The transcriptional dysregulation of choline catabolism genes was implicated in HCC stage-specific carcinogenesis

Abstract

Cancer cells often remodel their catabolic processes to support proliferation, growth, survival, and progression. This study investigated the transcriptional dysregulation of choline catabolism genes in pan-cancer, using TCGA and mRNA expression profiles from liver cancer cohorts. The studies revealed that choline catabolic genes, including choline kinase A, choline kinase B, choline dehydrogenase, and choline phosphotransferase, were prominently activated in stage-specific hepatocellular carcinoma (HCC) liver tumors with significant p-values (p < 0.0001). Additionally, these genes were further analyzed for their ontological functionality, showing that they play a crucial role in the biosynthesis of phosphatidylcholine, essential for membrane synthesis during cell proliferation and survival. Furthermore, ROC curve analysis demonstrated greater specificity and sensitivity for these genes in stage-specific HCC tumors with significant area under the curve values. Overall survival studies also confirmed that these genes were associated with poor survival in HCC patients with significant p-values (p < 0.05). Gene effect score analysis revealed higher negative scores for choline catabolic genes in liver tumor cell lines. Moreover, integrative genomic drug sensitivity studies identified a negative correlation with this catabolism, highlighting potential therapeutic targets such as Bryostatin1, Amuvatinib, FH535, Linsitinib, and DMOG. These findings could pave the way for the use of targeted therapies that focus on choline catabolic dysregulation in HCC treatment.

References

[1] Arlauckas SP, Popov AV, Delikatny EJ. Choline kinase alpha-putting the ChoK-hold on tumor metabolism. Progress in Lipid Research, 2016, 63: 28-40. 5360181

[2] Balakrishnan K. Hepatocellular carcinoma stage: An almost loss of fatty acid metabolism and gain of glucose metabolic pathways dysregulation. Medical Oncology (Northwood, London, England), 2022, 39(12): 247.

[3] Balakrishnan K. Salt-driven chromatin remodeling associated with senescence dysregulation plays a crucial role in the carcinogenesis of gastric cancer subtype. Computational Toxicology, 2023, 25. 100262

[4] Balakrishnan K. The hepatocellular carcinoma (HCC) stage carcinogenesis is associated with genomic instability features. Human Gene, 2023, 38. 201228

[5] Balakrishnan K. Lactate dehydrogenase isoform expressions differing impacts on gastrointestinal carcinogenesis. Human Gene, 2024, 39. 201243

[6] Balakrishnan K. Diffuse subtype-specific gastric carcinogenesis associated with dysregulation of Notch signaling pathways. Genome Instability & Disease, 2024.

[7] Balakrishnan K. Mitochondrial dysregulation is a key regulator of gastric cancer subtype carcinogenesis. Genome Instability & Disease, 2024, 5: 210-224.

[8] Balakrishnan K, Chen Y, Dong J. Amplification of hippo signaling pathway genes is governed and implicated in the serous subtype-specific ovarian carcino-genesis. Cancers, 2024, 16(9): 1781. 11082992

[9] Balakrishnan K, Chen Y, Dong J. Amplified cell cycle genes identified in high-grade serous ovarian cancer. Cancers, 2024, 16(16): 2783. 11352846

[10] Balakrishnan K, Ganesan K. Occurrence of differing metabolic dysregulations, a glucose driven and another fatty acid centric in gastric cancer subtypes. Functional & Integrative Genomics, 2020, 20(6): 813-824.

[11] Balakrishnan K, Ganesan K. Identification of oncogenic signaling pathways associated with the dimorphic metabolic dysregulations in gastric cancer subtypes. Medical Oncology (Northwood, London, England), 2022, 39(9): 132.

[12] Balakrishnan K, Panneerpandian P, Devanandan HJ, Sekar BT, Rayala SK, Ganesan K. Salt-mediated transcriptional and proteasomal dysregulations mimic the molecular dysregulations of stomach cancer. Toxicology in Vitro: An International Journal Published in Association with BIBRA, 2019, 61. 104588

[13] Balakrishnan K, Xiao Y, Chen Y, Dong J. Elevated expression of cell adhesion, metabolic, and mucus secretion gene clusters associated with tumorigenesis, metastasis, and poor survival in pancreatic ductal adenocarcinoma. Cancers, 2024, 16(23): 4049. 11640259

[14] Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: Archive for functional genomics data sets—Update. Nucleic Acids Research, 2013, 41(Database issue): D991-D995.

[15] Bland JM, Altman DG. The logrank test. BMJ (Clinical Research Edition), 2004, 328(7447): 1073.

