Biology subjects

Veerakumarasivam, A.

Publications and source records attributed to Veerakumarasivam, A..

4 recordsLinked to original sources

bioRxiv2025

Genomic alterations in persistently infecting oncolytic Newcastle disease virus reveal mechanisms of viral persistence in bladder cancer cells

AbstractsNewcastle disease virus (NDV) is a promising oncolytic agent with a non-segmented, negative-sense single-stranded RNA (ssRNA) genome of approximately 15 kb. While NDV selectively replicates in and lyses a wide range of human cancer cells, a subset of these cells develop persistent infections, potentially compromising the therapeutic efficacy of NDV-based treatments. To investigate the molecular basis of persistent infection, we performed transcriptome profiling of TCCSUP bladder cancer cells persistently infected with the NDV AF2240 strain. Deep sequencing using Illumina HiSeq 2000 was conducted in triplicate, and the resulting viral and host reads were separated and analyzed. Using Integrative Genomic Viewer (IGV) software, we identified several nucleotide variants linked to persistence. Specifically, nucleotide alterations included a deletion at 359A[->]C and a substitution at 1653C[->]T within the nucleoprotein (NP) gene, as well as an insertion at 3338C[->]T in the matrix protein (M) gene. Additionally, a GGG base insertion was detected at position 2290 in the phosphoprotein (P) gene. Crucially, we observed truncations in the hemagglutinin-neuraminidase (HN) gene (nt 8263-8390) and the large polymerase (L) gene (nt 6203-6342). These mutations and truncations suggest significant disruptions in viral replication, assembly, and host cell attachment, potentially facilitating viral persistence in bladder cancer cells. Understanding these genomic alterations provides valuable insights into the mechanisms driving viral persistence and could inform strategies to optimize the oncolytic efficacy of NDV in cancer therapy.

genomics↗

bioRxiv2022

Evaluation of EN2 Gene as a Potential Biomarker for Bladder Cancer

BackgroundAmong the most prevalent cancers in the urinary tract is bladder cancer, a caner with a high rate of recurrence and metastasis as compared to other malignancies. To date, there have been many genes reported as potential bladder cancer biomarkers among which is the EN2 gene, a member of the homeobox family containing transcriptional factors. Several studies suggested the overexpression of EN2 to be involved with the development of a number of tumors such as bladder cancer. However, the process of involvement of EN2 in the bladder tumorigenesis remains elusive. MethodsRT-qPCR was carried out to determine the gene expression of 17 cell lines. The short-term silencing of EN2 expression was then implemented in high-expressing cell lines using siRNAs. Using the scratch assay, the outcome of modulating the in vitro EN2 expression on the bladder cancer migration was determined. Correlation between the IC50 values with the EN2 expression was analyzed by correlating the viability of cells following the Newcastle Disease Virus infection with the fold change. Immunohistochemistry was then performed to determine the expression of the EN2 protein in the bladder cancer tissues. ResultsIn the current study, EN2 was differentially expressed in bladder cancer in vitro and upon modulating the expression of EN2, we found a reduction in the migratory effect of bladder cancer in vitro. In addition, following 24 hours post infection, a moderate correlation between EN2 gene expression and NDV-mediated oncolysis was observed. No expression of EN2 in bladder cancer tissues suggesting the need for further studies to investigate the expression of EN2 protein in bladder cancer. ConclusionEN2 may be a potential prognostic or diagnostic bladder cancer biomarker, however, further investigations are required to evaluate the EN2 gene as a potential bladder cancer biomarker.

cancer biology↗

bioRxiv2020

Analysis of PPI networks of transcriptomic expression identifies hub genes Associated with Newcastle disease virus persistent infection in bladder cancer

