sanger sequencing Methods 0.000 description 1
- 238000012216 screening Methods 0.000 description 1
- 210000000717 sertoli cell Anatomy 0.000 description 1
- 210000003491 skin Anatomy 0.000 description 1
- 210000001626 skin fibroblast Anatomy 0.000 description 1
- 239000004055 small Interfering RNA Substances 0.000 description 1
- 150000003384 small molecules Chemical class 0.000 description 1
- 238000000527 sonication Methods 0.000 description 1
- 210000000952 spleen Anatomy 0.000 description 1
- 238000010561 standard procedure Methods 0.000 description 1
- 210000000130 stem cell Anatomy 0.000 description 1
- 210000002784 stomach Anatomy 0.000 description 1
- 230000004960 subcellular localization Effects 0.000 description 1
- 230000001629 suppression Effects 0.000 description 1
- 238000003786 synthesis reaction Methods 0.000 description 1
- 231100000331 toxic Toxicity 0.000 description 1
- 230000002588 toxic effect Effects 0.000 description 1
- 238000013518 transcription Methods 0.000 description 1
- 230000035897 transcription Effects 0.000 description 1
- 230000002103 transcriptional effect Effects 0.000 description 1
- 230000037426 transcriptional repression Effects 0.000 description 1
- 238000012546 transfer Methods 0.000 description 1
- 230000007704 transition Effects 0.000 description 1
- 230000014616 translation Effects 0.000 description 1
- 230000005945 translocation Effects 0.000 description 1
- 102000035160 transmembrane proteins Human genes 0.000 description 1
- 108091005703 transmembrane proteins Proteins 0.000 description 1
- RXRGZNYSEHTMHC-BQBZGAKWSA-N troxacitabine Chemical compound O=C1N=C(N)C=CN1[C@H]1O[C@@H](CO)OC1 RXRGZNYSEHTMHC-BQBZGAKWSA-N 0.000 description 1
- 229950010147 troxacitabine Drugs 0.000 description 1
- 238000001195 ultra high performance liquid chromatography Methods 0.000 description 1
- 210000003708 urethra Anatomy 0.000 description 1
- 210000003932 urinary bladder Anatomy 0.000 description 1
- 230000002485 urinary effect Effects 0.000 description 1
- 238000010200 validation analysis Methods 0.000 description 1
- 125000002348 vinylic group Chemical group 0.000 description 1
- 230000003612 virological effect Effects 0.000 description 1
- 238000005406 washing Methods 0.000 description 1
- 238000012070 whole genome sequencing analysis Methods 0.000 description 1
Images
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
- A61P35/04—Antineoplastic agents specific for metastasis
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
- G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
- G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
- G01N33/57496—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving intracellular compounds
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/158—Expression markers
