158
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Liver Regeneration-Related Genes of Nontumor Liver Tissues Predict the Prognosis of Patients with Hepatocellular Carcinoma

, , , , , , & show all
Pages 2197-2209 | Received 08 Sep 2023, Accepted 22 Nov 2023, Published online: 06 Dec 2023

References

  • Sung H, Ferlay J, Siegel RL, et al. Global cancer statistics 2020: globocan estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–249. doi:10.3322/caac.21660
  • Kulik L, El-Serag HB. Epidemiology and management of hepatocellular carcinoma. Gastroenterology. 2019;156(2):477–491 e1. doi:10.1053/j.gastro.2018.08.065
  • Doycheva I, Thuluvath PJ. Systemic therapy for advanced hepatocellular carcinoma: an update of a rapidly evolving field. J Clin Exp Hepatol. 2019;9(5):588–596. doi:10.1016/j.jceh.2019.07.012
  • Goh EL, Chidambaram S, Ma S. Laparoscopic vs open hepatectomy for hepatocellular carcinoma in patients with cirrhosis: a meta-analysis of the long-term survival outcomes. Int J Surg. 2018;50:35–42. doi:10.1016/j.ijsu.2017.12.021
  • Xu LX, He MH, Dai ZH, et al. Genomic and transcriptional heterogeneity of multifocal hepatocellular carcinoma. Ann Oncol. 2019;30(6):990–997. doi:10.1093/annonc/mdz103
  • Fausto N, Campbell JS, Riehle KJ. Liver regeneration. Hepatology. 2006;43(2 Suppl 1):S45–53. doi:10.1002/hep.20969
  • Michalopoulos GK, Bhushan B. Liver regeneration: biological and pathological mechanisms and implications. Nat Rev Gastroenterol Hepatol. 2021;18(1):40–55. doi:10.1038/s41575-020-0342-4
  • Kwon YJ, Lee KG, Choi D. Clinical implications of advances in liver regeneration. Clin Mol Hepatol. 2015;21(1):7–13. doi:10.3350/cmh.2015.21.1.7
  • Yagi S, Hirata M, Miyachi Y, Uemoto S. Liver regeneration after hepatectomy and partial liver transplantation. Int J Mol Sci. 2020;21(21):8414. doi:10.3390/ijms21218414
  • Chen D, Aierken A, Li H, Chen R, Ren L, Wang K. Identification of subclusters and prognostic genes based on glycolysis/gluconeogenesis in hepatocellular carcinoma. Front Immunol. 2023;14. doi:10.3389/fimmu.2023.1232390
  • Peng X, Shi Y, Zhang B, Xu C, Lang J. Establishment of nucleic acid sensing pathways-based model in predicting response to immunotherapy and targeted drug in hepatitis virus-related hepatocellular carcinoma. J Med Virol. 2023;95(9): e29084.
  • Afra F, Mahboobipour AA, Salehi Farid A, Ala M. Recent progress in the immunotherapy of hepatocellular carcinoma: non-coding RNA-based immunotherapy may improve the outcome. Biomed Pharmacother. 2023;165:115104. doi:10.1016/j.biopha.2023.115104
  • Li B, Xu T, Liu C, et al. Liver-enriched genes are associated with the prognosis of patients with hepatocellular carcinoma. Sci Rep. 2018;8(1):11197. doi:10.1038/s41598-018-29237-5
  • Gong J, Li R, Chen Y, et al. HCC subtypes based on the activity changes of immunologic and hallmark gene sets in tumor and nontumor tissues. Briefings Bioinf. 2021;22(5). doi:10.1093/bib/bbaa427
  • Lin P, Wen DY, Pang JS, et al. Proteomics profiling of nontumor liver tissues identifies prognostic biomarkers in hepatitis B-related hepatocellular carcinoma. J Med Virol. 2023;95(1):e27732. doi:10.1002/jmv.27732
  • Aran D, Camarda R, Odegaard J, et al. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017;8(1):1077. doi:10.1038/s41467-017-01027-z
  • Jakubek YA, Chang K, Sivakumar S, et al. Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer. Nat Biotechnol. 2020;38(1):90–96. doi:10.1038/s41587-019-0297-6
  • Hoshida Y, Villanueva A, Kobayashi M, et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med. 2008;359(19):1995–2004. doi:10.1056/NEJMoa0804525
  • McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40(10):4288–4297. doi:10.1093/nar/gks042
  • Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33(1):1–22. doi:10.18637/jss.v033.i01
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
  • Mitchell C, Willenbring H. A reproducible and well-tolerated method for 2/3 partial hepatectomy in mice. Nat Protoc. 2008;3(7):1167–1170. doi:10.1038/nprot.2008.80
