|
1
|
Bray F, Ferlay J, Soerjomataram I, Siegel
RL, Torre LA and Jemal A: Global cancer statistics 2018: GLOBOCAN
estimates of incidence and mortality worldwide for 36 cancers in
185 countries. CA Cancer J Clin. 68:394–424. 2018.PubMed/NCBI View Article : Google Scholar
|
|
2
|
Luo Z, Lu L, Tang Q, Wei W, Chen P, Chen
Y, Pu J and Wang J: CircCAMSAP1 promotes hepatocellular carcinoma
progression through miR-1294/GRAMD1A pathway. J Cell Mol Med.
25:3793–3802. 2021.PubMed/NCBI View Article : Google Scholar
|
|
3
|
Forner A, Llovet JM and Bruix J:
Hepatocellular carcinoma. Lancet. 379:1245–1255. 2012.PubMed/NCBI View Article : Google Scholar
|
|
4
|
DiStefano JK and Davis B: Diagnostic and
prognostic Potential of AKR1B10 in human hepatocellular carcinoma.
Cancers (Basel). 11(486)2019.PubMed/NCBI View Article : Google Scholar
|
|
5
|
Lechner MS, Levitan I and Dressler GR:
PTIP, a novel BRCT domain-containing protein interacts with Pax2
and is associated with active chromatin. Nucleic Acids Res.
28:2741–2751. 2000.PubMed/NCBI View Article : Google Scholar
|
|
6
|
Shimizu K, Bourillot PY, Nielsen SJ, Zorn
AM and Gurdon JB: Swift is a novel BRCT domain coactivator of Smad2
in transforming growth factor beta signaling. Mol Cell Biol.
21:3901–3912. 2001.PubMed/NCBI View Article : Google Scholar
|
|
7
|
Cho YW, Hong T, Hong S, Guo H, Yu H, Kim
D, Guszczynski T, Dressler GR, Copeland TD, Kalkum M and Ge K: PTIP
associates with MLL3- and MLL4-containing histone H3 lysine 4
methyltransferase complex. J Biol Chem. 282:20395–20406.
2007.PubMed/NCBI View Article : Google Scholar
|
|
8
|
Munoz IM, Jowsey PA, Toth R and Rouse J:
Phospho-epitope binding by the BRCT domains of hPTIP controls
multiple aspects of the cellular response to DNA damage. Nucleic
Acids Res. 35:5312–5322. 2007.PubMed/NCBI View Article : Google Scholar
|
|
9
|
Patel SR, Kim D, Levitan I and Dressler
GR: The BRCT-domain containing protein PTIP links PAX2 to a histone
H3, lysine 4 methyltransferase complex. Dev Cell. 13:580–592.
2007.PubMed/NCBI View Article : Google Scholar
|
|
10
|
Escribano-Diaz C and Durocher D: DNA
repair pathway choice-a PTIP of the hat to 53BP1. EMBO Rep.
14:665–666. 2013.PubMed/NCBI View Article : Google Scholar
|
|
11
|
Issaeva I, Zonis Y, Rozovskaia T, Orlovsky
K, Croce CM, Nakamura T, Mazo A, Eisenbach L and Canaani E:
Knockdown of ALR (MLL2) reveals ALR target genes and leads to
alterations in cell adhesion and growth. Mol Cell Biol.
27:1889–1903. 2007.PubMed/NCBI View Article : Google Scholar
|
|
12
|
Mohan M, Herz HM, Smith ER, Zhang Y,
Jackson J, Washburn MP, Florens L, Eissenberg JC and Shilatifard A:
The COMPASS family of H3K4 methylases in Drosophila. Mol Cell Biol.
