Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians

Tane Kim; Danny Issa; Mykola Onyshchenko; Tane Kim; Danny Issa; Mykola Onyshchenko

doi:10.1159/000524576

2022 Volume 9

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RESEARCH ARTICLE Open Access

Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians

a.
Orange County School of the Arts, Santa Ana, California, USA
b.
Division of Digestive Diseases, Department of Medicine, UCLA School of Medicine, Los Angeles, California, USA
c.
Hematology-Oncology Division, Department of Medicine, Harbor-UCLA/Lundquist Institute, Torrance, California, USA

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Corresponding author: Mykola Onyshchenko, mykola.onyshchenko@lundquist.org

Received: 01 December 2021
Accepted: 13 March 2022
Published online: 20 April 2022
Gastrointestinal Tumors 9, Article number: 10.1159/000524576 (2022) | Cite this article

Abstract

Introduction: Liver cancer is the sixth most common and second most fatal type of cancer worldwide. Few treatment options are available as patients with liver cancer are often diagnosed in an advanced stage due to a lack of clinical symptoms. Effectively preventing and treating liver cancer relies heavily on early diagnosis; early diagnosis results from identifying and monitoring high-risk patients. Epigenetic risk factors, such as hepatitis B, hepatitis C, cirrhosis, nonalcoholic fatty liver disease, and alcohol/tobacco abuse, are highly prevalent in Asia and likely cause Asians to have a higher incidence and mortality rate of liver cancer. While these acquired risk factors are relatively well understood, the underlying genetic background of liver cancer in Asians has not been well established or correlated with clinical outcomes.
Methods: In this study, we accessed The Cancer Genome Atlas (TCGA) hepatocellular carcinoma clinical and mutation data through TCGAbiolinksGUI.
Results: We found that mutations in five genes (TP53, TTN, OBSCN, MUC5B, CSMD1) were statistically linked with increased mortality in Asians compared to non-Asians, four of which (TTN, OBSCN, MUC5B, CSMD1) were also more prevalent in the Asian population. Within the Asian cohort, two gene mutations (TTN, HMCN1) were statistically linked with worse outcomes. We also found that the TP53 mutation predicts worse outcomes within the non-Asian cohort but not within the Asian cohort
Discussion/Conclusion: Our findings can improve cancer care in the Asian population through better disease prognostication, evaluations for potential targeted therapy, and a deeper understanding of liver cancer pathogenesis.
- Asian,
- Hepatocellular carcinoma,
- The Cancer Genome Atlas,
- Bioinformatics,
- Prognostic marker

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Tane Kim, Danny Issa, Mykola Onyshchenko. 2022. Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians. Gastrointestinal Tumors. 9:524576 doi: 10.1159/000524576

Tane Kim, Danny Issa, Mykola Onyshchenko. 2022. Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians. Gastrointestinal Tumors. 9:524576 doi: 10.1159/000524576

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Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians

a.
Orange County School of the Arts, Santa Ana, California, USA
b.
Division of Digestive Diseases, Department of Medicine, UCLA School of Medicine, Los Angeles, California, USA
c.
Hematology-Oncology Division, Department of Medicine, Harbor-UCLA/Lundquist Institute, Torrance, California, USA

Corresponding author: Mykola Onyshchenko, mykola.onyshchenko@lundquist.org

Received: 01 December 2021
Accepted: 13 March 2022
Published online: 20 April 2022

Gastrointestinal Tumors 9, Article number: 10.1159/000524576 (2022) | Cite this article

Abstract:

Introduction: Liver cancer is the sixth most common and second most fatal type of cancer worldwide. Few treatment options are available as patients with liver cancer are often diagnosed in an advanced stage due to a lack of clinical symptoms. Effectively preventing and treating liver cancer relies heavily on early diagnosis; early diagnosis results from identifying and monitoring high-risk patients. Epigenetic risk factors, such as hepatitis B, hepatitis C, cirrhosis, nonalcoholic fatty liver disease, and alcohol/tobacco abuse, are highly prevalent in Asia and likely cause Asians to have a higher incidence and mortality rate of liver cancer. While these acquired risk factors are relatively well understood, the underlying genetic background of liver cancer in Asians has not been well established or correlated with clinical outcomes.

Methods: In this study, we accessed The Cancer Genome Atlas (TCGA) hepatocellular carcinoma clinical and mutation data through TCGAbiolinksGUI.

Results: We found that mutations in five genes (TP53, TTN, OBSCN, MUC5B, CSMD1) were statistically linked with increased mortality in Asians compared to non-Asians, four of which (TTN, OBSCN, MUC5B, CSMD1) were also more prevalent in the Asian population. Within the Asian cohort, two gene mutations (TTN, HMCN1) were statistically linked with worse outcomes. We also found that the TP53 mutation predicts worse outcomes within the non-Asian cohort but not within the Asian cohort

Discussion/Conclusion: Our findings can improve cancer care in the Asian population through better disease prognostication, evaluations for potential targeted therapy, and a deeper understanding of liver cancer pathogenesis.

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About this article

Cite this article

Tane Kim, Danny Issa, Mykola Onyshchenko. 2022. Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians. Gastrointestinal Tumors. 9:524576 doi: 10.1159/000524576

Tane Kim, Danny Issa, Mykola Onyshchenko. 2022. Analyzing TCGA Data to Identify Gene Mutations Linked to Hepatocellular Carcinoma in Asians. Gastrointestinal Tumors. 9:524576 doi: 10.1159/000524576