Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

Keynote webinar | Spotlight on medication adherence

LIVE: Thursday 27th June 2024, 18:00-19:30 (CEST)
Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.
ADVANCED SEARCH
Log in
Top
European Journal of Medical Research
Published in: European Journal of Medical Research 1/2023

Open Access 01-12-2023 | Hepatocellular Carcinoma | Research

SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma

Authors: Wonbeak Yoo, Seokho Kim, KyungHee Noh

Published in: European Journal of Medical Research | Issue 1/2023

Login to get access

Abstract

Hepatocellular carcinoma (HCC) is the most common form of liver cancer and the 5-year relative overall survival (OS) rate is less than 20%. Since there are no specific symptoms, most patients with HCC are diagnosed in an advanced stage with poor prognosis. Therefore, identifying novel prognostic biomarkers to improve the survival of patients with HCC is urgently needed. In the present study, we attempted to identify SAMD13 (Sterile Alpha Motif Domain-Containing Protein 13) as a novel biomarker associated with the prognosis of HCC using various bioinformatics tools. SAMD13 was found to be highly expressed pan-cancer; however, the SAMD13 expression was significantly correlated with the worst prognosis in HCC. Clinicopathological analysis revealed that SAMD13 upregulation was significantly associated with advanced HCC stage and high-grade tumor type. Simultaneously, high SAMD13 expression resulted in association with various immune markers in the immune cell subsets by TIMER databases and efficacy of immunotherapy. Methylation analysis showed SAMD13 was remarkably associated with prognosis. Furthermore, a six-hub gene signature associated with poor prognosis was correlated with the cell cycle, transcription, and epigenetic regulation and this analysis may support the connection between SAMD13 expression and drug-resistance. Our study illustrated the characteristics of SAMD13 role in patients with HCC using various bioinformatics tools and highlights its potential role as a therapeutic target and promising biomarker for prognosis in HCC.
Appendix
Available only for authorised users
Literature
1.
Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424.CrossRefPubMed
2.
3.
Liu PH, Hsu CY, Hsia CY, et al. Surgical resection versus radiofrequency ablation for single hepatocellular carcinoma </= 2 cm in a propensity score model. Ann Surg. 2016;263(3):538–45.PubMedCrossRef
4.
Ponziani FR, Bhoori S, Castelli C, et al. Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease. Hepatology. 2019;69(1):107–20.PubMedCrossRef
5.
6.
Peterson AJ, Kyba M, Bornemann D, et al. A domain shared by the Polycomb group proteins Scm and ph mediates heterotypic and homotypic interactions. Mol Cell Biol. 1997;17(11):6683–92.PubMedPubMedCentralCrossRef
7.
8.
Oberstrass FC, Lee A, Stefl R, et al. Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol. 2006;13(2):160–7.PubMedCrossRef
9.
Aviv T, Lin Z, Lau S, et al. The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat Struct Biol. 2003;10(8):614–21.PubMedCrossRef
10.
Li H, Fung KL, Jin DY, et al. Solution structures, dynamics, and lipid-binding of the sterile alpha-motif domain of the deleted in liver cancer 2. Proteins. 2007;67(4):1154–66.PubMedCrossRef
11.
12.
13.
Kanomata N, Kurebayashi J, Koike Y, Yamaguchi R, Moriya T. CD1d- and PJA2-related immune microenvironment differs between invasive breast carcinomas with and without a micropapillary feature. BMC Cancer. 2019;19(1):76.PubMedPubMedCentralCrossRef
14.
Chandrashekar DS, Bashel B, Balasubramanya SAH, et al. UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia. 2017;19(8):649–58.PubMedPubMedCentralCrossRef
15.
Tang Z, Li C, Kang B, et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–102.PubMedPubMedCentralCrossRef
16.
Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401–4.PubMedCrossRef
17.
Gyorffy B, Lanczky A, Eklund AC, et al. An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients. Breast Cancer Res Treat. 2010;123(3):725–31.PubMedCrossRef
18.
Ma L, Wang L, Khatib SA, et al. Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma. J Hepatol. 2021;75(6):1397–408.PubMedPubMedCentralCrossRef
19.
20.
21.
Modhukur V, Iljasenko T, Metsalu T, et al. MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data. Epigenomics. 2018;10(3):277–88.PubMedCrossRef
22.
Li Y, Ge D, Lu C. The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization. Epigenetics Chromatin. 2019;12(1):71.PubMedPubMedCentralCrossRef
23.
Rodchenkov I, Babur O, Luna A, et al. Pathway commons 2019 update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 2020;48(D1):D489–97.PubMed
24.
The Gene Ontology C. The gene ontology resource: 20 years and still going strong. Nucleic Acids Res. 2019;47(D1):D330–8.CrossRef
25.
Ponten F, Jirstrom K, Uhlen M. The human protein atlas–a tool for pathology. J Pathol. 2008;216(4):387–93.PubMedCrossRef
26.
Llovet JM, Zucman-Rossi J, Pikarsky E, et al. Hepatocellular carcinoma. Nat Rev Dis Primers. 2016;2:16018.PubMedCrossRef
27.
Kulik LM, Chokechanachaisakul A. Evaluation and management of hepatocellular carcinoma. Clin Liver Dis. 2015;19(1):23–43.PubMedCrossRef
28.