31:4310–4318. 2011.PubMed/NCBI View Article : Google Scholar
|
|
13
|
Cho EA, Prindle MJ and Dressler GR: BRCT
domain-containing protein PTIP is essential for progression through
mitosis. Mol Cell Biol. 23:1666–1673. 2003.PubMed/NCBI View Article : Google Scholar
|
|
14
|
Ray Chaudhuri A, Callen E, Ding X, Gogola
E, Duarte AA, Lee JE, Wong N, Lafarga V, Calvo JA, Panzarino NJ, et
al: Replication fork stability confers chemoresistance in
BRCA-deficient cells. Nature. 535:382–387. 2016.PubMed/NCBI View Article : Google Scholar
|
|
15
|
Willis S, Villalobos VM, Gevaert O,
Abramovitz M, Williams C, Sikic BI and Leyland-Jones B: Single gene
prognostic biomarkers in ovarian cancer: A meta-analysis. PLoS One.
11(e0149183)2016.PubMed/NCBI View Article : Google Scholar
|
|
16
|
De Gregoriis G, Ramos JA, Fernandes PV,
Vignal GM, Brianese RC, Carraro DM, Monteiro AN, Struchiner CJ,
Suarez-Kurtz G, Vianna-Jorge R and de Carvalho MA: DNA repair genes
PAXIP1 and TP53BP1 expression is associated with breast cancer
prognosis. Cancer Biol Ther. 18:439–449. 2017.PubMed/NCBI View Article : Google Scholar
|
|
17
|
Jhuraney A, Woods NT, Wright G, Rix L,
Kinose F, Kroeger JL, Remily-Wood E, Cress WD, Koomen JM, Brantley
SG, et al: PAXIP1 potentiates the combination of WEE1 inhibitor
AZD1775 and platinum agents in lung cancer. Mol Cancer Ther.
15:1669–1681. 2016.PubMed/NCBI View Article : Google Scholar
|
|
18
|
Han X, Zhu Y, Shen L, Zhou Y, Pang L, Zhou
W, Gu H, Han K, Yang Y, Jiang C, et al: PTIP inhibits cell invasion
in esophageal squamous cell carcinoma via modulation of EphA2
expression. Front Oncol. 11(629916)2021.PubMed/NCBI View Article : Google Scholar
|
|
19
|
Harland LTG, Simon CS, Senft AD, Costello
I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK,
Porcher C, et al: The T-box transcription factor Eomesodermin
governs haemogenic competence of yolk sac mesodermal progenitors.
Nat Cell Biol. 23:61–74. 2021.PubMed/NCBI View Article : Google Scholar
|
|
20
|
Livak KJ and Schmittgen TD: Analysis of
relative gene expression data using real-time quantitative PCR and
the 2(-Delta Delta C(T)) method. Methods. 25:402–408.
2001.PubMed/NCBI View Article : Google Scholar
|
|
21
|
Gertz J, Savic D, Varley KE, Partridge EC,
Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE and Myers RM:
Distinct properties of cell-type-specific and shared transcription
factor binding sites. Mol Cell. 52:25–36. 2013.PubMed/NCBI View Article : Google Scholar
|
|
22
|
Partridge EC, Chhetri SB, Prokop JW,
Ramaker RC, Jansen CS, Goh ST, Mackiewicz M, Newberry KM,
Brandsmeier LA, Meadows SK, et al: Occupancy maps of 208
chromatin-associated proteins in one human cell type. Nature.
583:720–728. 2020.PubMed/NCBI View Article : Google Scholar
|
|
23
|
Quinlan AR and Hall IM: BEDTools: A
flexible suite of utilities for comparing genomic features.
Bioinformatics. 26:841–842. 2010.PubMed/NCBI View Article : Google Scholar
|
|
24
|
Ramirez F, Ryan DP, Grüning B, Bhardwaj V,
Kilpert F, Richter AS, Heyne S, Dündar F and Manke T: deepTools2: A
next generation web server for deep-sequencing data analysis.