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2800/00—Detection or diagnosis of diseases
- G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
Landscapes
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Engineering & Computer Science (AREA)
- Immunology (AREA)
- Organic Chemistry (AREA)
- General Health & Medical Sciences (AREA)
- Molecular Biology (AREA)
- Analytical Chemistry (AREA)
- Pathology (AREA)
- Oncology (AREA)
- Cell Biology (AREA)
- Medicinal Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Urology & Nephrology (AREA)
- Hematology (AREA)
- Biomedical Technology (AREA)
- Biochemistry (AREA)
- Physics & Mathematics (AREA)
- Microbiology (AREA)
- Biotechnology (AREA)
- Hospice & Palliative Care (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Genetics & Genomics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Public Health (AREA)
- Chemical Kinetics & Catalysis (AREA)
- General Chemical & Material Sciences (AREA)
- Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
- Pharmacology & Pharmacy (AREA)
- Animal Behavior & Ethology (AREA)
- Veterinary Medicine (AREA)
- General Physics & Mathematics (AREA)
- Food Science & Technology (AREA)
- General Engineering & Computer Science (AREA)
- Biophysics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
Abstract
Description
本出願は、米国の35U.S.C.§119(e)の下で、2016年10月6日に出願された米国第62/405,155号の優先権の利益を主張し、その全体内容が参照によりその全体において本明細書に組み込まれる。
添付の配列表の材料は、参照により本出願に組み込まれる。付随する配列表のテキストファイル、ファイル名JHU4080_1WO_1WO_Sequence_Listingは、2017年10月4日に作成され、9kbである。ファイルは、Windows OSを使用しているコンピュータでMicrosoft Wordを使用して評価できる。
本研究は、NIH助成金CA38548(APF)、国立衛生研究所助成金CA140599、CA179991(CID)、AACR膵臓癌アクションネットワーク指導者助成金助成金(OGM)、Vanderbilt GI SPORE(OGM)、アメリカ癌協会からバンダービルト−イングラム癌センター(OGM)およびCA180682(AMM)からの助成金によって支援された。政府は本発明において一定の権利を有する。
本発明は、概して遺伝子分析に関し、より具体的には癌および癌の進行および転移に対する後成的影響に関する。
膵管腺癌(PDAC)の進行の進展中に、原発性腫瘍の増殖、領域の広がり、遠位転移、および患者の死亡を促進する不均一なサブクローン集団が出現する。しかしながら、転移の遺伝学は未治療の患者における原発腫瘍のそれを大部分反映しており、そしてPDACドライバー突然変異は全てのサブクローンによって共有されている。このことは、エピジェネティックな過程が転移の間に機能的であるかもしれないという可能性を高める。ここで我々は、遠位転移の自然な進化の歴史の間に全体的なクロマチン修飾の著しいエピジェネティックなリプログラミングを検出した。ゲノムワイドマッピングは、これらの全体的な変化が、ユークロマチンおよび大型組織化クロマチンK9修飾(LOCK)ヘテロクロマチンを含む悪性形質を集合的に特定する、ゲノム全体にわたる何千もの大クロマチンドメインを標的とすることを明らかにした。これらの変化と並行して、遠位転移はペントースリン酸経路(oxPPP)の酸化的分岐への依存を共進化させ、oxPPP阻害は再プログラムされたクロマチンを選択的に逆転させ、腫瘍形成能を遮断した。このように、多様な代謝、エピジェネティック、および腫瘍形成プログラムが膵臓癌進行の進展の間に出現した。
実施例1
ラージスケールエピゲノムのリプログラミングは、膵癌進行の進展中の同化グルコース代謝を遠位転移に結びつける
先に論じたように、1つの前転移候補はエピゲノム調節である。特に、大型組織化ヘテロクロマチンリジン(K)−9修飾ドメイン(LOCK)および大型DNA低メチル化ブロックを含む、特にヘテロクロマチンドメイン内での、PDACサブクローンの進展および遠位転移中のラージスケールエピゲノム変化の役割を調査したいと考えた。これらの領域は、ゲノムの半分以上を占め、互いに部分的に重複し、そしてPDACを含む多くのヒトの癌において見出されるので、ラージスケールエピジェネティックリプログラミングのための選択可能な標的を表し得る。したがって、本発明者らは、一貫した転移特異的ドライバー変異がないことを考えると、これらの領域内のエピゲノム異常調節が腫瘍進行の主要な選択的力となり得ると仮定した。
結果
遠位転移の進展の間の全体的なエピジェネティック状態のリプログラミング
aクローン由来は、以前に公表された(参考文献1)および他の未公表の(本文脚注1)全ゲノム配列決定データからの系統学的推定値を表す。
