Vishal Koparde | Virginia Commonwealth University (original) (raw)

Papers by Vishal Koparde

Methods in pharmacology and toxicology, 2015

Oncotarget, Apr 6, 2018

We report a novel mechanism of action of ONC201 as a mitochondria-targeting drug in cancer cells.... more We report a novel mechanism of action of ONC201 as a mitochondria-targeting drug in cancer cells. ONC201 was originally identified as a small molecule that induces transcription of TNF-related apoptosis-inducing ligand (TRAIL) and subsequently kills cancer cells by activating TRAIL death receptors. In this study, we examined ONC201 toxicity on multiple human breast and endometrial cancer cell lines. ONC201 attenuated cell viability in all cancer cell lines tested. Unexpectedly, ONC201 toxicity was not dependent on either TRAIL receptors nor caspases. Time-lapse live cell imaging revealed that ONC201 induces cell membrane ballooning followed by rupture, distinct from the morphology of cells undergoing apoptosis. Further investigation found that ONC201 induces phosphorylation of AMP-dependent kinase and ATP loss. Cytotoxicity and ATP depletion were significantly enhanced in the absence of glucose, suggesting that ONC201 targets mitochondrial respiration. Further analysis indicated that ONC201 indirectly inhibits mitochondrial respiration. Confocal and electron microscopic analysis demonstrated that ONC201 triggers mitochondrial structural damage and functional impairment. Moreover, ONC201 decreased mitochondrial DNA (mtDNA). RNAseq analysis revealed that ONC201 suppresses expression of multiple mtDNA-encoded genes and nuclear-encoded mitochondrial genes involved in oxidative phosphorylation and other mitochondrial functions. Importantly, fumarate www.oncotarget.com

Cancer Epidemiology, Biomarkers & Prevention, 2023

African American (AA) women are at increased risk of developing and dying from Triple-Negative Br... more African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remain underexplored. Using ATAC-sequencing, we characterized differences in chromatin accessibility between EA-derived versus AA-derived breast cancer cell lines across a range of breast cancer subtypes. Interestingly, our principal component analysis of the top 50,000 peaks with the most variance revealed separation of chromatin profiles by genetic ancestry specifically in TNBC cell lines (N=10). Digital footprinting analysis of differentially open chromatin regions using TOBIAS revealed significant differences in transcription factor (TF) binding by ancestry (61 TFs with a differential binding score > 0.25 or < -0.25 and FDR < 0.01). AA TNBC cell lines exhibited increased binding of transcription factors associated with epithelial-to-mesenchymal transition (ZEB1, SNAI1, GRHL2), cancer stemness and chemotherapeutic resistance (TFAP2C, NRF1), and others such as KAISO, whose aberrant expression has been previously linked to a distinct biology and poor outcomes in AA breast and prostate cancer patients. Pathway analysis of genes located within promoters of differentially open chromatin regions reveals enrichment of the following KEGG pathways in AA TNBC cells: inflammatory mediator regulation of TRP channels (p-adj = 0.009), Hippo signaling (p-adj = 0.006), Wnt signaling (p-adj = 0.031), and Rap-1 signaling (p-adj = 0.046). Together, these data reveal a differential chromatin landscape associated with the aberrant activity of critical TFs and downstream gene expression changes that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. Citation Format: Alexandra R. Harris, Vishal Koparde, Gatikrushna Panigrahi, Maeve Bailey-Whyte, Tiffany Dorsey, Stefan Ambs. Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C054.

TechConnect Briefs, May 8, 2005

During the vapor-phase synthesis of titanium dioxide (TiO 2) nanoparticles, sintering of the nano... more During the vapor-phase synthesis of titanium dioxide (TiO 2) nanoparticles, sintering of the nanoparticles is an important aspect of their behavior and an understanding of this phenomenon is therefore important. In this work, molecular dynamics (MD) simulations of the coalescence of TiO 2 nanoparticles have been carried out. The driving force for sintering of nanoparticles is the reduction in potential energy due to the decrease in surface area. The loss of potential energy manifests itself as an increase in the temperature of the sintering particles. This work concentrates on 3 and 4nm anatase and rutile nanoparticles. Dependence of particle orientation on sintering is reported along with ion mobility studies in the core and neck regions.

Molecular therapy. Nucleic acids, Jun 1, 2022

PLOS ONE, Jan 5, 2011

Background: The quality of X-ray crystallographic models for biomacromolecules refined from data ... more Background: The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at highresolution is assured by the data itself. However, at low-resolution, .3.0 Å , additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery. Methodology: An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology. Results: The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the lowresolution limit, 4.0A˚,thenewprotocolgeneratedmodelswithCapositionsthathaveRMSDsthatare0.18A˚moresimilartothereferencehigh−resolutionstructure,Ramachandranscoresimprovedby134.0 Å , the new protocol generated models with Ca positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions 4.0A˚,thenewprotocolgeneratedmodelswithCapositionsthathaveRMSDsthatare0.18A˚moresimilartothereferencehigh−resolutionstructure,Ramachandranscoresimprovedby134.0 Å , these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool.