Nucleic Acids Res. 44 (W1):W160–W165. 2016.PubMed/NCBI View Article : Google Scholar
|
|
25
|
Yu G, Wang LG and He QY: ChIPseeker: An
R/Bioconductor package for ChIP peak annotation, comparison and
visualization. Bioinformatics. 31:2382–2383. 2015.PubMed/NCBI View Article : Google Scholar
|
|
26
|
Huang da W, Sherman BT and Lempicki RA:
Systematic and integrative analysis of large gene lists using DAVID
bioinformatics resources. Nat Protoc. 4:44–57. 2009.PubMed/NCBI View Article : Google Scholar
|
|
27
|
Zhou Y, Zhou B, Pache L, Chang M,
Khodabakhshi AH, Tanaseichuk O, Benner C and Chanda SK: Metascape
provides a biologist-oriented resource for the analysis of
systems-level datasets. Nat Commun. 10(1523)2019.PubMed/NCBI View Article : Google Scholar
|
|
28
|
Lian Q, Wang S, Zhang G, Wang D, Luo G,
Tang J, Chen L and Gu J: HCCDB: A database of hepatocellular
carcinoma expression atlas. Genomics Proteomics Bioinformatics.
16:269–275. 2018.PubMed/NCBI View Article : Google Scholar
|
|
29
|
Riillo C, Polerà N, Di Martino MT, Juli G,
Hokanson CA, Odineca T, Signorelli S, Grillone K, Ascrizzi S,
Mancuso A, et al: A pronectin™ AXL-targeted
first-in-class bispecific T cell engager (pAXLxCD3ε) for ovarian
cancer. J Transl Med. 21(301)2023.PubMed/NCBI View Article : Google Scholar
|
|
30
|
Thul PJ and Lindskog C: The human protein
atlas: A spatial map of the human proteome. Protein Sci.
27:233–244. 2018.PubMed/NCBI View Article : Google Scholar
|
|
31
|
Cerami E, Gao J, Dogrusoz U, Gross BE,
Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et
al: The cBio cancer genomics portal: An open platform for exploring
multidimensional cancer genomics data. Cancer Discov. 2:401–404.
2012.PubMed/NCBI View Article : Google Scholar
|
|
32
|
de Bruijn I, Kundra R, Mastrogiacomo B,
Tran TN, Sikina L, Mazor T, Li X, Ochoa A, Zhao G, Lai B, et al:
Analysis and visualization of longitudinal genomic and clinical
data from the AACR project GENIE biopharma collaborative in
cBioPortal. Cancer Res. 83:3861–3867. 2023.PubMed/NCBI View Article : Google Scholar
|
|
33
|
Xue R, Chen L, Zhang C, Fujita M, Li R,
Yan SM, Ong CK, Liao X, Gao Q, Sasagawa S, et al: Genomic and
transcriptomic profiling of combined hepatocellular and
intrahepatic cholangiocarcinoma reveals distinct molecular
subtypes. Cancer Cell. 35:932–947.e8. 2019.PubMed/NCBI View Article : Google Scholar
|
|
34
|
Chen L, Zhang C, Xue R, Liu M, Bai J, Bao
J, Wang Y, Jiang N, Li Z, Wang W, et al: Deep whole-genome analysis
of 494 hepatocellular carcinomas. Nature. 627:586–593.
2024.PubMed/NCBI View Article : Google Scholar
|
|
35
|
Ng CKY, Dazert E, Boldanova T,
Coto-Llerena M, Nuciforo S, Ercan C, Suslov A, Meier MA, Bock T,
Schmidt A, et al: Integrative proteogenomic characterization of
hepatocellular carcinoma across etiologies and stages. Nat Commun.
13(2436)2022.PubMed/NCBI View Article : Google Scholar
|
|
36
|
Harding JJ, Nandakumar S, Armenia J,
Khalil DN, Albano M, Ly M, Shia J, Hechtman JF, Kundra R, El Dika
I, et al: Prospective genotyping of hepatocellular carcinoma:
Clinical implications of next-generation sequencing for matching
patients to targeted and immune therapies. Clin Cancer Res.
25:2116–2126. 2019.PubMed/NCBI View Article : Google Scholar
|
|
37
|
Cowzer D, White JB, Chou JF, Chen PJ, Kim
TH, Khalil DN, El Dika IH, Columna K, Yaqubie A, Light JS, et al:
Targeted molecular profiling of circulating cell-free DNA in
patients with advanced hepatocellular carcinoma. JCO Precis Oncol.