bウエスタンブロットデータは、A38Per対照(cont.)と比較したH3K9Me2シグナルのデンシトメトリー(濃度測定)パーセンテージを反映している。ウエスタンブロットを補足図1に示し、絶対濃度測定値を図の凡例に含まれるp値と共に図1gに示す。補足データファイル2のMbおよびRPKM値で詳述されているように、ChIP−seqデータは、A38Per対照(cont.)と比較してH3K9Me2が減少したLOCK Mbの割合を反映している。補足図1および2に詳述されるように、WGBSデータは、A124Pr対照(組織)およびA38Per対照(細胞株)に対するLOCK内のDNAメチル化の割合を反映する。
c化学療法治療を受けた患者からのこの転移は、SMARCA2において、不明瞭な意義のミスセンス変異を有していた。
dこれらの細胞株は、迅速剖検コホートからのものではなく、ドライバーの突然変異を過小評価している可能性がある、以前に公表された遺伝子型決定データに依存している。
eA32O細胞株は、広範囲の肺転移を含む非常に侵攻性のある疾患を有する患者の大網腫瘤病変から単離され、他の遠位(肺/肝臓)転移性サブクローンと同様の所見を示した。
我々は次に、PDACゲノム全体にわたって再プログラムされたクロマチン修飾の位置をマッピングすることを望んだ。この目的のために、我々は、PDAC進展のエピジェネティックなランドスケープをクロマチン免疫沈降とそれに続くハイスループットシークエンシング(ChIP−seq)を用いてよく理解された機能を有するヒストン修飾について包括的にマッピングした(ヘテロクロマチン:H3K9Me2、H3K9Me3、H3K27Me3;ユークロマチン:H3K27Ac、H3K36Me3)。サブクローン進展と悪性進行の多様性をとらえるために、同じ患者からの肺転移(A38Lg)合致した腹膜転移(A38Per)、および同じ患者からの肺転移(A13Lg)にも合致した2つの原発性腫瘍サブクローン(A13Pr1、A13Pr2)を含む、合致したサブクローンから単離された配列検証細胞株に対してChIP−seqを行った。各患者について、全てのサブクローンは、新しい転移特異的ドライバーを獲得することなく同一のドライバー遺伝子突然変異を共有した(表1)。合致する遺伝子発現の変化を同定するために、RNA−seqも並行して行った。最終的に、本発明者らは、図1に示すホルマリン固定腫瘍切片のサブセットに対応した、これらの細胞株および凍結腫瘍組織にわたる全ゲノム亜硫酸水素塩配列決定(WGBS)を用いてこれらのデータセットを補完した。ENCODEガイドライン(補足データ1)で推奨されているように、各ChIP実験について>15.0x106(中央値:32.3x106)のユニークアラインメントリードを含め、19.3x109のユニークアラインメントシークエンスリードで183データセットを生成した。実験は生物学的複製として実施し、複製間では良好な相関を示した(中央相関係数:0.956;範囲:0.746〜0.997、補足データ1)。我々の知る限りでは、これはヒトの癌の進展的進行の間のエピジェネティックなリプログラミングの最初の包括的なゲノムワイド解析を表している。
サブクローン進展は、個々の患者内で著しい表現型の不均一性を生み出す可能性があり、我々はそのような多様性が上記で検出されたものと同様の大規模なエピジェネティック変化によってコードされ得ると仮定した。したがって、我々は再プログラムされたクロマチンドメインが同じ患者からのPDACサブクローン間の不均一な悪性特性をコードしているかもしれないかどうかを徹底的に調査することを望んだ。この目的のために、本発明者らは、同じ患者(A38PerおよびA38Lg)から適合腹膜および肺転移サブクローンを選択し、サブクローン間で差次的に発現された再プログラム化LOCKおよびECD遺伝子に対して遺伝子オントロジー(GO)分析を行い(表4〜7、図2eおよび図11に示されるように再プログラムされた遺伝子に由来する)、その後、GOの結果が実験的アッセイによって測定された実際の表現型の差異と一致するかどうかを試験した。この分析は、再プログラムされたLOCKおよびECDが、以下に記載されるように、サブクローン進展の間に出現した実質的な表現型の違いをコードすることを明らかにした。
我々は次に、再発性の転移固有の経路が、全体的なエピジェネティック状態および腫瘍形成の可能性に対する上流制御を発揮するために、サブクローン進展中に選択されたのかどうかを尋ねた。最近のいくつかの研究では、栄養状態と代謝活性を世界レベルのヒストン修飾と結びつけた。急速剖検コホートにおける遠位転移は、グルコースの豊富な供給を提供する臓器(肝臓、肺)から大部分隔離されていたので、我々はこれらのサブクローンにおける再プログラムされたクロマチンおよび腫瘍形成性がグルコース代謝の特定の側面への依存を進化させたかどうか尋ねた。
一方、低減されたH3K27Acは、LOCKから抑制された遺伝子を特異的に標的とし、他のLOCK遺伝子またはECD調節遺伝子には影響を及ぼさなかった(図19c)。ウエスタンブロットの所見と同様に、6ANに応答してH3K27Me3のレベルは全ての領域にわたって安定したままであった(図19b、d)。まとめると、これらの実験は、6ANが、遠位転移の進展の間に出現したLOCK内のいくつかのクロマチン変化を選択的かつ定量的に標的とすることを実証した。
図の説明
a、6ANは、グルタミン/グルタメートに影響を与えずに、転移性サブクローンにおける細胞外グルコース消費および乳酸分泌の速度を選択的に遅くした。b、6ANは、PPPの下流の代謝産物への細胞内013標識グルコースの取り込みを減少させた。c、6ANは、PGD基質(6PG)および上流の代謝産物(G1、5L)の代謝産物レベルを大幅に増加させ、それに対応して下流の産物が減少した。
ディスカッション
我々は、そのような異質性は進展の時間の関数であると仮定する:後期の広範囲に転移性の疾患を呈する患者は、初期の疾患を呈する患者よりも腫瘍におけるサブクローン間のエピジェネティックかつ悪性の分岐を有する可能性がある。この可能性は、そのような悪性の異質性が生じる前に、癌を早期に発見することの差し迫った必要性を強調している。
データ保管
にオンラインで保管されている(GEO番号:GSE63126)。
方法概要
