Skip to main content

Advertisement

SpringerLink
Log in

Integrated analysis reveals an aspartate metabolism-related gene signature for predicting the overall survival in patients with hepatocellular carcinoma

  • RESEARCH ARTICLE
  • Published:
Clinical and Translational Oncology Aims and scope Submit manuscript

Abstract

Background

Deregulating cellular metabolism is one of the prominent hallmarks of malignancy, with a critical role in tumor survival and growth. However, the role of reprogramming aspartate metabolism in hepatocellular carcinoma (HCC) are largely unknown.

Methods

The multi-omics data of HCC patients were downloaded from public databases. Univariate and multivariate stepwise Cox regression were used to establish an aspartate metabolism-related gene signature (AMGS) in HCC. The Kaplan–Meier and receiver operating characteristic curve analyses were performed to evaluate the predictive ability for overall survival (OS) in HCC patients. Gene set enrichment analysis and immune infiltration analysis were operated to determine the potential mechanisms underlying the AMGS. Single-cell RNA sequencing (scRNA-seq) data of liver cancer stem cells were visualized by t-SNE algorithm. In vivo and in vitro experiments were implemented to investigate the biological function of CAD in HCC. In addition, a nomogram based on the AMGS and clinicopathologic characteristics was constructed by univariate and multivariate Cox regression analyses.

Results

Patients in the high-AMGS subgroup exerted advanced tumor status and poor prognosis. Mechanistically, the high-AMGS subgroup patients had significantly enhanced proliferation and stemness-related pathways, increased infiltration of regulatory T cells and upregulated expression levels of suppressive immune checkpoints in the tumor immune microenvironment. Notably, scRNA-seq data revealed CAD, one of the aspartate metabolism-related gene, is significantly upregulated in liver cancer stem cells. Silencing CAD inhibited proliferative capacity and stemness properties of HCC cells in vitro and in vivo. Finally, a novel nomogram based on the AMGS showed an accurate prediction in HCC patients.

Conclusions

The AMGS represents a promising prognostic value for HCC patients, providing a perspective for finding novel biomarkers and therapeutic targets for HCC.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

Data availability

The datasets used in this study can be downloaded in the TCGA (https://gdc.cancer.gov/), ICGC (https://dcc.icgc.org/projects/), GEO (https://www.ncbi.nlm.nih.gov/gds/), CPTAC (https://proteomic.datacommons.cancer.gov/pdc/) and KEGG database (https://www.kegg.jp/).

Abbreviations

HCC:

Hepatocellular carcinoma

AMGS:

Aspartate metabolism-related gene signature

TCGA:

The cancer genome atlas

ICGC:

International cancer genome consortium

GEO:

Gene expression omnibus

scRNA-seq:

Single-cell sequencing

CSCs:

Cancer stem cells

TIME:

Tumor immune microenvironment

References

  1. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: globocan estimates of incidence and mortality worldwide for 36 cancers in 185 countries. Ca: A Cancer J Clinicians. 2021;71(3):209–49. https://doi.org/10.3322/caac.21660

  2. Yang C, Zhang H, Zhang L, Zhu AX, Bernards R, Qin W, et al. Evolving therapeutic landscape of advanced hepatocellular carcinoma. Nat Rev Gastroenterol Hepatol. 2022. https://doi.org/10.1038/s41575-022-00704-9.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E, Roayaie S, et al. Hepatocellular carcinoma. Nature reviews. Dis Primers. 2021;7(1):6. https://doi.org/10.1038/s41572-020-00240-3

  4. Hanahan D. Hallmarks of cancer: new dimensions. Cancer Discov. 2022;12(1):31–46. https://doi.org/10.1158/2159-8290.CD-21-1059.

    Article  CAS  PubMed  Google Scholar 

  5. Martínez-Reyes I, Chandel NS. Cancer metabolism: looking forward. Nat Rev Cancer. 2021;21(10):669–80. https://doi.org/10.1038/s41568-021-00378-6.

    Article  CAS  PubMed  Google Scholar 

  6. Birsoy K, Wang T, Chen WW, Freinkman E, Abu-Remaileh M, Sabatini DM. An essential role of the mitochondrial electron transport chain in cell proliferation is to enable aspartate synthesis. Cell. 2015;162(3):540–51. https://doi.org/10.1016/j.cell.2015.07.016.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sullivan LB, Gui DY, Hosios AM, Bush LN, Freinkman E, Vander Heiden MG. Supporting aspartate biosynthesis is an essential function of respiration in proliferating cells. Cell. 2015;162(3):552–63. https://doi.org/10.1016/j.cell.2015.07.017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Choi B, Coloff JL. The diverse functions of non-essential amino acids in cancer. Cancers (Basel). 2019;11(5):675. https://doi.org/10.3390/cancers11050675.