[16] Chandrashekar DS, Karthikeyan SK, Korla PK, Patel H, Shovon AR, Athar M, Netto GJ, Qin ZS, Kumar S, Manne U, Creighton CJ, Varambally S. UALCAN: An update to the integrated cancer data analysis platform. Neoplasia (New York, N.y.), 2022, 25: 18-27.

[17] DeLong ER, DeLong DM, Clarke-Pearson DL. Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach. Biometrics, 1988, 44(3): 837-845.

[18] Dobransky T, Doherty-Kirby A, Kim AR, Brewer D, Lajoie G, Rylett RJ. Protein kinase C isoforms differentially phosphorylate human choline acetyltransferase regulating its catalytic activity. Journal of Biological Chemistry, 2004, 279(50): 52059-52068.

[19] Ducker GS, Rabinowitz JD. One-carbon metabolism in health and disease. Cell Metabolism, 2017, 25(1): 27-42.

[20] Gallego-Ortega D, Gómez del Pulgar T, Valdés-Mora F, Cebrián A, Lacal JC. Involvement of human choline kinase alpha and beta in carcinogenesis: A different role in lipid metabolism and biological functions. Advances in Enzyme Regulation, 2011, 51(1): 183-194.

[21] Glunde K, Penet M-F, Jiang L, Jacobs MA, Bhujwalla ZM. Choline metabolism-based molecular diagnosis of cancer: An update. Expert Review of Molecular Diagnostics, 2015, 15(6): 735-747. 4871254

[22] Glunde K, Raman V, Mori N, Bhujwalla ZM. RNA interference-mediated choline kinase suppression in breast cancer cells induces differentiation and reduces proliferation. Cancer Research, 2005, 65(23): 11034-11043.

[23] Glunde K, Serkova NJ. Therapeutic targets and biomarkers identified in cancer choline phospholipid metabolism. Pharmacogenomics, 2006, 7(7): 1109-1123.

[24] Gnocchi D, Afonso MB, Cavalluzzi MM, Lentini G, Ingravallo G, Sabbà C, et al.. Inhibition of lysophosphatidic acid receptor 6 upregulated by the choline-deficient l-amino acid-defined diet prevents hepatocarcinogenesis in mice. Molecular Carcinogenesis, 2023, 62(5): 577-582.

[25] Gougelet A, Sartor C, Senni N, Calderaro J, Fartoux L, Lequoy M, et al.. Hepatocellular carcinomas with mutational activation of beta-catenin require choline and can be detected by positron emission tomography. Gastroenterology, 2019, 157(3): 807-822.

[26] Hanahan D, Monje M. Cancer hallmarks intersect with neuroscience in the tumor microenvironment. Cancer Cell, 2023, 41(3): 573-580. 10202656

[27] Hanahan D, Weinberg RA. Hallmarks of cancer: The next generation. Cell, 2011, 144(5): 646-674.

[28] Inazu M. Choline transporter-like proteins CTLs/SLC44 family as a novel molecular target for cancer therapy. Biopharmaceutics & Drug Disposition, 2014, 35(8): 431-449.

[29] Ishikawa T, Suwanai H, Shikuma J, Suzuki R, Yamanaka T, Odawara M, Inazu M. Protein kinase C promotes choline transporter-like protein 1 function via improved cell surface expression in immortalized human hepatic cells. Molecular Medicine Reports, 2020, 21(2): 777-785

[30] Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research, 2023, 51(D1): D587-D592.

[31] Kansakar U, Trimarco V, Mone P, Varzideh F, Lombardi A, Santulli G. Choline supplements: An update. Frontiers in Endocrinology, 2023, 14: 1148166. 10025538

[32] Li C, Wong WH. Parmigiani G, Garrett ES, Irizarry RA, Zeger SL. DNA-chip analyzer (dChip). The analysis of gene expression data: Methods and software, 2003 Springer 120-141.

[33] Li T, Fu J, Zeng Z, Cohen D, Li J, Chen Q, Li B, Liu XS. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Research, 2020, 48(W1): W509-W514. 7319575

[34] Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics, 2011, 27(12): 1739-1740. 3106198

[35] Menyhart O, Nagy A, Gyorffy B. Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma. Royal Society Open Science, 2018, 5(12): 181006. 6304123

[36] Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, Dharia NV, Montgomery PG, Cowley GS, Pantel S, Goodale A, Lee Y, Ali LD, Jiang G, Lubonja R, Harrington WF, Strickland M, Wu T, Hawes DC, et al.. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics, 2017, 49(12): 1779-1784. 5709193

[37] Obeid R. The metabolic burden of methyl donor deficiency with focus on the betaine homocysteine methyltransferase pathway. Nutrients, 2013, 5(9): 3481-3495. 3798916

[38] Obeid R, Derbyshire E, Schön C. Association between maternal choline, fetal brain development, and child neurocognition: Systematic review and meta-analysis of human studies. Advances in Nutrition (Bethesda, Md.), 2022, 13(6): 2445-2457.