  • Chen Y, Chen L, Wu X, et al. Acute liver steatosis translationally controls the epigenetic regulator MIER1 to promote liver regeneration in a study with male mice. Nat Commun. 2023;14(1):1521. doi:10.1038/s41467-023-37247-9
  • Caldez MJ, Bjorklund M, Kaldis P. Cell cycle regulation in NAFLD: when imbalanced metabolism limits cell division. Hepatol Int. 2020;14(4):463–474. doi:10.1007/s12072-020-10066-6
  • Li G, Guo GL. Farnesoid X receptor, the bile acid sensing nuclear receptor, in liver regeneration. Acta Pharm Sin B. 2015;5(2):93–98. doi:10.1016/j.apsb.2015.01.005
  • Jia Y, Viswakarma N, Reddy JK. Med1 subunit of the mediator complex in nuclear receptor-regulated energy metabolism, liver regeneration, and hepatocarcinogenesis. Gene Expr. 2014;16(2):63–75. doi:10.3727/105221614X13919976902219
  • Braeuning A. Regulation of cytochrome P450 expression by Ras- and beta-catenin-dependent signaling. Curr Drug Metab. 2009;10(2):138–158. doi:10.2174/138920009787522160
  • Yang H, Guo J, Jin W, Chang C, Guo X, Xu C. A combined proteomic and metabolomic analyses of the priming phase during rat liver regeneration. Arch Biochem Biophys. 2020;693:108567. doi:10.1016/j.abb.2020.108567
  • Abu Rmilah A, Zhou W, Nelson E, Lin L, Amiot B, Nyberg SL. Understanding the marvels behind liver regeneration. Wiley Interdiscip Rev Dev Biol. 2019;8(3):e340. doi:10.1002/wdev.340
  • Li H, Li J, Qu X, et al. Establishment and validation of a novel lysosome-related gene signature for predicting prognosis and immune landscape in hepatocellular carcinoma. J Cancer Res Clin Oncol. 2023;149(19):17543–17557. doi:10.1007/s00432-023-05477-5
  • Wu R, Gao Y, Zhao X, et al. Tumor biology, immune infiltration and liver function define seven hepatocellular carcinoma subtypes linked to distinct drivers, survival and drug response. Comput Biol Med. 2023:167. doi:10.1016/j.compbiomed.2023.107593
  • Zhu H, Lin Y, Lu D, et al. Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma. Natl Sci Rev. 2023. doi:10.1093/nsr/nwad167
  • Budhu A, Forgues M, Ye QH, et al. Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Cancer Cell. 2006;10(2):99–111. doi:10.1016/j.ccr.2006.06.016
  • Wu J, Liu H, Wang H, et al. iTRAQ-based quantitative proteomic analysis of the liver regeneration termination phase after partial hepatectomy in mice. J Proteomics. 2022;267:104688. doi:10.1016/j.jprot.2022.104688
  • Xu WY, Shen Y, Zhu H, et al. 2-Aminoadipic acid protects against obesity and diabetes. J Endocrinol. 2019;243(2):111–123. doi:10.1530/joe-19-0157
  • Bezerra GA, Foster WR, Bailey HJ, et al. Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. IUCrJ. 2020;7(Pt 4):693–706. doi:10.1107/S205225252000696X
  • Morvay PL, Baes M, Van Veldhoven PP. Differential activities of peroxisomes along the mouse intestinal epithelium. Cell Biochem Funct. 2017;35(3):144–155. doi:10.1002/cbf.3255
  • Mizuno Y, Ninomiya Y, Nakachi Y, et al. Tysnd1 deficiency in mice interferes with the peroxisomal localization of PTS2 enzymes, causing lipid metabolic abnormalities and male infertility. PLoS Genet. 2013;9(2):e1003286. doi:10.1371/journal.pgen.1003286
  • Ferdinandusse S, Zomer AW, Komen JC, et al. Ataxia with loss of Purkinje cells in a mouse model for refsum disease. Proc Natl Acad Sci U S A. 2008;105(46):17712–17717. doi:10.1073/pnas.0806066105
  • Qian L, Zhou C, Wang K, Li L, Xia W, Fan Y. An investigation of the prognostic role of genes related to lipid metabolism in head and neck squamous cell carcinoma. Int J Genomics. 2023;2023:9708282. doi:10.1155/2023/9708282
  • Zhengqi Q, Zezhi G, Lei J, He Q, Jinyao P, Ying A. Prognostic role of PHYH for overall survival (OS) in clear cell renal cell carcinoma (ccRCC). Eur J Med Res. 2021;26(1):9. doi:10.1186/s40001-021-00482-1
  • Xiong Y, Si Y, Feng Y, Zhuo S, Cui B, Zhang Z. Prognostic value of lipid metabolism-related genes in head and neck squamous cell carcinoma. Immun Inflamm Dis. 2021;9(1):196–209. doi:10.1002/iid3.379
  • Xu R, Jiang W, Liu Y, et al. Single cell sequencing coupled with bioinformatics reveals PHYH as a potential biomarker in kidney ischemia reperfusion injury. Biochem Biophys Res Commun. 2022;602:156–162. doi:10.1016/j.bbrc.2022.02.095