The development and clinical applications of proteomics: an Indian perspective

INTRODUCTION

Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic.

AREAS COVERED

This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed.

EXPERT OPINION

The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.

dbGAPs: A comprehensive database of genes and genetic markers associated with psoriasis and its subtypes

Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data. The database contains annotation for 202 manually curated genes associated with psoriasis and its subtypes with cross-references. Functional enrichment of these genes, in context of Gene Ontology and pathways, provide insight into their important role in psoriasis etiology and pathogenesis. The dbGAPs interface is enriched with an interactive search engine for data retrieval along with unique customized tools for Single Nucleotide Polymorphism (SNP)/indel detection and SNP/indel annotations. dbGAPs is accessible at http://www.bmicnip.in/dbgaps/.

CXC chemokine‑7 inhibits growth and migration of oral tongue squamous cell carcinoma cells, mediated by the epithelial‑mesenchymal transition signaling pathway

Oral tongue squamous cell carcinoma (OTSCC) is the most common oral malignancy with different histopathological symptoms and etiology of tumorigenesis. Migration and invasion is the most important characteristics of OTSCC, and limits tumor therapy in clinics. The epithelial‑to‑mesenchymal transition (EMT) signaling pathway is an important process in the progress of tumor cell migration and invasion. Previous studies have indicated that C‑X‑C chemokine receptor‑7 (CXCR‑7) promotes the progression and metastasis of tumor cells, presenting a potential target molecule for cancer therapy. The present study investigated the inhibitory effects of C‑X‑C chemokine‑7 (CXC‑7) on human OTSCC cells both in vitro and in vivo. The results demonstrated that the Tca8113 human OTSCC cell line expressed higher levels of CXC‑7 mRNA compared with the hNOE human normal oral epithelial cell line. MTT assays indicated that CXC‑7 suppressed Tca8113 cell growth, and the cytotoxicity of CXC‑7 was indicated as the cell survival of the negative control group was significantly decreased compared with the blank control and hNOE cells. Migration and invasion assays revealed that CXC‑7 inhibited Tca8113 cell local expansion and distant metastasis. In addition, the results demonstrated that the extracellular signal‑regulated kinase (ERK)/protein kinase B (AKT) signaling pathway was inhibited after CXC‑7 treatment in Tca8113 cells. N‑cadherin, E‑Cadherin, Snail and Slug expression levels in the ERK/AKT signaling pathway were inhibited in Tca8113 cells after treatment with CXC‑7. It was demonstrated that important extracellular matrix proteins involved in cell migration, including Slug, collagen type I and Vimentin, were significantly downregulated by CXC‑7 treatment. In conclusion, CXC‑7 inhibited growth and migration in OTSCC cells, mediated by the EMT signaling pathway. This suggests that CXC‑7 serves an inhibitory role in OTSCC migration, implicating CXCR‑7 as a promising biomarker for chemokine receptor‑based drug development.

Micronome revealed miR-19a/b as key regulator of SOCS3 during cancer related inflammation of oral squamous cell carcinoma

Although significant advances have been established in molecular biology of Oral squamous cell carcinoma (OSCC), innovative strategies are still required to further understand detailed molecular mechanisms. Using bioinformatic approach, we aim to explore the potential miRNA-mRNA pairs in cancer related inflammatory response and investigate their potential roles as signature miRNA and proteins in the signaling pathway. Firstly, the differentially expressed genes of OSCC were selected which then underwent gene ontology to identify genes engaged in inflammatory response and its regulation. Validated miRNAs were retrieved and miRNAs with complete complementarily with their targets were visualized for miRNA-mRNA regulatory network. Protein-protein interactions of inflammatory and its regulatory genes were analyzed for interacting genes involved in signaling pathway. Eight universal miRNAs were obtained for inflammation and its regulation. miRNA-19a/b showed significant influence in controlling inflammatory response in OSCC. Therefore, micronome on deregulated genes in inflammation identifies miRNA-mRNA pairs which have high potential to be targeted for diagnostic and treatment applications in OSCC.