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Alotaibi A, Gadekar VP, Gundla PS, Mandarthi S, Jayendra N, Tungekar A, Lavanya BV, Bhagavath AK, Cordero MAW, Pitkaniemi J, Niazi SK, Upadhya R, Bepari A, Hebbar P. Global comparative transcriptomes uncover novel and population-specific gene expression in esophageal squamous cell carcinoma. Infect Agent Cancer 2023; 18:47. [PMID: 37641095 PMCID: PMC10463703 DOI: 10.1186/s13027-023-00525-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) has a poor prognosis and is one of the deadliest gastrointestinal malignancies. Despite numerous transcriptomics studies to understand its molecular basis, the impact of population-specific differences on this disease remains unexplored. AIMS This study aimed to investigate the population-specific differences in gene expression patterns among ESCC samples obtained from six distinct global populations, identify differentially expressed genes (DEGs) and their associated pathways, and identify potential biomarkers for ESCC diagnosis and prognosis. In addition, this study deciphers population specific microbial and chemical risk factors in ESCC. METHODS We compared the gene expression patterns of ESCC samples from six different global populations by analyzing microarray datasets. To identify DEGs, we conducted stringent quality control and employed linear modeling. We cross-compared the resulting DEG lists of each populations along with ESCC ATLAS to identify known and novel DEGs. We performed a survival analysis using The Cancer Genome Atlas Program (TCGA) data to identify potential biomarkers for ESCC diagnosis and prognosis among the novel DEGs. Finally, we performed comparative functional enrichment and toxicogenomic analysis. RESULTS Here we report 19 genes with distinct expression patterns among populations, indicating population-specific variations in ESCC. Additionally, we discovered 166 novel DEGs, such as ENDOU, SLCO1B3, KCNS3, IFI35, among others. The survival analysis identified three novel genes (CHRM3, CREG2, H2AC6) critical for ESCC survival. Notably, our findings showed that ECM-related gene ontology terms and pathways were significantly enriched among the DEGs in ESCC. We also found population-specific variations in immune response and microbial infection-related pathways which included genes enriched for HPV, Ameobiosis, Leishmaniosis, and Human Cytomegaloviruses. Our toxicogenomic analysis identified tobacco smoking as the primary risk factor and cisplatin as the main drug chemical interacting with the maximum number of DEGs across populations. CONCLUSION This study provides new insights into population-specific differences in gene expression patterns and their associated pathways in ESCC. Our findings suggest that changes in extracellular matrix (ECM) organization may be crucial to the development and progression of this cancer, and that environmental and genetic factors play important roles in the disease. The novel DEGs identified may serve as potential biomarkers for diagnosis, prognosis and treatment.
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Grants
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
- 43- PRFA-P-8 the Deanship of Scientific Research, Princess Nourah bint Abdulrahman University, through the Program of Research Project Funding After Publication
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Affiliation(s)
- Amal Alotaibi
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Sumana Mandarthi
- Mbiomics LLC, 16192 Coastal Highway, Lewes, DE, 19958, USA
- Meta Biosciences Pvt Ltd, Manipal-GOK Bioincubator, Manipal, India
| | - Nidhi Jayendra
- Mbiomics LLC, 16192 Coastal Highway, Lewes, DE, 19958, USA
| | - Asna Tungekar
- Mbiomics LLC, 16192 Coastal Highway, Lewes, DE, 19958, USA
| | - B V Lavanya
- Mbiomics LLC, 16192 Coastal Highway, Lewes, DE, 19958, USA
| | - Ashok Kumar Bhagavath
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX, USA
| | - Mary Anne Wong Cordero
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Janne Pitkaniemi
- Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Shaik Kalimulla Niazi
- Department of Preparatory Health Sciences, Riyadh Elm University, Riyadh, Saudi Arabia
| | - Raghavendra Upadhya
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - Asmatanzeem Bepari
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
| | - Prashantha Hebbar
- Mbiomics LLC, 16192 Coastal Highway, Lewes, DE, 19958, USA.
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India.