    Article  CAS  PubMed  Google Scholar 

  9. De Falco P, Lazzarino G, Felice F, Desideri E, Castelli S, Salvatori I, et al. Hindering nat8l expression in hepatocellular carcinoma increases cytosolic aspartate delivery that fosters pentose phosphate pathway and purine biosynthesis promoting cell proliferation. Redox Biol. 2023;59:102585. https://doi.org/10.1016/j.redox.2022.102585.

    Article  CAS  PubMed  Google Scholar 

  10. Rabinovich S, Adler L, Yizhak K, Sarver A, Silberman A, Agron S, et al. Diversion of aspartate in ass1-deficient tumours fosters de novo pyrimidine synthesis. Nature. 2015;527(7578):379–83. https://doi.org/10.1038/nature15529.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  11. Son J, Lyssiotis CA, Ying H, Wang X, Hua S, Ligorio M, et al. Glutamine supports pancreatic cancer growth through a kras-regulated metabolic pathway. Nature. 2013;496(7443):101–5. https://doi.org/10.1038/nature12040.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  12. Helenius IT, Madala HR, Yeh JJ. An asp to strike out cancer? Therapeutic possibilities arising from aspartate’s emerging roles in cell proliferation and survival. Biomolecules. 2021;11(11):1666. https://doi.org/10.3390/biom11111666.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Mering CV. String: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003;31(1):258–61. https://doi.org/10.1093/nar/gkg034.

    Article  CAS  Google Scholar 

  14. Zheng H, Pomyen Y, Hernandez MO, Li C, Livak F, Tang W, et al. Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma. Hepatology. 2018;68(1):127–40. https://doi.org/10.1002/hep.29778.

    Article  PubMed  Google Scholar 

  15. Wilkerson MD, Hayes DN. Consensusclusterplus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–3. https://doi.org/10.1093/bioinformatics/btq170.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Blanche P, Dartigues J, Jacqmin-Gadda H. Estimating and comparing time-dependent areas under receiver operating characteristic curves for censored event times with competing risks. Stat Med. 2013;32(30):5381–97. https://doi.org/10.1002/sim.5958.

    Article  MathSciNet  PubMed  Google Scholar 

  17. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for rna-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7): e47. https://doi.org/10.1093/nar/gkv007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database hallmark gene set collection. Cell Syst. 2015;1(6):417–25. https://doi.org/10.1016/j.cels.2015.12.004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–7. https://doi.org/10.1038/nmeth.3337.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411–20. https://doi.org/10.1038/nbt.4096.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. He X, Peng Y, He G, Ye H, Liu L, Zhou Q, et al. Increased co-expression of pd1 and tim3 is associated with poor prognosis and immune microenvironment heterogeneity in gallbladder cancer. J Transl Med. 2023;21(1):717. https://doi.org/10.1186/s12967-023-04589-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhou Q, Lin J, Yan Y, Meng S, Liao H, Chen R, et al. Inpp5f translocates into cytoplasm and interacts with asph to promote tumor growth in hepatocellular carcinoma. J Exp Clin Cancer Res. 2022;41(1). https://doi.org/10.1186/s13046-021-02216-x

  23. Tauriello DVF, Sancho E, Batlle E. Overcoming tgfβ-mediated immune evasion in cancer. Nat Rev Cancer. 2022;22(1):25–44. https://doi.org/10.1038/s41568-021-00413-6.

    Article  CAS  PubMed  Google Scholar 

  24. Gorgoglione R, Impedovo V, Riley CL, Fratantonio D, Tiziani S, Palmieri L, et al. Glutamine-derived aspartate biosynthesis in cancer cells: role of mitochondrial transporters and new therapeutic perspectives. Cancers (Basel). 2022;14(1):245. https://doi.org/10.3390/cancers14010245.

    Article  CAS  PubMed  Google Scholar 

  25. Ridder DA, Schindeldecker M, Weinmann A, Berndt K, Urbansky L, Witzel HR, et al. Key enzymes in pyrimidine synthesis, cad and cps1, predict prognosis in hepatocellular carcinoma. Cancers (Basel). 2021;13(4):744. https://doi.org/10.3390/cancers13040744.

    Article  CAS  PubMed  Google Scholar 

  26. Li Y, Li B, Xu Y, Qian L, Xu T, Meng G, et al. Got2 silencing promotes reprogramming of glutamine metabolism and sensitizes hepatocellular carcinoma to glutaminase inhibitors. Cancer Res. 2022;82(18):3223–35. https://doi.org/10.1158/0008-5472.CAN-22-0042.