YSI代謝物の分析。代謝産物消費量(グルコースおよびグルタミン)および生産量(乳酸塩およびグルタミン酸塩)は、YSI7100 Bioanalyzerを使用して測定した。指示された細胞株を、−1日目に6ウェルプレートにプレーティングした。0日目に、細胞をカウントするか(3ウェル)、または通常の培地または指示された化合物を補充した培地のいずれかで培養した。細胞プレーティングの72時間後に、組織培養上清(1mL、n=3、各条件)を回収した。組織培養条件は、栄養素の利用可能性および指数関数的な細胞増殖を確実にするために最適化された。代謝産物消費/産生データは、以前に記載されているように(Lee et al.、2014:PMID:24998913)、曲線下の細胞数面積に対して正規化した。曲線下面積(AUC)は、N(T)d/In2(1−2−T/d)として計算され、ここで、N(T)は最終細胞数、dは倍増時間、そしてTは実験時間である。倍増時間はd=(T)[log(2)/log(Q2/Q1)]として計算され、ここでQ1は血球計を用いた手動計数により決定されるように開始細胞数でありそしてQ2は最終細胞数である。
補足データ1.これは、ChIP−seq、WGBS、およびRNA−seq実験のすべての複製サンプルのシーケンス読み取り数(トータル読み取り数とユニークアラインメント読み取り数)を示し、複製サンプル間の相関係数を含む。
Claims (26)
- エピジェネティックリプログラミングのための標的の同定方法であって、
癌を有する対象由来のDNAを含有する試料中の大型組織化ヘテロクロマチンリジン(K)−9修飾ドメイン(LOCK)および大型DNA低メチル化ブロックを検出することを含む、方法。 - 前記試料は固形腫瘍由来である、請求項1に記載の方法。
- 前記対象は、PDACを有する、または、PDACおよび/もしくはその転移を有する危険性がある、請求項1に記載の方法。
- 前記検出は、H3K9Me2/3および/またはH4K20Me3の分析を含む、請求項1に記載の方法。
- 前記検出は、H3K27Acおよび/またはH3K9Acの分析を含む、請求項1に記載の方法。
- 前記検出は、ウエスタンブロッティングによる、請求項1に記載の方法。
- 前記検出は、H3K9Me2/3および/またはH4K20Me3に対する抗体についてのChIPによるものであり、任意にその後に配列決定が続く、請求項1に記載の方法。
- 前記検出は、H3K27Acおよび/またはH3K9Acに対する抗体についてのChIPによるものであり、任意にその後に配列決定が続く、請求項1に記載の方法。
- 前記検出は、全ゲノム亜硫酸水素塩配列決定によるものである、請求項1に記載の方法。
- 遺伝子発現分析をさらに含む、請求項2〜8のいずれか1つに記載の方法。
- 転移についてのドライバー変異が存在しない、請求項1〜10のいずれか1つに記載の方法。
- ユークロマチンアイランドおよび/またはユークロマチンLOCKの分析をさらに含む、請求項1〜11のいずれか1つに記載の方法。
- DNA試料中のユークロマチンドメイン(ECD)ECDの変化を同定する方法であって、
治療計画の前後でのECDの分析を含み、治療計画に対する応答性の予後または分析を提供する、方法。 - DNA試料中のLOCKの変化を同定する方法であって、
治療計画の前後でのLOCKの分析を含み、治療計画に対する応答性の予後または分析を提供する、方法。 - 前記分析がコンビナトリアル法によるものである、請求項13または14に記載の方法。
- 原発腫瘍における転移傾向を同定するための、差次的に発現される遺伝子の使用であって、
該遺伝子は、本明細書の表中の遺伝子、酸化ストレス遺伝子、EMT遺伝子、免疫学的応答遺伝子、DNA修復遺伝子、グルコース代謝遺伝子、oxPPP遺伝子、およびPGD遺伝子から選択される、使用。 - oxPPP阻害を含むエピゲノム変化を逆転させるかまたはそれに影響を及ぼすための方法。
- PGDRNAiを含むエピゲノム変化を逆転させるかまたはそれに影響を及ぼすための方法。
- 6ANを含むエピゲノム変化を逆転させるかまたはそれに影響を及ぼすための方法。
- エピゲノム変化に影響を与える作用物質または化合物を同定するための方法であって、
作用物質または化合物と接触させる前後に、請求項1に記載の対象由来の試料を分析し、oxPPPの阻害を含むエピゲノム変化に対する作用物質または化合物の効果を測定することを含む、方法。 - 前記方法が、腫瘍球アッセイ、マトリゲルアッセイ、器官型間質への細胞の注入からなる群から選択される方法を含む、請求項17〜19のいずれか1つに記載の方法。
- それを必要とする対象を治療するのに使用するための、請求項20に記載の方法によって同定された作用物質または化合物。
- 前記対象が癌を患っている、請求項20に記載の方法。
- 前記対象がPDACを有する、請求項20に記載の方法。
- 前記使用が転移治療および/または予防のためのものである、請求項20に記載の方法。
- 前記作用物質または化合物が、化学療法または放射線療法または他の治療計画による治療の前に、それと同時に、またはその後に、投与される、請求項20に記載の方法。
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201662405155P | 2016-10-06 | 2016-10-06 | |
US62/405,155 | 2016-10-06 | ||
PCT/US2017/055376 WO2018067840A1 (en) | 2016-10-06 | 2017-10-05 | Large-scale epigenomic reprogramming links anabolic glucose metabolism to distant metastasis during the evolution of pancreatic caner progression |
Publications (3)
Publication Number | Publication Date |
---|---|
JP2019535017A true JP2019535017A (ja) | 2019-12-05 |
JP2019535017A5 JP2019535017A5 (ja) | 2020-10-15 |
JP7239468B2 JP7239468B2 (ja) | 2023-03-14 |
Family
ID=61831296
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
JP2019518463A Active JP7239468B2 (ja) | 2016-10-06 | 2017-10-05 | ラージスケールエピゲノムのリプログラミングは、膵癌進行の進展中の同化グルコース代謝を遠位転移に結びつける |