Neoplasia, Apr 1, 2019

Chromosomal aneuploidy is a defining feature of carcinomas and results in tumor-entity specific g... more Chromosomal aneuploidy is a defining feature of carcinomas and results in tumor-entity specific genomic imbalances. For instance, most sporadic colorectal carcinomas carry extra copies of chromosome 7, an aneuploidy that emerges already in premalignant adenomas, and is maintained throughout tumor progression and in derived cell lines. A comprehensive understanding on how chromosomal aneuploidy affects nuclear organization and gene expression, i.e., the nucleome, remains elusive. We now analyzed a cell line established from healthy colon mucosa with a normal karyotype (46,XY) and its isogenic derived cell line that acquired an extra copy of chromosome 7 as its sole anomaly (47,XY,+7). We studied structure/function relationships consequent to aneuploidization using genome-wide chromosome conformation capture (Hi-C), RNA sequencing and protein profiling. The gain of chromosome 7 resulted in an increase of transcript levels of resident genes as well as genome-wide gene and protein expression changes. The Hi-C analysis showed that the extra copy of chromosome 7 is reflected in more interchromosomal contacts between the triploid chromosomes. Chromatin organization changes are observed genome-wide, as determined by changes in A/B compartmentalization and topologically associating domain (TAD) boundaries. Most notably, chromosome 4 shows a profound loss of chromatin organization, and chromosome 14 contains a large A/B compartment switch region, concurrent with resident gene expression changes. No changes to the nuclear position of the additional chromosome 7 territory were observed when measuring distances of chromosome painting probes by interphase FISH. Genome and protein data showed enrichment in signaling pathways crucial for malignant transformation, such as the HGF/MET-axis.

BMC Bioinformatics, Dec 1, 2016

Background: Recent advances in next-generation sequencing have revolutionized genomic research. 1... more Background: Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis. Results: We have developed the Merging and Filtering Tool (MeFiT) to combine these pre-processing steps into one simple, intuitive pipeline. MeFiT invokes CASPER (context-aware scheme for paired-end reads) for merging paired-end reads and provides users the option to quality filter the reads using the traditional average Q-score metric or using a maximum expected error cutoff threshold.

Methods, Dec 1, 2021

Circular forms of RNA were first discovered in plant viroids and later found in a variety of anim... more Circular forms of RNA were first discovered in plant viroids and later found in a variety of animal viruses. These circular RNAs lack free 5’ and 3’ ends, granting protection from exonucleases. This review is focused on the methods that are used to investigate virus-encoded circular RNAs. Using DNA viruses that are prevalent among human as examples, we begin with features of circular RNAs and the unique methods to enrich for circular RNAs. Next, we discuss the computational methods for RNA-sequencing analysis to discover new virus-encoded circular RNAs. Many strategies are similar to analyzing cellular RNAs, but some unique aspects of virus-encoded circular RNAs that are likely due to highly packed viral genomes and non-canonical use of splicing machinery, are described herein. We illustrate the various methods of validating expression of specific virus-encoded circular RNAs. Finally, we discuss methods to study functions of circular RNAs and the current technical challenges that remain for investigating virus-encoded circular RNAs.

Journal of Physical Chemistry C, Apr 24, 2007

... Vishal N. Koparde* and Peter T. Cummings. Department of Chemical Engineering, Vanderbilt Univ... more ... Vishal N. Koparde* and Peter T. Cummings. Department of Chemical Engineering, Vanderbilt University, VU Station B 351604, Nashville, Tennessee 37235. J. Phys. Chem. C , 2007, 111 (19), pp 69206926. DOI: 10.1021/jp0666380. ...

Nature Immunology, Jul 13, 2023

Journal of Immunology, Feb 1, 2021

The expression and turnover of Ag-specific peptide–MHC class II (pMHC-II) on the surface of dendr... more The expression and turnover of Ag-specific peptide–MHC class II (pMHC-II) on the surface of dendritic cells (DCs) is essential for their ability to efficiently activate CD4 T cells. Ubiquitination of pMHC-II by the E3 ubiquitin ligase March-I regulates surface expression and survival of pMHC-II in DCs. We now show that despite their high levels of surface pMHC-II, MHC class II (MHC-II) ubiquitination–deficient mouse DCs are functionally defective; they are poor stimulators of naive CD4 T cells and secrete IL-12 in response to LPS stimulation poorly. MHC-II ubiquitination–mutant DC defects are cell intrinsic, and single-cell RNA sequencing demonstrates that these DCs have an altered gene expression signature as compared with wild-type DCs. Curiously, these functional and gene transcription defects are reversed by activating the DCs with LPS. These results show that dysregulation of MHC-II turnover suppresses DC development and function.