    Article  CAS  PubMed  Google Scholar 

  27. Long PM, Moffett JR, Namboodiri AMA, Viapiano MS, Lawler SE, Jaworski DM. N-acetylaspartate (naa) and n-acetylaspartylglutamate (naag) promote growth and inhibit differentiation of glioma stem-like cells. J Biol Chem. 2013;288(36):26188–200. https://doi.org/10.1074/jbc.M113.487553.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sun C, Gu Y, Chen G, Du Y. Bioinformatics analysis of stromal molecular signatures associated with breast and prostate cancer. J Comput Biol. 2019;26(10):1130–9. https://doi.org/10.1089/cmb.2019.0045.

    Article  CAS  PubMed  Google Scholar 

  29. Clarke MF. Clinical and therapeutic implications of cancer stem cells. N Engl J Med. 2019;380(23):2237–45. https://doi.org/10.1056/NEJMra1804280.

    Article  CAS  PubMed  Google Scholar 

  30. Lytle NK, Barber AG, Reya T. Stem cell fate in cancer growth, progression and therapy resistance. Nat Rev Cancer. 2018;18(11):669–80. https://doi.org/10.1038/s41568-018-0056-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Lee TK, Guan X, Ma S. Cancer stem cells in hepatocellular carcinoma—from origin to clinical implications. Nat Rev Gastroenterol Hepatol. 2022;19(1):26–44. https://doi.org/10.1038/s41575-021-00508-3.

    Article  PubMed  Google Scholar 

  32. Loong JHC, Wong T, Tong M, Sharma R, Zhou L, Ng K, et al. Glucose deprivation–induced aberrant fut1-mediated fucosylation drives cancer stemness in hepatocellular carcinoma. J Clin Invest. 2021;131(11): e143377. https://doi.org/10.1172/JCI143377.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Mok EHK, Leung CON, Zhou L, Lei MML, Leung HW, Tong M, et al. Caspase-3–induced activation of srebp2 drives drug resistance via promotion of cholesterol biosynthesis in hepatocellular carcinoma. Cancer Res. 2022;82(17):3102–15. https://doi.org/10.1158/0008-5472.CAN-21-2934.

    Article  CAS  PubMed  Google Scholar 

  34. Wang X, Yang K, Wu Q, Kim LJY, Morton AR, Gimple RC, et al. Targeting pyrimidine synthesis accentuates molecular therapy response in glioblastoma stem cells. Sci Transl Med. 2019;11(504):eaau4972. https://doi.org/10.1126/scitranslmed.aau4972

  35. Llovet JM, Castet F, Heikenwalder M, Maini MK, Mazzaferro V, Pinato DJ, et al. Immunotherapies for hepatocellular carcinoma. Nat Rev Clin Oncol. 2022;19(3):151–72. https://doi.org/10.1038/s41571-021-00573-2.

    Article  CAS  PubMed  Google Scholar 

  36. Yau T, Park J, Finn RS, Cheng A, Mathurin P, Edeline J, et al. Nivolumab versus sorafenib in advanced hepatocellular carcinoma (checkmate 459): a randomised, multicentre, open-label, phase 3 trial. Lancet Oncol. 2022;23(1):77–90. https://doi.org/10.1016/S1470-2045(21)00604-5.

    Article  CAS  PubMed  Google Scholar 

  37. Verset G, Borbath I, Karwal M, Verslype C, Van Vlierberghe H, Kardosh A, et al. Pembrolizumab monotherapy for previously untreated advanced hepatocellular carcinoma: data from the open-label, phase ii keynote-224 trial. Clin Cancer Res. 2022;28(12):2547–54. https://doi.org/10.1158/1078-0432.CCR-21-3807.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Donne R, Lujambio A. The liver cancer immune microenvironment: therapeutic implications for hepatocellular carcinoma. Hepatology. 2022:n/a–n/a. https://doi.org/10.1002/hep.32740

  39. Li X, Wenes M, Romero P, Huang SC, Fendt S, Ho P. Navigating metabolic pathways to enhance antitumour immunity and immunotherapy. Nat Rev Clin Oncol. 2019;16(7):425–41. https://doi.org/10.1038/s41571-019-0203-7.

    Article  CAS  PubMed  Google Scholar 

  40. Zhou J, Ding T, Pan W, Zhu L, Li L, Zheng L. Increased intratumoral regulatory t cells are related to intratumoral macrophages and poor prognosis in hepatocellular carcinoma patients. Int J Cancer. 2009;125(7):1640–8. https://doi.org/10.1002/ijc.24556.