Country Status (5)
Country | Link |
---|---|
US (2) | US11795510B2 (ja) |
EP (1) | EP3522924A4 (ja) |
JP (1) | JP7239468B2 (ja) |
AU (1) | AU2017340743A1 (ja) |
WO (1) | WO2018067840A1 (ja) |
Families Citing this family (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN115927608B (zh) * | 2022-01-28 | 2023-10-10 | 臻智达生物技术(上海)有限公司 | 用于预测胰腺癌发生风险的生物标志物、方法和诊断设备 |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JP2006506610A (ja) * | 2002-11-13 | 2006-02-23 | ジー6・サイエンス・コーポレイション | 疾患を検出するための、dnaユークロマチンを同定し評価する方法 |
JP2011504462A (ja) * | 2007-11-02 | 2011-02-10 | エージェンシー フォー サイエンス,テクノロジー アンド リサーチ | 腫瘍の予防および治療のための方法および化合物 |
JP2014519319A (ja) * | 2011-05-12 | 2014-08-14 | ザ・ジョンズ・ホプキンス・ユニバーシティー | エピジェネティックドメインの安定性の全般的な損失を通して癌を検出する方法およびその組成物 |
Family Cites Families (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2013152186A1 (en) * | 2012-04-04 | 2013-10-10 | Beth Israel Deaconess Medical Center, Inc. | Methods and compositions for 6-phosphogluconate dehydrogenase (6-pgd) as a target for lung cancer therepy |
WO2013192274A2 (en) * | 2012-06-19 | 2013-12-27 | The Broad Institute, Inc. | Diagnostic and treatment methods in subjects having or at risk of developing resistance to cancer therapy |
JP2015533130A (ja) * | 2012-10-12 | 2015-11-19 | ハイ−シュテム ゲマインヌートツィヒェ ゲゼルシャフト ミット ベシュレンクテル ハフツング | 膵管腺癌の個別化療法のための新規手法 |
WO2016144371A1 (en) * | 2015-03-06 | 2016-09-15 | Mitchell Woods Pharmaceuticals, Inc. | Methods of treating cancer |
WO2016172332A1 (en) * | 2015-04-22 | 2016-10-27 | The University Of North Carolina At Chapel Hill | A novel compound for the treatment of ewing sarcoma and high-throughput assays for identifying small molecules that modulate aberrant chromatin accessibility |
-
2017
- 2017-10-05 WO PCT/US2017/055376 patent/WO2018067840A1/en unknown
- 2017-10-05 JP JP2019518463A patent/JP7239468B2/ja active Active
- 2017-10-05 AU AU2017340743A patent/AU2017340743A1/en active Pending
- 2017-10-05 EP EP17859197.0A patent/EP3522924A4/en active Pending
- 2017-10-05 US US16/340,069 patent/US11795510B2/en active Active
-
2023
- 2023-08-01 US US18/229,064 patent/US20240011100A1/en active Pending
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JP2006506610A (ja) * | 2002-11-13 | 2006-02-23 | ジー6・サイエンス・コーポレイション | 疾患を検出するための、dnaユークロマチンを同定し評価する方法 |
JP2011504462A (ja) * | 2007-11-02 | 2011-02-10 | エージェンシー フォー サイエンス,テクノロジー アンド リサーチ | 腫瘍の予防および治療のための方法および化合物 |
JP2014519319A (ja) * | 2011-05-12 | 2014-08-14 | ザ・ジョンズ・ホプキンス・ユニバーシティー | エピジェネティックドメインの安定性の全般的な損失を通して癌を検出する方法およびその組成物 |
Non-Patent Citations (4)
Title |
---|
KARAGIANNIS G. S. ET AL.: "Signatures of breast cancer metastasis at a glance", JOURNAL OF CELL SCIENCE, vol. 129(9), JPN7021003343, 1 May 2016 (2016-05-01), pages 1751 - 1758, XP002798961, ISSN: 0004897893, DOI: 10.1242/jcs.183129 * |
