Biology subjects

Thomas, M. D.

Publications and source records attributed to Thomas, M. D..

5 recordsLinked to original sources

bioRxiv2025

Molecular Plasticity of T Cells Informs Their Possible Adaptation in 4T1 Tumors

BackgroundThe triple-negative breast cancer (TNBC) microenvironment (TME) undergoes progressive reprogramming, transitioning from an early immune-active state to a late immune-suppressed state. While tumor cell plasticity has been extensively studied, the molecular plasticity of T cells in vivo remains poorly defined. ObjectivesTo characterize transcriptional changes in T cells during TNBC progression and identify stage-specific shifts in T cell function, polarization, and antigen-presenting cell (APC)-T cell interactions. ResultsTranscriptional analysis of T cells from BALB/c mice bearing 4T1 tumors at 1, 3, and 6 weeks revealed a decline in T cell-associated genes from 194 at 1 week to 156 at 6 weeks, with a significant late-stage loss of TCR diversity and contraction of natural killer T (NKT)- and {gamma}{delta} T cell-related transcripts. Cytokine and transcription factor dynamics reflected temporal T cell polarization: early (1 week) IL-12/{beta}-STAT4 signaling supports CD4+ type 1 T helper cell (Th1) and type 1 CD8+ cytotoxic T cell (Tc1) responses; intermediate (3 weeks) IL-21 and BCL6 expression suggest transient CD8+ cytotoxic follicular T cell (Tfc) skewing; and late (6 weeks) AhR and IL-1{beta} induction reflect interleukin 17/22 producing CD8+ T cell (Tc17/Tc22) transition. Pro-inflammatory cytokines and chemokines increased over time, while immunosuppressive mediators (e.g., IL-10) declined significantly. Antigen-presenting cell (APC)-T cell crosstalk deteriorated at 6 weeks, characterized by a reduction in the expression of co-stimulatory and APC genes. Despite an early dominance of M1-like macrophage signals (e.g., IL-12/{beta}), persistent expression of arginase 1 (ARG1) and other M2-associated genes indicated a stable tolerogenic niche. ConclusionsTNBC progression is characterized by progressive T cell functional decline, narrowing of TCR diversity, impaired APC-T cell interactions, and sustained macrophage-driven immunosuppression. These temporally coordinated immune shifts suggest tumor-driven adaptation toward immune evasion and identify potential windows for stage-specific immunotherapeutic intervention.

cancer biology↗

bioRxiv2025

Molecular Phenotypic Plasticity Informs Possible Adaptive Change of Triple-Negative Breast Cancer Cells In Vivo

Background and ObjectivesCancer evolves via interconnected mechanisms, including changes in extrachromosomal DNA (ecDNA), genetic instability, and interactions with the tumor microenvironment (TME). These mechanisms allow for some clones to evolve metastatic traits, evade the immune system, and resist chemotherapy. However, how cancer cells evolve in vivo remains poorly understood. This study investigates the in vivo changes in gene expression of triple-negative breast cancer (TNBC) cells implanted in BALB/c mice. MethodologyWe analyzed RNA-seq data from 4T1 TNBC cells and tumors at different growth stages (1-, 3-, and 6-week) to identify differentially expressed genes, protein-protein interactions, and ecDNA alterations. We also assessed how ecDNA and genomic instability proteins interact with anti-TNBC drugs ResultsOur results reveal early transcriptional shifts within one week of tumor implantation, showing rapid acclimation. Changes in gene expression continued over time, with significant molecular reprogramming observed at six weeks under in vivo environmental pressures, including ecDNA alterations and immune evasion. The shift from the earlier generation (1 week) to the later generation (6 weeks) suggests cumulative alterations in key oncogenic pathways related to tumor progression. Additionally, we found that mutations in ecDNA and genomic instability proteins influence drug binding affinity, suggesting that adaptive changes may impact chemotherapy response. Conclusions and ImplicationsThis study provides new insights into how TNBC tumors may evolve over time and novel ecDNA-related mechanisms of possible tumor adaptation, highlighting potential biomarkers for tumor aggression and immune evasion, which could help develop more effective therapeutic strategies against TNBC.

