Last update 01 Nov 2024

Institute of Bioinformatics & Applied Biotechnology

Private Company|

Karnataka, India

www.ibab.ac.in

Private Company|

Karnataka, India

www.ibab.ac.in

Last update 01 Nov 2024

Overview

Pipeline

Deal

Translational Medicine

Overview

Clinical Trials associated with Institute of Bioinformatics & Applied Biotechnology

CTRI/2022/02/040198 / Not yet recruitingNot Applicable

Whole genome, exome, transcriptome and small-RNA sequencing for AML/ALL samples

Start Date21 Feb 2022

Sponsor / Collaborator

Institute of Bioinformatics & Applied Biotechnology

100 Clinical Results associated with Institute of Bioinformatics & Applied Biotechnology

0 Patents (Medical) associated with Institute of Bioinformatics & Applied Biotechnology

254

Literatures (Medical) associated with Institute of Bioinformatics & Applied Biotechnology

01 Dec 2024·Cellular and Molecular Life Sciences

Delineating the mechanism of fragility at BCL6 breakpoint region associated with translocations in diffuse large B cell lymphoma

Article

Author: Choudhary, Bibha ; Roy, Urbi ; Sharma, Shivangi ; Javedakar, Saniya M ; Gopalakrishnan, Vidya ; Srivastava, Shikha ; Raghavan, Sathees C ; Kariya, Khyati M

BCL6 translocation is one of the most common chromosomal translocations in cancer and results in its enhanced expression in germinal center B cells. It involves the fusion of BCL6 with any of its twenty-six Ig and non-Ig translocation partners associated with diffuse large B cell lymphoma (DLBCL). Despite being discovered long back, the mechanism of BCL6 fragility is largely unknown. Analysis of the translocation breakpoints in 5' UTR of BCL6 reveals the clustering of most of the breakpoints around a region termed Cluster II. In silico analysis of the breakpoint cluster sequence identified sequence motifs that could potentially fold into non-B DNA. Results revealed that the Cluster II sequence folded into overlapping hairpin structures and identified sequences that undergo base pairing at the stem region. Further, the formation of cruciform DNA blocked DNA replication. The sodium bisulfite modification assay revealed the single-strandedness of the region corresponding to hairpin DNA in both strands of the genome. Further, we report the formation of intramolecular parallel G4 and triplex DNA, at Cluster II. Taken together, our studies reveal that multiple non-canonical DNA structures exist at the BCL6 cluster II breakpoint region and contribute to the fragility leading to BCL6 translocation in DLBCL patients.

15 Oct 2024·The Journal of Immunology

Understanding the Role of miR-29a in the Regulation of RAG1, a Gene Associated with the Development of the Immune System

Article

Author: Roy, Urbi ; Raghavan, Sathees C. ; Choudhary, Bibha ; Desai, Sagar Sanjiv ; Kumari, Susmita ; Bushra, Tanzeem

AbstractThe process of Ag receptor diversity is initiated by RAGs consisting of RAG1 and RAG2 in developing lymphocytes. Besides its role as a sequence-specific nuclease during V(D)J recombination, RAGs can also act as a structure-specific nuclease leading to genome instability. Thus, regulation of RAG expression is essential to maintaining genome stability. Previously, the role of miR29c in the regulation of RAG1 was identified. In this article, we report the regulation of RAG1 by miR-29a in the lymphocytes of both mice (Mus musculus) and humans (Homo sapiens). The level of RAG1 could be modulated by overexpression of miR-29a and inhibition using anti-miRs. Argonaute2-immunoprecipitation and high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation studies established the association of miR-29a and RAG1 with Argonaute proteins. We observed a negative correlation between miR-29a and RAG1 levels in mouse B and T cells and leukemia patients. Overexpression of pre–miR-29a in the bone marrow cells of mice led to the generation of mature miR-29a transcripts and reduced RAG1 expression, which led to a significant reduction in V(D)J recombination in pro-B cells. Importantly, our studies are consistent with the phenotype reported in miR-29a knockout mice, which showed impaired immunity and survival defects. Finally, we show that although both miR-29c and miR-29a can regulate RAG1 at mRNA and protein levels, miR-29a substantially impacts immunity and survival. Our results reveal that the repression of RAG1 activity by miR-29a in B cells of mice and humans is essential to maintain Ig diversity and prevent hematological malignancies resulting from aberrant RAG1 expression in lymphocytes.

04 Oct 2024·Journal of Proteome Research

AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function

Article

Author: Vishwakarma, Aman ; Thiyagarajan, Saravanamuthu ; Padmashali, Namrata

The rapid expansion of biological sequence databases due to high-throughput genomic and proteomic sequencing methods has left a considerable number of identified protein sequences with unclear or incomplete functional annotations. Domains of unknown function (DUFs) are protein domains that lack functional annotations but are present in numerous proteins. To address the challenge of finding functional annotations for DUFs, we have developed a computational method that efficiently identifies and annotates these enigmatic protein domains by utilizing the position-specific iterative basic local alignment search tool (PSI-BLAST) and data mining techniques. Our pipeline identifies putative potential functionalities of DUFs, thereby decreasing the gap between known sequences and functions. The tool can also take user input sequences to annotate. We executed our pipeline on 5111 unique DUF sequences obtained from Pfam, resulting in putative annotations for 2007 of these. These annotations were subsequently incorporated into a comprehensive database and interfaced with a web-based server named "AnnoDUF". AnnoDUF is freely accessible to both academic and industrial users, via the World Wide Web at the link http://bts.ibab.ac.in/annoduf.php. All scripts used in this study are uploaded to the GitHub repository, and these can be accessed from https://github.com/BioToolSuite/AnnoDUF.

100 Deals associated with Institute of Bioinformatics & Applied Biotechnology

100 Translational Medicine associated with Institute of Bioinformatics & Applied Biotechnology

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Institute of Bioinformatics & Applied Biotechnology

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