KASPER DANIEL HANSEN, ET AL.: "Increased methylation variation in epigenetic domains across cancer types", NATURE GENETICS, vol. 43(8), JPN7021003342, 26 June 2011 (2011-06-26), pages 768 - 775, ISSN: 0004897892 * |
OLIVER G. MCDONALD ET AL.: "Genome-scale epigenetic reprogramming during epithelial to mesenchymal transition", NATURE STRUCTURAL & MOLECULAR BIOLOGY, vol. 18(8), JPN7021003344, 3 July 2011 (2011-07-03), pages 867 - 874, ISSN: 0004897894 * |
WINSTON TIMP, ET AL.: "Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors", GENOME MEDICINE, vol. 6(8), JPN7021003341, 26 August 2014 (2014-08-26), pages 61, ISSN: 0004897891 * |
Also Published As
Publication number | Publication date |
---|---|
EP3522924A4 (en) | 2020-07-08 |
US20190233903A1 (en) | 2019-08-01 |
US20240011100A1 (en) | 2024-01-11 |
WO2018067840A8 (en) | 2018-06-28 |
AU2017340743A1 (en) | 2019-04-18 |
WO2018067840A1 (en) | 2018-04-12 |
US11795510B2 (en) | 2023-10-24 |
EP3522924A1 (en) | 2019-08-14 |
JP7239468B2 (ja) | 2023-03-14 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
McDonald et al. | Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis | |
Alonso-Curbelo et al. | A gene–environment-induced epigenetic program initiates tumorigenesis | |
Zhao et al. | PRMT1 regulates the tumour-initiating properties of esophageal squamous cell carcinoma through histone H4 arginine methylation coupled with transcriptional activation | |
Buczacki et al. | Itraconazole targets cell cycle heterogeneity in colorectal cancer | |
Ito et al. | Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification | |
Martín-Martín et al. | Stratification and therapeutic potential of PML in metastatic breast cancer | |
Gong et al. | Epigenetic silencing of TET2 and TET3 induces an EMT-like process in melanoma | |
Kim et al. | Myc-induced microRNAs integrate Myc-mediated cell proliferation and cell fate | |
Zhu et al. | CD44s is a crucial ATG7 downstream regulator for stem-like property, invasion, and lung metastasis of human bladder cancer (BC) cells | |
Lorenzo-Martín et al. | VAV2 signaling promotes regenerative proliferation in both cutaneous and head and neck squamous cell carcinoma | |
Tiedemann et al. | Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome | |
Lin et al. | Podocalyxin-like 1 is associated with tumor aggressiveness and metastatic gene expression in human oral squamous cell carcinoma | |
Huang et al. | RNA m6A demethylase ALKBH5 protects against pancreatic ductal adenocarcinoma via targeting regulators of iron metabolism | |
de Wet et al. | SOX2 mediates metabolic reprogramming of prostate cancer cells | |
Wang et al. | Identification of new hypoxia‐regulated epithelial‐mesenchymal transition marker genes labeled by H3K4 acetylation | |
Patani et al. | Transition to naïve human pluripotency mirrors pan-cancer DNA hypermethylation | |