arXiv (Cornell University), Dec 10, 2015

Next generation sequencing technology rapidly produces massive volume of data and quality control... more Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on maximum expected error as a percentage of read length (MEEP score) to filter, trim, truncate and assess next generation DNA sequencing data in FASTQ file format. MEEPTOOLS provides a non-traditional approach towards read filtering/trimming based on maximum error probabilities of the bases in the read on a nonlogarithmic scale. This method simultaneously retains more reliable bases and removes more unreliable bases than the traditional quality filtering strategies.

Journal of Translational Medicine

Background Kaposi sarcoma (KS) is a multicentric tumor caused by Kaposi sarcoma herpesvirus (KSHV... more Background Kaposi sarcoma (KS) is a multicentric tumor caused by Kaposi sarcoma herpesvirus (KSHV) that leads to morbidity and mortality among people with HIV worldwide. KS commonly involves the skin but can occur in the gastrointestinal tract (GI) in severe cases. Methods RNA sequencing was used to compare the cellular and KSHV gene expression signatures of skin and GI KS lesions in 44 paired samples from 19 participants with KS alone or with concurrent KSHV-associated diseases. Analyses of KSHV expression from KS lesions identified transcriptionally active areas of the viral genome. Results The transcript of an essential viral lytic gene, ORF75, was detected in 91% of KS lesions. Analyses of host genes identified 370 differentially expressed genes (DEGs) unique to skin KS and 58 DEGs unique to GI KS lesions as compared to normal tissue. Interleukin (IL)-6 and IL-10 gene expression were higher in skin lesions as compared to normal skin but not in GI KS lesions. Twenty-six cellular ...

Figure 2B). Transcriptome analysis by Nanostring technology comparing 10 days post-HCT CD4 T cell... more Figure 2B). Transcriptome analysis by Nanostring technology comparing 10 days post-HCT CD4 T cells from MyD88-/versus WT recipients showed lower levels of Irak1, Il1rl1 (gene of ST2), Ifng, Csf2, Stat5, and Jak2 (Figure 2C) as well as a decrease in systemic plasma sST2 (Figure 2D) and IFN-γ levels (Figure 2E). As we have previously shown for ST2 deficient donor T cells, we hypothesize that MyD88 deficiency in donor T cells will reduce the ratio of sST2-secreting T cells to mST2expressing T cells during aGVHD. We are currently repeating these experiments to confirm these data at the protein level. We found that loss of MyD88 signaling in donor CD4 Tconvs increases Tregs suppression through loss of ST2 signaling in Tconvs, alleviating aGVHD. This suggests that Tregs suppression from lack of MyD88 signaling in Tconvs during alloreactivity uses the ST2 but not the IL-1R pathway, possibly by different antigen stimulation. MyD88 represents an aGVHD therapeutic target sparing Treg function.

Biology of Blood and Marrow Transplantation, May 1, 2016

Microbiology, Mar 1, 2016

Vaginal lactobacilli can inhibit colonization by and growth of other bacteria, thereby preventing... more Vaginal lactobacilli can inhibit colonization by and growth of other bacteria, thereby preventing development of bacterial vaginosis (BV). Amongst the lactobacilli, Lactobacillus crispatus appears to be particularly effective at inhibiting growth of BV-associated bacteria. Nonetheless, some women who are colonized with this species can still develop clinical BV. Therefore, we sought to determine whether strains of L. crispatus that colonize women with lactobacillidominated vaginal microbiomes are distinct from strains that colonize women who develop BV. The genomes of L. crispatus isolates from four women with lactobacilli-dominated vaginal microbiomes (,1 % 16S rRNA reads above threshold from genera other than Lactobacillus) and four women with microbiomes containing BV-associated bacteria (.12 % 16S rRNA reads from bacterial taxa associated with BV) were sequenced and compared. Lactic acid production by the different strains was quantified. Phage induction in the strains was also analysed. There was considerable genetic diversity between strains, and several genes were exclusive to either the strains from Lactobacillus-dominated microbiomes or those containing BV-associated bacteria. Overall, strains from microbiomes dominated by lactobacilli did not differ from strains from microbiomes containing BV-associated bacteria with respect to lactic acid production. All of the strains contained multiple phage, but there was no clear distinction between the presence or absence of BV-associated bacteria with respect to phage-induced lysis. Genes found to be exclusive to the Lactobacillus-dominated versus BV-associated bacteria-containing microbiomes could play a role in the maintenance of vaginal health and the development of BV, respectively.

International Journal of Computational Biology and Drug Design, 2017