7(e2300272)2023.PubMed/NCBI View Article : Google Scholar
|
|
38
|
Schulze K, Imbeaud S, Letouzé E,
Alexandrov LB, Calderaro J, Rebouissou S, Couchy G, Meiller C,
Shinde J, Soysouvanh F, et al: Exome sequencing of hepatocellular
carcinomas identifies new mutational signatures and potential
therapeutic targets. Nat Genet. 47:505–511. 2015.PubMed/NCBI View Article : Google Scholar
|
|
39
|
Zheng J, Sadot E, Vigidal JA, Klimstra DS,
Balachandran VP, Kingham TP, Allen PJ, D'Angelica MI, DeMatteo RP,
Jarnagin WR and Ventura A: Characterization of hepatocellular
adenoma and carcinoma using microRNA profiling and targeted gene
sequencing. PLoS One. 13(e0200776)2018.PubMed/NCBI View Article : Google Scholar
|
|
40
|
Ahn SM, Jang SJ, Shim JH, Kim D, Hong SM,
Sung CO, Baek D, Haq F, Ansari AA, Lee SY, et al: Genomic portrait
of resectable hepatocellular carcinomas: Implications of RB1 and
FGF19 aberrations for patient stratification. Hepatology.
60:1972–1982. 2014.PubMed/NCBI View Article : Google Scholar
|
|
41
|
Fujimoto A, Totoki Y, Abe T, Boroevich KA,
Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, et al:
Whole-genome sequencing of liver cancers identifies etiological
influences on mutation patterns and recurrent mutations in
chromatin regulators. Nat Genet. 44:760–764. 2012.PubMed/NCBI View Article : Google Scholar
|
|
42
|
Pilati C, Letouzé E, Nault JC, Imbeaud S,
Boulai A, Calderaro J, Poussin K, Franconi A, Couchy G, Morcrette
G, et al: Genomic profiling of hepatocellular adenomas reveals
recurrent FRK-activating mutations and the mechanisms of malignant
transformation. Cancer Cell. 25:428–441. 2014.PubMed/NCBI View Article : Google Scholar
|
|
43
|
Vasaikar SV, Straub P, Wang J and Zhang B:
LinkedOmics: Analyzing multi-omics data within and across 32 cancer
types. Nucleic Acids Res. 46 (D1):D956–D963. 2018.PubMed/NCBI View Article : Google Scholar
|
|
44
|
Chen Y, Li B, Wang J, Liu J, Wang Z, Mao
Y, Liu S, Liao X and Chen J: Identification and verification of the
prognostic value of the glutathione S-transferase Mu genes in
gastric cancer. Oncol Lett. 20(100)2020.PubMed/NCBI View Article : Google Scholar
|
|
45
|
Zhang Z, Lin E, Zhuang H, Xie L, Feng X,
Liu J and Yu Y: Construction of a novel gene-based model for
prognosis prediction of clear cell renal cell carcinoma. Cancer
Cell Int. 20(27)2020.PubMed/NCBI View Article : Google Scholar
|
|
46
|
Zhang Q, Liu W, Zhang HM, Xie GY, Miao YR,
Xia M and Guo AY: hTFtarget: A comprehensive database for
regulations of human transcription factors and their targets.
Genomics Proteomics Bioinformatics. 18:120–128. 2020.PubMed/NCBI View Article : Google Scholar
|
|
47
|
Thorvaldsdóttir H, Robinson JT and Mesirov
JP: Integrative genomics viewer (IGV): High-performance genomics
data visualization and exploration. Brief Bioinform. 14:178–192.
2013.PubMed/NCBI View Article : Google Scholar
|
|
48
|
Geeleher P, Cox N and Huang RS:
pRRophetic: An R package for prediction of clinical
chemotherapeutic response from tumor gene expression levels. PLoS
One. 9(e107468)2014.PubMed/NCBI View Article : Google Scholar
|
|
49
|
Li H, Han D, Hou Y, Chen H and Chen Z:
Statistical inference methods for two crossing survival curves: A
comparison of methods. PLoS One. 10(e0116774)2015.PubMed/NCBI View Article : Google Scholar
|
|
50
|
Huang da W, Sherman BT and Lempicki RA:
Bioinformatics enrichment tools: Paths toward the comprehensive
functional analysis of large gene lists. Nucleic Acids Res.