    Article  CAS  PubMed  Google Scholar 

  41. Kalathil S, Lugade AA, Miller A, Iyer R, Thanavala Y. Higher frequencies of garp+ctla-4+foxp3+ t regulatory cells and myeloid-derived suppressor cells in hepatocellular carcinoma patients are associated with impaired t-cell functionality. Cancer Res. 2013;73(8):2435–44. https://doi.org/10.1158/0008-5472.CAN-12-3381.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Chang H, Jung W, Kim A, Kim HK, Kim WB, Kim JH, et al. Expression and prognostic significance of programmed death protein 1 and programmed death ligand-1, and cytotoxic t lymphocyte-associated molecule-4 in hepatocellular carcinoma. APMIS. 2017;125(8):690–8. https://doi.org/10.1111/apm.12703.

    Article  CAS  PubMed  Google Scholar 

  43. Liu X, Li M, Wang X, Dang Z, Jiang Y, Wang X, et al. Pd-1+ tigit+ cd8+ t cells are associated with pathogenesis and progression of patients with hepatitis b virus-related hepatocellular carcinoma. Cancer Immunol Immunother. 2019;68(12):2041–54. https://doi.org/10.1007/s00262-019-02426-5.

    Article  CAS  PubMed  Google Scholar 

  44. Li H, Wu K, Tao K, Chen L, Zheng Q, Lu X, et al. Tim-3/galectin-9 signaling pathway mediates t-cell dysfunction and predicts poor prognosis in patients with hepatitis b virus-associated hepatocellular carcinoma. Hepatology. 2012;56(4):1342–51. https://doi.org/10.1002/hep.25777.

    Article  CAS  PubMed  Google Scholar 

  45. Han Y, Chen Z, Yang Y, Jiang Z, Gu Y, Liu Y, et al. Human cd14+ ctla-4+ regulatory dendritic cells suppress t-cell response by cytotoxic t-lymphocyte antigen-4-dependent il-10 and indoleamine-2,3-dioxygenase production in hepatocellular carcinoma. Hepatology. 2014;59(2):567–79. https://doi.org/10.1002/hep.26694.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank all the databases that provided public data downloads and the researchers who proposed the algorithms used in this study.

Funding

This research was funded by National Natural Science Foundation of China (No. 82073045, 82103090), Guangdong Basic and Applied Basic Research Foundation (No. 2021A1515012107, 2022A1515012391, 2020A1515010232), Beijing Xisike Clinical Oncology Research Foundation (Y-MSDPU2022-0826), Science and Technology Program of Guangzhou (No.202201020311), China Postdoctoral Science Foundation (2020TQ0384, 2021M703742), the Guangdong Science and Technology Department (2020B1212060018), the Key Laboratory of Malignant Tumour Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat‐sen University (Grant KLB09001), and the Key Laboratory of Malignant Tumour Molecular Mechanism and Translational Medicine of Guangzhou Bureau of Science and Information Technology ([2013]163).

Author information

Author notes

  1. Juanyi Shi, Kai Wen, and Sintim Mui have contributed equally to this work.

Authors and Affiliations

  1. Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China

    Juanyi Shi, Kai Wen, Sintim Mui, Huoming Li, Hao Liao, Chuanchao He, Yongcong Yan, Zhenyu Zhou & Zhiyu Xiao

  2. Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China

    Juanyi Shi

  3. Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China

    Juanyi Shi, Kai Wen, Sintim Mui, Huoming Li, Hao Liao, Chuanchao He, Yongcong Yan, Zhenyu Zhou & Zhiyu Xiao

  4. Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Shanwei, 516621, Guangdong, China

    Zhiyu Xiao

Authors
  1. Juanyi Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kai Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sintim Mui
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Huoming Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hao Liao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chuanchao He
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yongcong Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zhenyu Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Zhiyu Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: ZZ and ZX. Methodology: JS and YY. Software: KW. Data collection: JS. Manuscript preparation: HL, HL and CH. Manuscript editing: SM and ZZ. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Yongcong Yan, Zhenyu Zhou or Zhiyu Xiao.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Ethical approval

The study was approved by the Animal Ethics Committee of Sun Yat-sen University and conducted in accordance with institutional guidelines.

Informed consent

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shi, J., Wen, K., Mui, S. et al. Integrated analysis reveals an aspartate metabolism-related gene signature for predicting the overall survival in patients with hepatocellular carcinoma. Clin Transl Oncol (2024). https://doi.org/10.1007/s12094-024-03431-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12094-024-03431-6

Keywords

Search

Navigation