[39] Pessi G, Choi J-Y, Reynolds JM, Voelker DR, Mamoun CB. In vivo evidence for the specificity of Plasmodium falciparum phosphoethanolamine methyltransferase and its coupling to the Kennedy pathway. The Journal of Biological Chemistry, 2005, 280(13): 12461-12466.

[40] Ramírez de Molina A, Sarmentero-Estrada J, Belda-Iniesta C, Tarón M, Ramírez de Molina V, Cejas P, Skrzypski M, Gallego-Ortega D, de Castro J, Casado E, García-Cabezas MA, Sánchez JJ, Nistal M, Rosell R, González-Barón M, Lacal JC. Expression of choline kinase alpha to predict outcome in patients with early-stage non-small-cell lung cancer: A retrospective study. The Lancet. Oncology, 2007, 8(10): 889-897.

[41] Sanchez-Lopez E, Zhong Z, Stubelius A, Sweeney SR, Booshehri LM, Antonucci L, Liu-Bryan R, Lodi A, Terkeltaub R, Lacal JC, Murphy AN, Hoffman HM, Tiziani S, Guma M, Karin M. Choline uptake and metabolism modulate macrophage IL-1β and IL-18 production. Cell Metabolism, 2019, 29(6): 1350-1362.e7. 6675591

[42] Siegel, R. L., Giaquinto, A. N., & Jemal, A. (2024). Cancer statistics, 2024. CA: a cancer journal for clinicians, 74(1).

[43] Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer statistics, 2022. CA: A Cancer Journal for Clinicians, 2022, 72(1): 7-33.

[44] Snider SA, Margison KD, Ghorbani P, LeBlond ND, O’Dwyer C, Nunes JRC, Nguyen T, Xu H, Bennett SAL, Fullerton MD. Choline transport links macrophage phospholipid metabolism and inflammation. The Journal of Biological Chemistry, 2018, 293(29): 11600-11611. 6065184

[45] Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 2015, 43(Database issue): D447-D452. Epub 2014 Oct 28

[46] Tarca AL, Romero R, Draghici S. Analysis of microarray experiments of gene expression profiling. American Journal of Obstetrics and Gynecology, 2006, 195(2): 373-388. 2435252

[47] Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, et al.. Tissue-based map of the human proteome. Science, 2015, 347(6220): 1260419.

[48] Wang X, Zheng Z, Caviglia JM, Corey KE, Herfel TM, Cai B, Masia R, Chung RT, Lefkowitch JH, Schwabe RF, Tabas I. Hepatocyte TAZ/WWTR1 promotes inflammation and fibrosis in nonalcoholic steatohepatitis. Cell Metabolism, 2016, 24(6): 848-862. 5226184

[49] Wu G, Sher RB, Cox GA, Vance DE. Understanding the muscular dystrophy caused by deletion of choline kinase beta in mice. Biochimica Et Biophysica Acta, 2009, 1791(5): 347-356.

[50] Xie Z, Bailey A, Kuleshov MV, Clarke DJ, Evangelista JE, Jenkins SL, et al.. Gene set knowledge discovery with Enrichr. Current Protocols, 2021, 1(3): e90. 8152575

[51] Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, Bindal N, Beare D, Smith JA, Thompson IR, Ramaswamy S, Futreal PA, Haber DA, Stratton MR, Benes C, McDermott U, Garnett MJ. Genomics of Drug Sensitivity in Cancer (GDSC): A resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Research, 2013, 41(Database issue): D955-961.

[52] Yao N, Li W, Xu G, Duan N, Yu G, Qu J. Choline metabolism and its implications in cancer. Frontiers in Oncology, 2023, 13: 1234887. 10646347

[53] Yao Z, Dai C, Yang J, Xu M, Meng H, Hu X, Lin N. Time-trends in liver cancer incidence and mortality rates in the U.S. from 1975 to 2017: A study based on the Surveillance, Epidemiology, and End Results database. Journal of Gastrointestinal Oncology, 2023, 14(1): 312-324. 10007921

[54] Zeisel SH. Gene response elements, genetic polymorphisms and epigenetics influence the human dietary requirement for choline. IUBMB Life, 2007, 59(6): 380-387. 2430110

RIGHTS & PERMISSIONS

Shenzhen University School of Medicine; Fondazione Istituto FIRC di Oncologia Molecolare