37:1–13. 2009.PubMed/NCBI View Article : Google Scholar
|
|
51
|
Anders S: Visualization of genomic data
with the Hilbert curve. Bioinformatics. 25:1231–1235.
2009.PubMed/NCBI View Article : Google Scholar
|
|
52
|
Goodall GJ and Wickramasinghe VO: RNA in
cancer. Nat Rev Cancer. 21:22–36. 2021.PubMed/NCBI View Article : Google Scholar
|
|
53
|
Shetron SG: Large-scale ecosystem
restoration: Five case studies from the United States. Choice:
Current Reviews for Academic Libraries. 46:715–716. 2008.
|
|
54
|
Wang Y, Guo X, Niu Z, Huang X, Wang B and
Gao L: DeepCBS: Shedding light on the impact of mutations occurring
at CTCF binding sites. Front Genet. 15(1354208)2024.PubMed/NCBI View Article : Google Scholar
|
|
55
|
Srinivasan P, Wu X, Basu M, Rossi C and
Sandler AD: PD-L1 checkpoint inhibition and anti-CTLA-4 whole tumor
cell vaccination counter adaptive immune resistance: A mouse
neuroblastoma model that mimics human disease. PLoS Med.
15(e1002497)2018.PubMed/NCBI View Article : Google Scholar
|
|
56
|
Yang JD, Hainaut P, Gores GJ, Amadou A,
Plymoth A and Roberts LR: A global view of hepatocellular
carcinoma: Trends, risk, prevention and management. Nat Rev
Gastroenterol Hepatol. 16:589–604. 2019.PubMed/NCBI View Article : Google Scholar
|
|
57
|
Zhang F, Wei M, Chen H, Ji L, Nie Y and
Kang J: The genomic stability regulator PTIP is required for proper
chromosome segregation in mitosis. Cell Div. 17(5)2022.PubMed/NCBI View Article : Google Scholar
|
|
58
|
Liu B and Li Z: PTIP-associated protein 1:
More than a component of the MLL3/4 complex. Front Genet.
13(889109)2022.PubMed/NCBI View Article : Google Scholar
|
|
59
|
Cheng Q, Xie H, Zhang XY, Wang MY, Bi CL,
Wang Q, Wang R and Fang M: An essential role for PTIP in mediating
Hox gene regulation along PcG and trxG pathways. FEBS J.
289:6324–6341. 2022.PubMed/NCBI View Article : Google Scholar
|
|
60
|
Xu Y, Zhu D, Yang Q, Su D and Chen YQ:
PTIP deficiency in B lymphocytes reduces subcutaneous fat
deposition in mice. Biochemistry (Mosc). 86:568–576.
2021.PubMed/NCBI View Article : Google Scholar
|
|
61
|
Callen E, Zong D, Wu W, Wong N, Stanlie A,
Ishikawa M, Pavani R, Dumitrache LC, Byrum AK, Mendez-Dorantes C,
et al: 53BP1 Enforces distinct pre- and post-resection blocks on
homologous recombination. Mol Cell. 77:26–38.e7. 2020.PubMed/NCBI View Article : Google Scholar
|
|
62
|
Das P, Veazey KJ, Van HT, Kaushik S, Lin
K, Lu Y, Ishii M, Kikuta J, Ge K, Nussenzweig A and Santos MA:
Histone methylation regulator PTIP is required to maintain normal
and leukemic bone marrow niches. Proc Natl Acad Sci USA.
115:E10137–E10146. 2018.PubMed/NCBI View Article : Google Scholar
|
|
63
|
Cenik BK and Shilatifard A: COMPASS and
SWI/SNF complexes in development and disease. Nat Rev Genet.
22:38–58. 2021.PubMed/NCBI View Article : Google Scholar
|
|
64
|
Wu J, Prindle MJ, Dressler GR and Yu X:
PTIP regulates 53BP1 and SMC1 at the DNA damage sites. J Biol Chem.
