Biology subjects

Dhamija, S.

Publications and source records attributed to Dhamija, S..

4 recordsLinked to original sources

bioRxiv2026

5-Iodotubercidin inhibits Epithelial to Mesenchymal Transition by inhibiting IKK/NFκB-dependent gene expression

Epithelial to mesenchymal transition (EMT) is a process of trans-differentiation important for development, inflammation and cancer. Transforming Growth Factor-{beta} (TGF{beta}) is a physiologically relevant inducer of EMT. We had recently characterized the adenosine analogue, adenosine kinase inhibitor 5-Iodotubercidin (5-ITu), as a compound which preferentially sensitizes MK2-deficient cells to TNF-induced, RIPK1-dependent cell death. Here we investigated the effect of 5-ITu on TGF{beta}-induced EMT. 5-ITu suppressed TGF{beta}-induced morphological changes and migration in A549 (lung cancer) and PANC1 (pancreatic cancer) cell lines. Consistent with these effects, there was significant suppression of EMT markers as indicated by qPCR, immunoblotting and immunofluorescence and confocal microscopy. Mechanistic investigations revealed that 5-ITu-mediated EMT suppression was independent of adenosine kinase inhibition and RIPK1 activation. 5-ITu suppressed NF{kappa}B activity in cells undergoing EMT and IKK inhibition phenocopied the effect of 5-ITu on EMT. Kinase assays revealed IKK{beta} as a potential direct target of 5-ITu. We identified a TGF{beta}-associated, NF{kappa}B-dependent gene signature consisting of 4 genes, which are differentially regulated upon 5-ITu treatment. Interestingly, this 4 gene signature could predict survival in lung and pancreatic cancer. The identification of this role for the multitarget kinase inhibitor 5-ITu in NF{kappa}B activity-dependent EMT, in addition to RIPK1-dependent necroptosis has potential implications in anticancer strategies.

cell biology↗

bioRxiv2026

Genome-wide annotation and analyses of bifunctional genes in the human genome

Conventional gene annotation pipelines classify eukaryotic genes into protein-coding and non-coding. Alternative splicing may generate non-coding transcript variants from protein-coding genes, that are expressed in tissue- or disease- specific manner. We and others have described the genes which transcribe both coding and non-coding transcripts as bifunctional genes. Here we present a genome-wide analyses of bifunctional genes and reannotate the genes in the human genome reference assembly into coding, non-coding and bifunctional. We identify over 4000 bifunctional genes in the human genome, constituting approximately 10% of the transcribed genes, and present evidence that these genes are conserved in evolution and their number correlate well with genome size and complexity. These genes are enriched in gene sets involved in vesicular transport, autophagy, RNA/DNA binding, glycosylation and splicing. By monitoring the expression of non-coding exons in long-read sequencing datasets and by quantitative RT-PCR, we provide evidence for the expression of non-coding variants from bifunctional genes. The ncRNA transcripts from these genes might have similar or different roles from their cognate mRNA counterparts. They may act as miRNA sponges or harbour non-canonical open-reading frames that encode microproteins, while also competing for binding with RNA-binding proteins. We present evidence for establishing potential biological functions of bifunctional genes and summarise the findings in a searchable database. Further studies and functional characterization focused on this special group of genes may reveal interesting gene regulatory mechanisms relevant to physiology and pathology.

genomics↗

bioRxiv2023

Kinase inhibitor-induced cell-type specific vacuole formation in the absence of canonical ATG5-dependent autophagy

Pyridinyl imidazole class p38 MAPK/{beta} (MAPK14/MAPK11) inhibitors including SB202190 have been shown to induce a cell-type specific defective autophagy response resulting in micron-scale vacuole formation, autophagy-dependent death, and tumor growth suppression in vivo. We had earlier shown that this is an off-target effect of SB202190. Here we provide evidence that the cell-type specific vacuole formation is independent of canonical autophagy pathway. While SB202190 seems to interfere with autophagic flux in many cell lines in parallel to vacuolation, autophagy-deficient DU-145 cells and CRISPR/Cas9 gene-edited ATG5 knockout A549 cells also undergo vacuolation upon SB202190 treatment. Late-endosomal GTPase RAB7 colocalizes with these compartments and RAB7 GTP-binding seems to be essential for SB202190-induced vacuolation. RAB7 is a driver of tumor progression and interfering with RAB7-positive endo/lysosomal compartments may enhance cytotoxicity. A screen for modulators of SB202190-induced vacuolation revealed molecules including multi-kinase inhibitor Sorafenib as inhibitor of vacuolation and sorafenib co-treatment enhanced the cytotoxicity of SB202190. Moreover VE-821, an ATR kinase inhibitor was found to phenocopy the cell-type specific vacuolation response of SB202190. To identify the factors determining the cell-type specificity of the vacuolation response induced by SB-compounds and VE-821, we compared the transcriptomics data from vacuole forming and non-vacuole forming cancer cell lines and identified a gene expression signature which may define sensitivity of cancer cells to these small-molecule kinase inhibitors. Further analyses using the small molecule tools and the gene signature discovered here, could reveal novel mechanisms regulating this interesting phenotype relevant to anti-cancer therapy.

cell biology↗

bioRxiv2020

Mutation landscape of SARS-CoV-2 reveals three mutually exclusive clusters of leading and trailing single nucleotide substitutions

The COVID-19 pandemic has spread across the globe at an alarming rate. However, unlike any of the previous global outbreaks the availability of a large number of SARS-CoV-2 sequences provides us with a unique opportunity to understand viral evolution in real time. We analysed 1448 full-length (>29000 nt) sequences available and identified 40 single-nucleotide substitutions occurring in >1% of the genomes. Majority of the substitutions were C to T or G to A. We identify C/Gs with an upstream TTT trinucleotide motif as hotspots for mutations in the SARS-CoV-2 genome. Interestingly, three of the 40 substitutions occur within highly conserved secondary structures in the 5 and 3 regions of the genomic RNA that are critical for the virus life cycle. Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. Of note, we observed several co-occurring mutations that almost never occur individually. We define five mutually exclusive lineages (A1, B1, C1, D1 and E1) of SARS-CoV-2 which account for about three quarters of the genomes analysed. We identify lineage-defining leading mutations in the SARS-CoV-2 genome which precede the occurrence of sub-lineage defining trailing mutations. The identification of mutually exclusive lineage-defining mutations with geographically restricted patterns of distribution has potential implications for diagnosis, pathogenesis and vaccine design. Our work provides novel insights on the temporal evolution of SARS-CoV-2. ImportanceThe SARS-CoV-2 / COVID-19 pandemic has spread far and wide with high infectivity. However, the severeness of the infection as well as the mortality rates differ greatly across different geographic areas. Here we report high frequency mutations in the SARS-CoV-2 genomes which show the presence of linage-defining, leading and trailing mutations. Moreover, we propose for the first time, five mutually exclusive clusters of SARS-CoV-2 which account for 75% of the genomes analysed. This will have implications in diagnosis, pathogenesis and vaccine design

genomics↗