Miura et al. | Oncogenic potential of human pluripotent stem cell‐derived lung organoids with HER2 overexpression | |
Zhang et al. | TIP60 inhibits metastasis by ablating DNMT1− SNAIL2-driven epithelial-mesenchymal transition program | |
Lambert et al. | ΔNp63/p73 drive metastatic colonization by controlling a regenerative epithelial stem cell program in quasi-mesenchymal cancer stem cells | |
Zaidan et al. | HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells | |
Hoetker et al. | H3K36 methylation maintains cell identity by regulating opposing lineage programmes | |
Xu et al. | Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation | |
US20240011100A1 (en) | Large-scale epigenomic reprogramming links anabolic glucose metabolism to distant metastasis during the evolution of pancreatic cancer progression | |
Téllez‐Gabriel et al. | High RAB 25 expression is associated with good clinical outcome in patients with locally advanced head and neck squamous cell carcinoma | |
Looney et al. | Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
A521 | Request for written amendment filed |
Free format text: JAPANESE INTERMEDIATE CODE: A523 Effective date: 20200902 |
|
A621 | Written request for application examination |
Free format text: JAPANESE INTERMEDIATE CODE: A621 Effective date: 20200902 |
|
A977 | Report on retrieval |
Free format text: JAPANESE INTERMEDIATE CODE: A971007 Effective date: 20210728 |
|
A131 | Notification of reasons for refusal |
Free format text: JAPANESE INTERMEDIATE CODE: A131 Effective date: 20210824 |
|
A601 | Written request for extension of time |
Free format text: JAPANESE INTERMEDIATE CODE: A601 Effective date: 20211122 |
|
A521 | Request for written amendment filed |
Free format text: JAPANESE INTERMEDIATE CODE: A523 Effective date: 20220111 |
|
A131 | Notification of reasons for refusal |
Free format text: JAPANESE INTERMEDIATE CODE: A131 Effective date: 20220510 |
|
A521 | Request for written amendment filed |
Free format text: JAPANESE INTERMEDIATE CODE: A523 Effective date: 20220809 |
|
A131 | Notification of reasons for refusal |
Free format text: JAPANESE INTERMEDIATE CODE: A131 Effective date: 20221018 |
|
A521 | Request for written amendment filed |
Free format text: JAPANESE INTERMEDIATE CODE: A523 Effective date: 20230117 |
|
TRDD | Decision of grant or rejection written | ||
A01 | Written decision to grant a patent or to grant a registration (utility model) |
Free format text: JAPANESE INTERMEDIATE CODE: A01 Effective date: 20230207 |
|
A61 | First payment of annual fees (during grant procedure) |
Free format text: JAPANESE INTERMEDIATE CODE: A61 Effective date: 20230302 |
|
R150 | Certificate of patent or registration of utility model |
Ref document number: 7239468 Country of ref document: JP Free format text: JAPANESE INTERMEDIATE CODE: R150 |