284:18078–18084. 2009.PubMed/NCBI View Article : Google Scholar
|
|
65
|
Chang J, Wu H, Wu J, Liu M, Zhang W, Hu Y,
Zhang X, Xu J, Li L, Yu P and Zhu J: Constructing a novel
mitochondrial-related gene signature for evaluating the tumor
immune microenvironment and predicting survival in stomach
adenocarcinoma. J Transl Med. 21(191)2023.PubMed/NCBI View Article : Google Scholar
|
|
66
|
Li P, Yu Z, He L, Zhou D, Xie S, Hou H and
Geng X: Knockdown of FOXK1 inhibited the proliferation, migration
and invasion in hepatocellular carcinoma cells. Biomed
Pharmacother. 92:270–276. 2017.PubMed/NCBI View Article : Google Scholar
|
|
67
|
Yang L, Peng F, Qin J, Zhou H and Wang B:
Downregulation of microRNA-196a inhibits human liver cancer cell
proliferation and invasion by targeting FOXO1. Oncol Rep.
38:2148–2154. 2017.PubMed/NCBI View Article : Google Scholar
|
|
68
|
Noh JH, Chang YG, Kim MG, Jung KH, Kim JK,
Bae HJ, Eun JW, Shen Q, Kim SJ, Kwon SH, et al: MiR-145 functions
as a tumor suppressor by directly targeting histone deacetylase 2
in liver cancer. Cancer Lett. 335:455–462. 2013.PubMed/NCBI View Article : Google Scholar
|
|
69
|
Wei T, Weiler SME, Tóth M, Sticht C, Lutz
T, Thomann S, De La Torre C, Straub B, Merker S, Ruppert T, et al:
YAP-dependent induction of UHMK1 supports nuclear enrichment of the
oncogene MYBL2 and proliferation in liver cancer cells. Oncogene.
38:5541–5550. 2019.PubMed/NCBI View Article : Google Scholar
|
|
70
|
Wang L, Zhao Z, Meyer MB, Saha S, Yu M,
Guo A, Wisinski KB, Huang W, Cai W, Pike JW, et al: CARM1
methylates chromatin remodeling factor BAF155 to enhance tumor
progression and metastasis. Cancer Cell. 25:21–36. 2014.PubMed/NCBI View Article : Google Scholar
|
|
71
|
Todisco S, Convertini P, Iacobazzi V and
Infantino V: TCA cycle rewiring as emerging metabolic signature of
hepatocellular carcinoma. Cancers (Basel). 12(68)2019.PubMed/NCBI View Article : Google Scholar
|
|
72
|
Li F, Wang S, Cui X, Jing J, Yu L, Xue B
and Shi H: Adipocyte utx deficiency promotes high-fat diet-induced
metabolic dysfunction in mice. Cells. 11(181)2022.PubMed/NCBI View Article : Google Scholar
|
|
73
|
Daniel JA, Santos MA, Wang Z, Zang C,
Schwab KR, Jankovic M, Filsuf D, Chen HT, Gazumyan A, Yamane A, et
al: PTIP promotes chromatin changes critical for immunoglobulin
class switch recombination. Science. 329:917–923. 2010.PubMed/NCBI View Article : Google Scholar
|
|
74
|
Callen E, Faryabi RB, Luckey M, Hao B,
Daniel JA, Yang W, Sun HW, Dressler G, Peng W, Chi H, et al: The
DNA damage- and transcription-associated protein paxip1 controls
thymocyte development and emigration. Immunity. 37:971–985.
2012.PubMed/NCBI View Article : Google Scholar
|
|
75
|
Miao Y, Li Z, Feng J, Lei X, Shan J, Qian
C and Li J: The role of CD4+T cells in nonalcoholic
steatohepatitis and hepatocellular carcinoma. Int J Mol Sci.
25(6895)2024.PubMed/NCBI View Article : Google Scholar
|
|
76
|
Zheng X, Jin W, Wang S and Ding H:
Progression on the roles and mechanisms of tumor-infiltrating T
lymphocytes in patients with hepatocellular carcinoma. Front
Immunol. 12(729705)2021.PubMed/NCBI View Article : Google Scholar
|