cancer biology↗

bioRxiv2022

Mutant huntingtin exon-1 impaired GTPCH and DHFR expression in plants and mice

Pathophysiology associated with Huntingtons disease (HD) has been studied extensively in various cell and animal models since the 1993 discovery of the mutant huntingtin (mHtt) with abnormally expanded polyglutamine (polyQ) tracts as the causative factor. However, the sequence of early pathophysiological events leading to HD still remains elusive. To gain new insights into the polyQ-induced early pathogenic events, we expressed Htt exon1 (Httex1) with a normal (21), or an extended (42 or 63) number of polyQ in tobacco plants, which lack an Htt ortholog to avoid any associated effects from endogenous Htt. Here, we show that transgenic plants accumulated Httex1 proteins with corresponding polyQ tracts, and that mHttex1 induced protein aggregation and affected plant growth, especially root and root hair development, in a polyQ length-dependent manner. Quantitative proteomic analysis of young roots from severely affected Httex1Q63 and unaffected Httex1Q21 plants showed that the most impaired protein by polyQ63 is a GTP cyclohydrolase I (GTPCH) along with many its related one-carbon (C1) metabolic pathway enzymes. GTPCH is a key enzyme involved in folate biosynthesis in plants and tetrahydrobiopterin (BH4) biosynthesis in mammals. Validating studies in 4-week-old R6/2 HD mice expressing a mHttex1 showed reduced levels of GTPCH and dihydrofolate reductase (DHFR, a key folate utilization/alternate BH4 biosynthesis enzyme), and impaired C1 and BH4 metabolisms. Our findings from mHttex1 plants and mice reveal impaired expressions of GTPCH and DHFR and contribute to a better understanding of mHtt-altered C1 metabolism and C1 interconnected BH4 metabolism leading to the pathogenesis of HD.

molecular biology↗

bioRxiv2020

Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli

Antibiotic resistance is a growing health concern. Efforts to control resistance would benefit from an improved ability to forecast when and how it will evolve. Epistatic interactions between mutations can promote divergent evolutionary trajectories, which complicates our ability to predict evolution. We recently showed that differences between genetic backgrounds can lead to idiosyncratic responses in the evolvability of phenotypic resistance, even among closely related Escherichia coli strains. In this study, we examined whether a strains genetic background also influences the genotypic evolution of resistance. Do lineages founded by different genotypes take parallel or divergent mutational paths to achieve their evolved resistance states? We addressed this question by sequencing the complete genomes of antibiotic-resistant clones that evolved from several different genetic starting points during our earlier experiments. We first validated our statistical approach by quantifying the specificity of genomic evolution with respect to antibiotic treatment. As expected, mutations in particular genes were strongly associated with each drug. Then, we determined that replicate lines evolved from the same founding genotypes had more parallel mutations at the gene level than lines evolved from different founding genotypes, although these effects were more subtle than those showing antibiotic specificity. Taken together with our previous work, we conclude that historical contingency can alter both genotypic and phenotypic pathways to antibiotic resistance. SignificanceA fundamental question in evolution is the repeatability of adaptation. Will independently evolving populations respond similarly when facing the same environmental challenge? This question also has important public-health implications related to the growing problem of antibiotic resistance. For example, efforts to control resistance might benefit from accurately predicting mutational paths to resistance. However, this goal is complicated when a lineages prior history alters its subsequent evolution. We recently found that differences between genetic backgrounds can lead to unpredictable responses in phenotypic resistance. Here, we report that genetic background can similarly alter genotypic paths to resistance. This historical contingency underscores the importance of accounting for stochasticity, in the past as well as at present, when designing evolutionarily informed treatment strategies.

evolutionary biology↗

bioRxiv2017

Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes cis-Regulatory Elements

PurposeDNA methylation is a well characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of synthesizing a strand of RNA from DNA, or transcription, is controlled by proteins that regulate RNA polymerase activity by binding to specific gene regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell specific gene expression. While much is known about the functions and DNA binding specificity of CRX, less is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements.\n\nMethodsWe used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO, PDE6B, PAX6, and LINE. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences.\n\nResultsIn this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to our DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate that changes to the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX dependent transcription.\n\nConclusionCollectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.

molecular biology↗