Ruth Cruz-Cosme

Pathogenic variants of MSH3 can increase mutational load within colorectal cells, which may drive initiation and progression of colorectal cancer (CRC). We identified several variants within MSH3 among CRCs from African Americans (AA). To predict and assess the functional significance of these MSH3 variants, we employed a combination of in silico analyses and in vitro functionality assays. Our objective was to elucidate the correlation between computational predictions and functional outcomes. Methods: A CRISPR‐Cas9 knock‐in approach was used to introduce and generate specific point mutations in Exons 21, 22, and 23 of MSH3 in the wild‐type (WT) MSH3 CRC cell line SW620, which was confirmed with Sanger sequencing. We employed cell proliferation, microsatellite instability assays, and whole genome sequencing to assess biological and genetic consequences. We utilized immunofluorescence, Western blot, and coimmunoprecipitation methods to assess subcellular localization and differences in heterodimer MSH2 binding between WT and variant MSH3 proteins. Results: We previously identified six novel, potentially pathogenic nonsynonymous variants (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, and c.G3241A) within six exons (Exons 8 (E413K), 9 (S466N), 20 (S920F), 21 (E976K), 22 (H1010Y), and 23 (E1081K), respectively) of MSH3 among AA CRCs as assessed by computational bioinformatic and molecular dynamic simulation analysis. We successfully knocked in three of the MSH3 variants (Exons 21, 22, and 23). Biological phenotypic assays revealed no observable changes in cell morphology or proliferation between WT and MSH3 ‐variant knocked‐in cells, and no differences were observed in microsatellite assays. Subcellular localization of variant MSH3 protein was unaffected compared with WT, whereas the interaction between MSH3 and MSH2 was not impacted. Short tandem repeats (STRs), or microsatellites, are short DNA motifs of two to six base pairs repeated consecutively, and they serve as powerful genetic markers for studying inheritance patterns and disease‐associated repeat instability. In our analysis, STR profiling revealed both repeat expansions and contractions across multiple motifs, with tetranucleotide repeats showing the most pronounced alterations. Notably, loci flanking LINC00550 (ATTT), FBXL7 (AGAT), and DUSP28 (CTTT/GTTT) displayed consistent repeat expansions (+1.5 to +2), whereas intronic regions within GPC5 , TMEM232 , and ABCA13 exhibited contractions. Trinucleotide STRs revealed a mix of instability, with repeat gains at SLC25A12 and losses near GTF3C3 and AKAP12 . Pentanucleotide and hexanucleotide motifs were more stable overall, but expansions were still noted at CNTN5 , CPEB1 , and CBSL , and contractions at SGO1 and FER . These findings highlight the bidirectional and motif‐specific nature of STR instability driven by MSH3 deficiency. Our results support the utility of STR‐based assays as sensitive tools to detect nonclassical MSI events and deepen our understanding of MSH3 ′s role in preserving microsatellite integrity across the genome. Conclusion: This study investigated the functional consequences of MSH3 variants identified among AA CRCs. While CRISPR‐Cas9 knock‐in of MSH3 variants (Exons 21, 22, and 23) in SW620 cells did not alter cell morphology, proliferation, protein localization, or MSH2 binding, we observed genetic changes that collectively underscore the bidirectional nature of STR instability in MSH3 ‐deficient cells and reinforce this protein′s pivotal role in suppressing slippage at longer repeat motifs. This study advances our understanding of how MSH3 deficiency contributes to genomic instability beyond canonically defined MSI loci, offering novel insights into the mutational landscapes of MMR‐deficient tumors and how these MSH3 mutations can potentially contribute to the outcome of AA CRC patients.

Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150’s binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single point mutation at the pp150-MCP interface significantly attenuated viral replication, unlike the situation of pp150-deletion mutation where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150 K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.

Circular RNAs (circRNAs) are a newly recognized component of the transcriptome with critical roles in autoimmune diseases and viral pathogenesis. To address the importance of circRNA in RNA viral transcriptome, we systematically identified and characterized circRNAs encoded by the RNA genomes of betacoronaviruses using both bioinformatical and experimental approaches. We predicted 351, 224, and 2764 circRNAs derived from severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), SARS‐CoV, and Middle East respiratory syndrome coronavirus, respectively. We experimentally identified 75 potential SARS‐CoV‐2 circRNAs from RNA samples extracted from SARS‐CoV‐2‐infected Vero E6 cells. A systematic comparison of viral and host circRNA features, including abundance, strand preference, length distribution, circular exon numbers, and breakpoint sequences, demonstrated that coronavirus‐derived circRNAs had a spliceosome‐independent origin. We further showed that back‐splice junctions (BSJs) captured by inverse reverse‐transcription polymerase chain reaction have different level of resistance to RNase R. Through northern blotting with a BSJ‐spanning probe targeting N gene, we identified three RNase R‐resistant bands that represent SARS‐CoV‐2 circRNAs that are detected cytoplasmic by single‐molecule and amplified fluorescence in situ hybridization assays. Lastly, analyses of 169 sequenced BSJs showed that both back‐splice and forward‐splice junctions were flanked by homologous and reverse complementary sequences, including but not limited to the canonical transcriptional regulatory sequences. Our findings highlight circRNAs as an important component of the coronavirus transcriptome, offer important evaluation of bioinformatic tools in the analysis of circRNAs from an RNA genome, and shed light on the mechanism of discontinuous RNA synthesis.