Yuzugullu H, Benhaj K, Ozturk N, et al. Canonical Wnt signaling is antagonized by noncanonical Wnt5a in hepatocellular carcinoma cells. Mol Cancer. 2009;8:90.PubMedPubMedCentralCrossRef
29.
Ge Z, Ding S. The crosstalk between Tumor-Associated Macrophages (TAMs) and tumor cells and the corresponding targeted therapy. Front Oncol. 2020;10:590941.PubMedPubMedCentralCrossRef
30.
Obradovic A, Chowdhury N, Haake SM, et al. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Cell. 2021;184(11):2988–3005.PubMedPubMedCentralCrossRef
31.
Guo Y, Yang J, Ren K, et al. The heterogeneity of immune cell infiltration landscape and its immunotherapeutic implications in hepatocellular carcinoma. Front Immunol. 2022;13:861525.PubMedPubMedCentralCrossRef
32.
Pappas DJ, Coppola G, Gabatto PA, et al. Longitudinal system-based analysis of transcriptional responses to type I interferons. Physiol Genomics. 2009;38(3):362–71.PubMedCrossRef
33.
Margetts J, Ogle LF, Chan SL, et al. Neutrophils: driving progression and poor prognosis in hepatocellular carcinoma? Br J Cancer. 2018;118(2):248–57.PubMedCrossRef
34.
Arvanitakis K, Koletsa T, Mitroulis I, Germanidis G. Tumor-associated macrophages in hepatocellular carcinoma pathogenesis, prognosis and therapy. Cancers (Basel). 2022;14(1):226.PubMedCrossRef
35.
Zhang X, Fu X, Li T, Yan H. The prognostic value of myeloid derived suppressor cell level in hepatocellular carcinoma: a systematic review and meta-analysis. PLoS ONE. 2019;14(12):e0225327.PubMedPubMedCentralCrossRef
36.
Hao X, Luo H, Krawczyk M, et al. DNA methylation markers for diagnosis and prognosis of common cancers. Proc Natl Acad Sci U S A. 2017;114(28):7414–9.PubMedPubMedCentralCrossRef
37.
38.
Cheng Y, He C, Wang M, et al. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Transduct Target Ther. 2019;4:62.PubMedPubMedCentralCrossRef
39.
Hernandez-Vargas H, Lambert MP, Le Calvez-Kelm F, et al. Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS ONE. 2010;5(3):e9749.PubMedPubMedCentralCrossRef
40.
41.
Hlady RA, Zhou D, Puszyk W, et al. Initiation of aberrant DNA methylation patterns and heterogeneity in precancerous lesions of human hepatocellular cancer. Epigenetics. 2017;12(3):215–25.PubMedPubMedCentralCrossRef
42.
Casalino L, Verde P. Multifaceted roles of DNA methylation in neoplastic transformation, from tumor suppressors to EMT and metastasis. Genes (Basel). 2020;11(8):922.PubMedCrossRef
43.
Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet. 2002;3(6):415–28.PubMedCrossRef
44.
45.
46.
Shaulian E. AP-1–the Jun proteins: oncogenes or tumor suppressors in disguise? Cell Signal. 2010;22(6):894–9.PubMedCrossRef
47.
48.
Kinkel SA, Galeev R, Flensburg C, et al. Jarid2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2. Blood. 2015;125(12):1890–900.PubMedPubMedCentralCrossRef
49.
Pasini D, Cloos PA, Walfridsson J, et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature. 2010;464(7286):306–10.PubMedCrossRef
50.
Lei X, Xu JF, Chang RM, et al. JARID2 promotes invasion and metastasis of hepatocellular carcinoma by facilitating epithelial-mesenchymal transition through PTEN/AKT signaling. Oncotarget. 2016;7(26):40266–84.PubMedPubMedCentralCrossRef
51.
Li S, Wu Z, Li Q, et al. The prognostic value of AT-Rich Interaction Domain (ARID) family members in patients with hepatocellular carcinoma. Evid Based Complement Alternat Med. 2022;2022:1150390.PubMedPubMedCentral
52.
Chan BC, Ching AK, To KF, et al. BRE is an antiapoptotic protein in vivo and overexpressed in human hepatocellular carcinoma. Oncogene. 2008;27(9):1208–17.PubMedCrossRef
53.
Chui YL, Ching AK, Chen S, et al. BRE over-expression promotes growth of hepatocellular carcinoma. Biochem Biophys Res Commun. 2010;391(3):1522–5.PubMedCrossRef
54.
Qiu J, Zhang S, Wang P, et al. BUB1B promotes hepatocellular carcinoma progression via activation of the mTORC1 signaling pathway. Cancer Med. 2020;9(21):8159–72.PubMedPubMedCentralCrossRef
55.
Zhuang L, Yang Z, Meng Z. Upregulation of BUB1B, CCNB1, CDC7, CDC20, and MCM3 in tumor tissues predicted worse overall survival and disease-free survival in hepatocellular carcinoma patients. Biomed Res Int. 2018;2018:7897346.PubMedPubMedCentralCrossRef
56.
57.
Metadata
Title
SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma
Authors
Wonbeak Yoo
Seokho Kim
KyungHee Noh
Publication date
01-12-2023
Publisher
BioMed Central
Published in
European Journal of Medical Research / Issue 1/2023
Electronic ISSN: 2047-783X
DOI
https://doi.org/10.1186/s40001-023-01347-5

Other articles of this Issue 1/2023

European Journal of Medical Research 1/2023 Go to the issue

Review

Exploring the potential of vagus nerve stimulation in treating brain diseases: a review of immunologic benefits and neuroprotective efficacy

Review

The direct prognosis comparison of 125I low-dose-rate brachytherapy versus laparoscopic radical prostatectomy for patients with intermediate-risk prostate cancer

Research

Top 100 cited articles in the thromboangiitis obliterans: a bibliometric analysis and visualized study

Research

Role of hyperbaric oxygen therapy in PDGF-BB-mediated astrogliosis in traumatic brain injury rats associated with ERK1/2 signaling pathway inhibition

Research

A novel scoring system for early assessment of the risk of the COVID-19-associated mortality in hospitalized patients: COVID-19 BURDEN

Review

Research progress of metabolomics in cervical cancer