Integrated In Silico Analysis of Proteogenomic and Drug Targets for Pancreatic Cancer Survival

Alakesh Bera; Digonto Chatterjee; Jack Hester; Meera Srivastava

doi:10.1007/978-1-0716-3163-8_19

Integrated In Silico Analysis of Proteogenomic and Drug Targets for Pancreatic Cancer Survival

Alakesh Bera
, Digonto Chatterjee
, Jack Hester
, Meera Srivastava^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

1 Scopus citations

Abstract

Pancreatic cancer remains a major health concern, being among the deadliest forms of cancer with over 80% of the patients presenting with metastatic disease. According to the American Cancer Society, for all stages of pancreatic cancer combined, the 5-year survival rate is less than 10%. Genetic research on pancreatic cancer has generally been focused on familial pancreatic cancer, which is only 10% of all pancreatic cancer patients. This study focuses on finding genes that impact the survival of pancreatic cancer patients which can be used as biomarkers and potential targets to develop personalized treatment options. We used cBioPortal platform using NCI-initiated The Cancer Genome Atlas (TCGA) dataset to find genes that were altered differently in different ethnic groups which can serve as potential biomarkers and analyzed the genes’ impact on patient survival. MD Anderson Cell Lines Project (MCLP) and genecards.org were also utilized to identify potential drug candidates that can target the proteins encoded by the genes. The results showed that there are unique genes that are associated with each race category which may influence the survival outcomes of patients, and their potential drug candidates were identified.

Original language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	273-282
Number of pages	10
DOIs	https://doi.org/10.1007/978-1-0716-3163-8_19
State	Published - 2023

Publication series

Name	Methods in Molecular Biology
Volume	2660
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

cBioPortal
Copy number alterations (CNAs)
Disease-free survival (DFS)
Drug targets
Genomics
MD Anderson Cell Lines Project (MCLP)
Overall survival (OS)
Pancreatic cancer
Proteogenomics
Proteomics
Socioeconomic status (SES)
Survival outcomes
The Cancer Genome Atlas (TCGA)

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10.1007/978-1-0716-3163-8_19

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title = "Integrated In Silico Analysis of Proteogenomic and Drug Targets for Pancreatic Cancer Survival",

abstract = "Pancreatic cancer remains a major health concern, being among the deadliest forms of cancer with over 80\% of the patients presenting with metastatic disease. According to the American Cancer Society, for all stages of pancreatic cancer combined, the 5-year survival rate is less than 10\%. Genetic research on pancreatic cancer has generally been focused on familial pancreatic cancer, which is only 10\% of all pancreatic cancer patients. This study focuses on finding genes that impact the survival of pancreatic cancer patients which can be used as biomarkers and potential targets to develop personalized treatment options. We used cBioPortal platform using NCI-initiated The Cancer Genome Atlas (TCGA) dataset to find genes that were altered differently in different ethnic groups which can serve as potential biomarkers and analyzed the genes{\textquoteright} impact on patient survival. MD Anderson Cell Lines Project (MCLP) and genecards.org were also utilized to identify potential drug candidates that can target the proteins encoded by the genes. The results showed that there are unique genes that are associated with each race category which may influence the survival outcomes of patients, and their potential drug candidates were identified.",

keywords = "cBioPortal, Copy number alterations (CNAs), Disease-free survival (DFS), Drug targets, Genomics, MD Anderson Cell Lines Project (MCLP), Overall survival (OS), Pancreatic cancer, Proteogenomics, Proteomics, Socioeconomic status (SES), Survival outcomes, The Cancer Genome Atlas (TCGA)",

author = "Alakesh Bera and Digonto Chatterjee and Jack Hester and Meera Srivastava",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",

year = "2023",

doi = "10.1007/978-1-0716-3163-8\_19",

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AU - Bera, Alakesh

AU - Chatterjee, Digonto

AU - Hester, Jack

AU - Srivastava, Meera

PY - 2023

Y1 - 2023

N2 - Pancreatic cancer remains a major health concern, being among the deadliest forms of cancer with over 80% of the patients presenting with metastatic disease. According to the American Cancer Society, for all stages of pancreatic cancer combined, the 5-year survival rate is less than 10%. Genetic research on pancreatic cancer has generally been focused on familial pancreatic cancer, which is only 10% of all pancreatic cancer patients. This study focuses on finding genes that impact the survival of pancreatic cancer patients which can be used as biomarkers and potential targets to develop personalized treatment options. We used cBioPortal platform using NCI-initiated The Cancer Genome Atlas (TCGA) dataset to find genes that were altered differently in different ethnic groups which can serve as potential biomarkers and analyzed the genes’ impact on patient survival. MD Anderson Cell Lines Project (MCLP) and genecards.org were also utilized to identify potential drug candidates that can target the proteins encoded by the genes. The results showed that there are unique genes that are associated with each race category which may influence the survival outcomes of patients, and their potential drug candidates were identified.

AB - Pancreatic cancer remains a major health concern, being among the deadliest forms of cancer with over 80% of the patients presenting with metastatic disease. According to the American Cancer Society, for all stages of pancreatic cancer combined, the 5-year survival rate is less than 10%. Genetic research on pancreatic cancer has generally been focused on familial pancreatic cancer, which is only 10% of all pancreatic cancer patients. This study focuses on finding genes that impact the survival of pancreatic cancer patients which can be used as biomarkers and potential targets to develop personalized treatment options. We used cBioPortal platform using NCI-initiated The Cancer Genome Atlas (TCGA) dataset to find genes that were altered differently in different ethnic groups which can serve as potential biomarkers and analyzed the genes’ impact on patient survival. MD Anderson Cell Lines Project (MCLP) and genecards.org were also utilized to identify potential drug candidates that can target the proteins encoded by the genes. The results showed that there are unique genes that are associated with each race category which may influence the survival outcomes of patients, and their potential drug candidates were identified.

KW - cBioPortal

KW - Copy number alterations (CNAs)

KW - Disease-free survival (DFS)

KW - Drug targets

KW - Genomics

KW - MD Anderson Cell Lines Project (MCLP)

KW - Overall survival (OS)

KW - Pancreatic cancer

KW - Proteogenomics

KW - Proteomics

KW - Socioeconomic status (SES)

KW - Survival outcomes

KW - The Cancer Genome Atlas (TCGA)

UR - https://www.scopus.com/pages/publications/85159739817

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DO - 10.1007/978-1-0716-3163-8_19

M3 - Chapter

C2 - 37191804

AN - SCOPUS:85159739817

T3 - Methods in Molecular Biology

SP - 273

EP - 282

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

Integrated In Silico Analysis of Proteogenomic and Drug Targets for Pancreatic Cancer Survival

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