Omics data-driven analysis identifies laminin-integrin-mediated signaling pathway as a determinant for cell differentiation in oral squamous cell carcinoma

Spoorti Kulkarni, Riaz Abdulla, Maji Jose, Soniya Adyanthaya, D. A.B. Rex, Arun H. Patil, Sneha M. Pinto, Yashwanth Subbannayya

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: In recent years, high-throughput omics technologies have been widely used globally to identify potential biomarkers and therapeutic targets in various cancers. However, apart from large consortiums such as The Cancer Genome Atlas, limited attempts have been made to mine existing datasets pertaining to cancers. Methods and Results: In the current study, we used an omics data analysis approach wherein publicly available protein expression data were integrated to identify functionally important proteins that revealed consistent dysregulated expression in head and neck squamous cell carcinomas. Our analysis revealed members of the integrin family of proteins to be consistently altered in expression across disparate datasets. Additionally, through association evidence and network analysis, we also identified members of the laminin family to be significantly altered in head and neck cancers. Members of both integrin and laminin families are known to be involved in cell-extracellular matrix adhesion and have been implicated in tumor metastatic processes in several cancers. To this end, we carried out immunohistochemical analyses to validate the findings in a cohort (n = 50) of oral cancer cases. Laminin-111 expression (composed of LAMA1, LAMB1, and LAMC1) was found to correlate with cell differentiation in oral cancer, showing a gradual decrease from well differentiated to poorly differentiated cases. Conclusion: This study serves as a proof-of-principle for the mining of multiple omics datasets coupled with selection of functionally important group of molecules to provide novel insights into tumorigenesis and cancer progression.

Original languageEnglish
Pages (from-to)529-536
Number of pages8
JournalIndian Journal of Pathology and Microbiology
Volume62
Issue number4
DOIs
Publication statusPublished - 01-10-2019
Externally publishedYes

Fingerprint

Laminin
Integrins
Cell Differentiation
Squamous Cell Carcinoma
Neoplasms
Mouth Neoplasms
Cell-Matrix Junctions
Proteins
Atlases
Head and Neck Neoplasms
Extracellular Matrix
Carcinogenesis
Biomarkers
Genome
Technology
Datasets

All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Microbiology (medical)

Cite this

Kulkarni, Spoorti ; Abdulla, Riaz ; Jose, Maji ; Adyanthaya, Soniya ; Rex, D. A.B. ; Patil, Arun H. ; Pinto, Sneha M. ; Subbannayya, Yashwanth. / Omics data-driven analysis identifies laminin-integrin-mediated signaling pathway as a determinant for cell differentiation in oral squamous cell carcinoma. In: Indian Journal of Pathology and Microbiology. 2019 ; Vol. 62, No. 4. pp. 529-536.
@article{dec36002581347fb999351003cf4de5f,
title = "Omics data-driven analysis identifies laminin-integrin-mediated signaling pathway as a determinant for cell differentiation in oral squamous cell carcinoma",
abstract = "Background: In recent years, high-throughput omics technologies have been widely used globally to identify potential biomarkers and therapeutic targets in various cancers. However, apart from large consortiums such as The Cancer Genome Atlas, limited attempts have been made to mine existing datasets pertaining to cancers. Methods and Results: In the current study, we used an omics data analysis approach wherein publicly available protein expression data were integrated to identify functionally important proteins that revealed consistent dysregulated expression in head and neck squamous cell carcinomas. Our analysis revealed members of the integrin family of proteins to be consistently altered in expression across disparate datasets. Additionally, through association evidence and network analysis, we also identified members of the laminin family to be significantly altered in head and neck cancers. Members of both integrin and laminin families are known to be involved in cell-extracellular matrix adhesion and have been implicated in tumor metastatic processes in several cancers. To this end, we carried out immunohistochemical analyses to validate the findings in a cohort (n = 50) of oral cancer cases. Laminin-111 expression (composed of LAMA1, LAMB1, and LAMC1) was found to correlate with cell differentiation in oral cancer, showing a gradual decrease from well differentiated to poorly differentiated cases. Conclusion: This study serves as a proof-of-principle for the mining of multiple omics datasets coupled with selection of functionally important group of molecules to provide novel insights into tumorigenesis and cancer progression.",
author = "Spoorti Kulkarni and Riaz Abdulla and Maji Jose and Soniya Adyanthaya and Rex, {D. A.B.} and Patil, {Arun H.} and Pinto, {Sneha M.} and Yashwanth Subbannayya",
year = "2019",
month = "10",
day = "1",
doi = "10.4103/IJPM.IJPM_1_19",
language = "English",
volume = "62",
pages = "529--536",
journal = "Indian Journal of Pathology and Microbiology",
issn = "0377-4929",
publisher = "Medknow Publications and Media Pvt. Ltd",
number = "4",