MotivationBladder cancer cells acquire persistent infection associated with oncolytic Newcastle disease virus (NDV) in which its molecular events are still unclear. This poses a potential problem for oncolytic virus application for cancer therapy. To unravel the molecular mechanism underlying the development of NDV persistent infection in bladder cancer, we used mRNA expression profile of the persistently infected bladder cancer cells to construct PPI network. ResultsBased on path and module exploring in the PPI network, the bridges were found mainly from pathways of p53 signalling, ECM-receptor interaction, and TGF-beta signalling by the upregulated mRNAs, to the antigen processing and presentation, protein processing in endoplasmic reticulum, completement and coagulation cascades by the downregulated mRNAs in NDV persistent TCCSUPPi cells. In persistent EJ28Pi cells comparatively, connections were identified mainly from pathways of renal carcinoma, viral carcinogenesis, Ras signalling and cell cycle by the upregulated mRNAs, to the Wnt signalling, HTLV-I infection and pathways in cancer by the downregulated mRNAs. This connection was mainly dependent on of RPL8- HSPA1A/HSPA4 in TCCSUPPi cells and EP300, PTPN11, RAC1 - TP53, SP1, CCND1 and XPO1 in EJ28Pi cells. Oncomine validation showed that the top hub genes identified in the network that includes RPL8, THBS1, F2 from TCCSUPPi and TP53 and RAC1 from EJ28Pi are involved in the development and progression of bladder cancer. Protein-drug interaction network, have identified several drugs targets that could be used to disconnect the linkages between modules and prevent bladder cancer cells from acquiring NDV persistent infection. This is the first time reporting the PPI network analysis of differentially expressed mRNAs of the NDV persistently infected bladder cancer cell lines which provide an insight into screening drugs that could be used together with NDV to manage bladder cancer resistance to therapy and progression.

bioinformatics↗

bioRxiv2020

Functional Transcriptome Analysis of Bladder Cancer Cell Lines Persistently Infected with Oncolytic Newcastle Disease Virus

BackgroundNewcastle disease virus (NDV) has been an attractive virotherapy agent that targets various type of human cancers while leaving normal cells unharmed. Wild-type NDV strain AF2240 has been found to persistently infect subpopulation of cancer cells in vitro, making the cells less susceptible to NDV-mediated oncolysis. It is proposed that transcriptome profiling of NDV persistently infected bladder cancer cell lines will provide insights to understand such occurrence by identifying specific pathways associated with NDV persistent infection due to transcriptomic dysregulation. ResultsTranscriptome profiling revealed a total of 63 and 134 differentially expressed genes (DEGs) from NDV persistently infected TCCSUPPi and EJ28Pi bladder cancer cells relative to their uninfected controls, respectively. Of the 63 DEGs identified for TCCSUPPi cells, 25 DEGs were upregulated (log2 fold-change [≥] 0) and 38 DEGs were downregulated (log2 fold-change [≤] 0). These genes were significantly enriched in the molecular function of calcium binding (GO:0005509) and DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227) and the enriched important upregulated pathways were mainly heme metabolism, TGF-beta signaling and spermatogenesis. As for EJ28Pi, 55 DEGs were upregulated (log2 fold-change [≥] 0) and 79 DEGs were downregulated (log2 fold-change [≤] 0). These DEGs resulted in significantly enriched molecular function such as protein domain specific binding (GO:0019904) and RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977). The enriched important upregulated pathways were allograft rejection, KRAS signaling up and interferon gamma response. Other important pathways that were downregulated in both the NDV-persistently infected cell lines were angiogenesis, apoptosis, and xenobiotic metabolism. ConclusionThe transcriptome profiles (RNA-Seq) of these cell lines suggest that evasion of apoptosis and increase in TGF-beta signaling and interferon gamma response activities are crucial for establishment of NDV persistent infection in bladder cancer cells. Findings from this study provide the molecular basis that warrant further study on how bladder cancer cells acquired NDV persistent infection. Resolving the mechanism of persistent infection will facilitate the application of NDV for more effective treatment of bladder cancer.

cancer biology↗