- Meta Biosciences Pvt Ltd, Manipal-GOK Bioincubator, Manipal, India.
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Alotaibi A, Gadekar VP, Gundla PS, Mandarthi S, Ravi S, Mallya D, Tungekar A, Lavanya BV, Bhagavath AK, Cordero MW, Pitkaniemi J, Seetharam RN, Bepari A, Hebbar P. A comprehensive analysis of mRNA expression profiles of Esophageal Squamous Cell Carcinoma reveals downregulation of Desmoglein 1 and crucial genomic targets. Cancer Biomark 2023; 38:465-487. [PMID: 38073377 DOI: 10.3233/cbm-230145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
AIM Esophageal Squamous Cell Carcinoma (ESCC) is a histological subtype of esophageal cancer that begins in the squamous cells in the esophagus. In only 19% of the ESCC-diagnosed patients, a five-year survival rate has been seen. This necessitates the identification of high-confidence biomarkers for early diagnosis, prognosis, and potential therapeutic targets for the mitigation of ESCC. METHOD We performed a meta-analysis of 10 mRNA datasets and identified consistently perturbed genes across the studies. Then, integrated with ESCC ATLAS to segregate 'core' genes to identify consequences of primary gene perturbation events leading to gene-gene interactions and dysregulated molecular signaling pathways. Further, by integrating with toxicogenomics data, inferences were drawn for gene interaction with environmental exposures, trace elements, chemical carcinogens, and drug chemicals. We also deduce the clinical outcomes of candidate genes based on survival analysis using the ESCC related dataset in The Cancer Genome Atlas. RESULT We identified 237 known and 18 novel perturbed candidate genes. Desmoglein 1 (DSG1) is one such gene that we found significantly downregulated (Fold Change =-1.89, p-value = 8.2e-06) in ESCC across six different datasets. Further, we identified 31 'core' genes (that either harbor genetic variants or are regulated by epigenetic modifications) and found regulating key biological pathways via adjoining genes in gene-gene interaction networks. Functional enrichment analysis showed dysregulated biological processes and pathways including "Extracellular matrix", "Collagen trimmer" and "HPV infection" are significantly overrepresented in our candidate genes. Based on the toxicogenomic inferences from Comparative Toxicogenomics Database we report the key genes that interacted with risk factors such as tobacco smoking, zinc, nitroso benzylmethylamine, and drug chemicals such as cisplatin, Fluorouracil, and Mitomycin in relation to ESCC. We also point to the STC2 gene that shows a high risk for mortality in ESCC patients. CONCLUSION We identified novel perturbed genes in relation to ESCC and explored their interaction network. DSG1 is one such gene, its association with microbiota and a clinical presentation seen commonly with ESCC hints that it is a good candidate for early diagnostic marker. Besides, in this study we highlight candidate genes and their molecular connections to risk factors, biological pathways, drug chemicals, and the survival probability of ESCC patients.
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Affiliation(s)
- Amal Alotaibi
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Veerendra P Gadekar
- Mbiomics LLC, Lewes DE, USA
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | - Ashok Kumar Bhagavath
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, Texas, TX, USA
| | - MaryAnne Wong Cordero
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Janne Pitkaniemi
- Finnish Cancer Registry, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Raviraja N Seetharam
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - Asmatanzeem Bepari
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Prashantha Hebbar
- Mbiomics LLC, Lewes DE, USA
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Meta Biosciences Pvt Ltd., Manipal - GOK Bioincubator, Advanced Research Center, Manipal, India
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018. [PMID: 30143675 DOI: 10.1038/s41598-018-30579-3,] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India.,Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India.,Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.,Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India.,Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India.,Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India.,Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India.,Infosys Technologies Ltd, Bangalore, Karnataka, India.,Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India. .,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India. .,Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India. .,School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India. .,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018; 8:12715. [PMID: 30143675 PMCID: PMC6109081 DOI: 10.1038/s41598-018-30579-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India
- Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
- Infosys Technologies Ltd, Bangalore, Karnataka, India
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India.
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India.
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India.
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India.
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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