}

Omics data-driven analysis identifies laminin-integrin-mediated signaling pathway as a determinant for cell differentiation in oral squamous cell carcinoma. / Kulkarni, Spoorti; Abdulla, Riaz; Jose, Maji; Adyanthaya, Soniya; Rex, D. A.B.; Patil, Arun H.; Pinto, Sneha M.; Subbannayya, Yashwanth.

In: Indian Journal of Pathology and Microbiology, Vol. 62, No. 4, 01.10.2019, p. 529-536.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Omics data-driven analysis identifies laminin-integrin-mediated signaling pathway as a determinant for cell differentiation in oral squamous cell carcinoma

AU - Kulkarni, Spoorti

AU - Abdulla, Riaz

AU - Jose, Maji

AU - Adyanthaya, Soniya

AU - Rex, D. A.B.

AU - Patil, Arun H.

AU - Pinto, Sneha M.

AU - Subbannayya, Yashwanth

PY - 2019/10/1

Y1 - 2019/10/1

N2 - Background: In recent years, high-throughput omics technologies have been widely used globally to identify potential biomarkers and therapeutic targets in various cancers. However, apart from large consortiums such as The Cancer Genome Atlas, limited attempts have been made to mine existing datasets pertaining to cancers. Methods and Results: In the current study, we used an omics data analysis approach wherein publicly available protein expression data were integrated to identify functionally important proteins that revealed consistent dysregulated expression in head and neck squamous cell carcinomas. Our analysis revealed members of the integrin family of proteins to be consistently altered in expression across disparate datasets. Additionally, through association evidence and network analysis, we also identified members of the laminin family to be significantly altered in head and neck cancers. Members of both integrin and laminin families are known to be involved in cell-extracellular matrix adhesion and have been implicated in tumor metastatic processes in several cancers. To this end, we carried out immunohistochemical analyses to validate the findings in a cohort (n = 50) of oral cancer cases. Laminin-111 expression (composed of LAMA1, LAMB1, and LAMC1) was found to correlate with cell differentiation in oral cancer, showing a gradual decrease from well differentiated to poorly differentiated cases. Conclusion: This study serves as a proof-of-principle for the mining of multiple omics datasets coupled with selection of functionally important group of molecules to provide novel insights into tumorigenesis and cancer progression.

AB - Background: In recent years, high-throughput omics technologies have been widely used globally to identify potential biomarkers and therapeutic targets in various cancers. However, apart from large consortiums such as The Cancer Genome Atlas, limited attempts have been made to mine existing datasets pertaining to cancers. Methods and Results: In the current study, we used an omics data analysis approach wherein publicly available protein expression data were integrated to identify functionally important proteins that revealed consistent dysregulated expression in head and neck squamous cell carcinomas. Our analysis revealed members of the integrin family of proteins to be consistently altered in expression across disparate datasets. Additionally, through association evidence and network analysis, we also identified members of the laminin family to be significantly altered in head and neck cancers. Members of both integrin and laminin families are known to be involved in cell-extracellular matrix adhesion and have been implicated in tumor metastatic processes in several cancers. To this end, we carried out immunohistochemical analyses to validate the findings in a cohort (n = 50) of oral cancer cases. Laminin-111 expression (composed of LAMA1, LAMB1, and LAMC1) was found to correlate with cell differentiation in oral cancer, showing a gradual decrease from well differentiated to poorly differentiated cases. Conclusion: This study serves as a proof-of-principle for the mining of multiple omics datasets coupled with selection of functionally important group of molecules to provide novel insights into tumorigenesis and cancer progression.

UR - http://www.scopus.com/inward/record.url?scp=85073180274&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85073180274&partnerID=8YFLogxK

U2 - 10.4103/IJPM.IJPM_1_19

DO - 10.4103/IJPM.IJPM_1_19

M3 - Article

C2 - 31611435

AN - SCOPUS:85073180274

VL - 62

SP - 529

EP - 536

JO - Indian Journal of Pathology and Microbiology

JF - Indian Journal of Pathology and Microbiology

SN - 0377-4929

IS - 4

ER -