Biology subjects

Bakhle, K. M.

Publications and source records attributed to Bakhle, K. M..

5 recordsLinked to original sources

bioRxiv2026

MHC-I downregulation is associated with immune-evasion in breast cancers with heterogeneous activation of epithelial-mesenchymal plasticity

Cancer cell-intrinsic epithelial-mesenchymal plasticity (EMP) drives carcinoma progression through increased intratumoral heterogeneity and an immunosuppressive tumor microenvironment (TME). Specifically, EMP activation in murine mammary carcinomas results in exclusion of CD8+ T-cells and recruitment of immunosuppressive M2-like macrophages, resulting in resistance to anti-CTLA-4 immune checkpoint blockade (ICB) therapy. Notably, mixed E-qM tumors in which only 10% of cancer cells have activated EMP are resistant anti-CTLA-4 immune checkpoint blockade (ICB) therapy. This suggests that minority fractions of qM cancer cells could, in theory, exert immunosuppressive effects on surrounding E cancer and immune cells to shield the entire heterogeneous tumor against immune attack. However, this has not yet been demonstrated. Here, we use spatial transcriptomic profiling to demonstrate that mixed E-qM tumors assemble immunosuppressive cellular niches. Furthermore, E cancer cells within mixed E-qM tumors experience long-term MHC-I downregulation leading to resistance to elimination by CD8+ T-cells. This is associated with the exclusion of T-cells from the tumor core and a dysfunctional phenotype in the remaining CD8+ T-cells. qM cancer cells recruit immunosuppressive M2-like macrophages to mixed tumors, which further downregulates E cancer cell-intrinsic MHC-I levels. Finally, we demonstrate that human triple-negative breast cancers with increased EMP activation exclude T-cells from the tumor core. Together, these findings reveal that qM cancer cells modulate the immune infiltrate of mixed tumors, promoting MHC-I downregulation and evasion of immunological control by CD8+ T-cells.

cancer biology↗

bioRxiv2026

Feline mammary carcinomas display evidence of stemness, epithelial-mesenchymal plasticity, and metastasis-associated M2-like macrophage infiltration

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer-a consequence of high proliferation rates, stemness, epithelial-mesenchymal plasticity, and immune evasion. Feline mammary carcinomas (FMCs) are spontaneous mammary gland cancers associated with high rates of metastasis and death. The aggressive biological behavior of FMCs, as well as their lack of expression of hormone receptors, make FMCs an excellent naturally-occurring model of human triple-negative breast cancer (TNBC). Therefore, we investigated whether FMCs of increasing histologic grade (I-III) harbor characteristics comparable to human TNBC. We performed immunohistochemistry using markers of proliferation (Ki67), stemness (Sox2), and epithelial-mesenchymal plasticity (E-cadherin, vimentin). We found that FMCs expressed high levels of Sox2 and vimentin together with a grade-associated increase in Ki67 expression. Apart from these cancer cell-intrinsic properties, knowledge on the tumor microenvironment of FMCs is limited. To this end, we assessed the presence of T-cells (CD3), total macrophages (Iba1), and immunosuppressive M2-like macrophages (CD204) in FMCs. High-grade FMCs showed increased M2-like macrophage infiltration. Moreover, samples with evidence of vascular invasion and lymph node metastasis displayed increased total and M2-like macrophage infiltration. These findings suggest that the presence of intratumoral macrophages is associated with the biological aggressiveness and metastatic potential of FMCs. Taken together, our results support FMCs as a translational model of human TNBC.

cancer biology↗

bioRxiv2025

Epithelial-Mesenchymal Plasticity is Associated with Immunosuppressive Features in Canine Mammary Carcinomas

Epithelial-mesenchymal plasticity (EMP) is a cellular process activated in carcinoma cells to drive invasiveness, metastasis, and chemoresistance. Recently, we have demonstrated that activation of the EMP program also results in the assembly of an immunosuppressive tumor microenvironment and resistance to immunotherapy in an immunocompetent orthotopic murine model. However, it has yet to be shown whether these findings can be translated to canine carcinomas. Here, we show that in spontaneous canine mammary carcinomas (CMCs), which share similar histopathologic, molecular, and clinical features with human breast cancers, EMP activation is linked to the recruitment of immunosuppressive cells including regulatory T-cells and M2-like macrophages. Additionally, through transcriptomic profiling of CMCs, we identify that the glycoprotein CD109 is associated with EMP-mediated immunosuppression across canine, murine, and human breast cancer models. CD109 has been previously associated with tumorigenicity, but not immunosuppression in cancers of any species. Finally, we identified upregulation of several immunosuppressive paracrine factors across multiple canine carcinomas, including oral squamous cell carcinoma, urothelial carcinoma, and pulmonary carcinoma samples. These findings demonstrate for the first time that the EMP program is associated with immunosuppression in canine carcinomas, with direct translational implications for human breast cancers.

cancer biology↗

bioRxiv2022

Establishing the contribution of active histone methylation marks to the aging transcriptional landscape of Drosophila photoreceptors

Studies in multiple organisms have shown that aging is accompanied by several molecular phenotypes that include dysregulation of chromatin. Since chromatin regulates DNA-based processes such as transcription, alterations in chromatin modifications could impact the transcriptome and function of aging cells. In flies, as in mammals, the aging eye undergoes changes in gene expression that correlate with declining visual function and increased risk of retinal degeneration. However, the causes of these transcriptome changes are poorly understood. Here, we profiled chromatin marks associated with active transcription in the aging Drosophila eye to understand how chromatin modulates transcriptional outputs. We found that both H3K4me3 and H3K36me3 globally decrease across all actively expressed genes with age. However, we found no correlation with changes in differential gene expression. Downregulation of the H3K36me3 methyltransferase Set2 in young photoreceptors revealed significant changes in splicing events that overlapped significantly with those observed in aging photoreceptors. These overlapping splicing events impacted multiple genes involved in phototransduction and neuronal function. Since proper splicing is essential for visual behavior, and because aging Drosophila undergo a decrease in visual function, our data suggest that H3K36me3 plays a role in maintaining visual function in the aging eye through regulating alternative splicing.

genomics↗

bioRxiv2021

The Clock:cycle complex is a major transcriptional regulator of Drosophila photoreceptors that protects the eye from retinal degeneration and oxidative stress

The aging eye experiences physiological changes that include decreased visual function and increased risk of retinal degeneration. Although there are transcriptomic signatures in the aging retina that correlate with these physiological changes, the gene regulatory mechanisms that contribute to cellular homeostasis during aging remain to be determined. Here, we integrated ATAC-seq and RNA-seq data to identify 61 transcription factors that showed differential activity in aging Drosophila photoreceptors. These 61 age-regulated transcription factors include two circadian regulators, Clock and cycle, that showed sustained increases in activity during aging. When we disrupted Clock activity in adult photoreceptors, we observed changes in expression of 15 - 20% of genes including key components of the phototransduction machinery and many eye-specific transcription factors. Using ATAC-seq, we showed that loss of Clock activity leads to changes in activity of 31 transcription factors and causes a progressive decrease in global levels of chromatin accessibility in photoreceptors. Supporting a key role for Clock-dependent transcription in the eye, disruption of Clock activity in photoreceptors also induced light-dependent retinal degeneration and increased oxidative stress, independent of light exposure. Together, our data suggests that the circadian regulators Clock and cycle act as neuroprotective factors in the aging eye by directing gene regulatory networks that maintain expression of the phototransduction machinery and counteract oxidative stress.

genomics↗