Biology subjects

Tharmapalan, P.

Publications and source records attributed to Tharmapalan, P..

5 recordsLinked to original sources

bioRxiv2026

Germline BRCA1 Mutation Deregulates Irradiation-Induced Cell Cycle Checkpoints in Human Mammary Luminal Progenitors

Mammary ductal tree comprises two epithelial lineages, basal and luminal, which harbour stem and progenitor cell subsets essential to breast physiology and are cancer-initiating precursors. Dysregulated cellular stress response is an early event in tumorigenesis, yet lineage-rooted study of primary breast epithelium pertinent to familial mutation carriers is limited. Here, we establish a lineage-resolved monolayer culture system that enables propagation of primary human mammary epithelial populations while preserving lineage identity across passages. We identify intrinsically distinct cell cycle response of luminal progenitors and basal cells to irradiation stress where the former engages both G1/S and G2/M checkpoints to achieve cell cycle arrest and the latter relies on the G2/M checkpoint. These lineage distinctions are diminished in germline BRCA1 mutation carriers with an attenuated G1/S checkpoint in luminal progenitors. Paired transcriptomic-proteomic profiling of acute irradiation response uncovers BRCA1+/- luminal progenitor population with sustained AKT-mTOR signaling and compromised cell cycle arrest marking an early deviation in the stress response of these purported cells-of-origin of aggressive breast cancers known to arise in BRCA1 germline mutation carriers. Our study provides a functional framework for determining critical events in the expansion of genomically altered mammary epithelial cells in the high-risk breast to enable future preventive interventions.

cell biology↗

bioRxiv2026

Mapping lineage and functional diversity in the high-risk human mammary epithelium

BackgroundBreast cancer risk is shaped by the vast heterogeneity of mammary epithelial cells, comprising basal, luminal progenitor, and mature luminal populations. While transcriptional variation among these lineages has been extensively studied, protein-level features - particularly in high-risk women - remain underexplored, limiting insight into early cellular and molecular determinants of susceptibility. Moreover, little is known about how clinical covariates influence clonogenic capacity, proteomic states, and epithelial proportions, complicating the design of properly controlled human studies of early breast cancer risk. ResultsWe combined low-input proteomics with functional clonogenic assays to profile mammary epithelial cell subpopulations from a cohort of 21 breast tissues encompassing different germline mutation backgrounds, parity status and age. We quantified over 5,555 proteins and observed marked inter-donor variation in epithelial composition, proteomic programs, and colony-forming capacity. Multivariable modeling revealed that clinical covariates - including age, parity, and germline mutation status - modulate both global proteomic architecture and lineage-specific pathway activity. Parity was associated with reduced basal cell abundance, altered luminal progenitor and mature luminal proteomes, and changes in clonogenicity. Pathway analyses identified both conserved and lineage-restricted responses to shared risk factors. Projection of clonogenic signatures onto METABRIC and TCGA tumors further linked functional programs to tumor subtypes and clinical outcomes. ConclusionsThis study provides the most comprehensive proteomic atlas of cell-type resolved diversity in the high-risk breast to date. By defining how clinical covariates remodel epithelial composition and molecular state, it clarifies key sources of biological variability that challenge controlled study design and offers a resource for improving mechanistic insight, risk assessment, and prevention strategies.

cancer biology↗

bioRxiv2025

Progesterone Receptor Expressing Basal Cells and Progesterone Receptor-Primed Progenitors Redefine the Mammary Epithelial Hierarchy

The central role of progesterone in breast biology and cancer is undeniable. Progesterone is a potent mitogen for mammary stem cell expansion and essential for mammopoiesis, yet only a fraction of the luminal epithelium is described to express the progesterone receptor (PR). Progestins in contraceptives and HRT regimens increases breast cancer risk, whilst progesterone inhibition reduces mammary tumorigenesis. Understanding PR within mammary epithelial dynamics is imperative, especially given mammary stem/progenitors cells are the cells-of-origin in breast cancer. Here, we show PR-primed progenitors contribute to both mammary lineages and expose a novel PR+ basal population, challenging current dogma in the field. PR lineage-tracing yields an unprecedented contribution to the luminal and basal compartments. We uncover an asymmetrically dividing PR-primed subpopulation, which has unique bipotent clonogenic capacity and forms TEB-like outgrowths upon transplantation. We enumerate PR+ basal cells and dissect their proteomic landscape, establishing PR+ basal cells as a discrete basal subset, disparate from luminal PR+ cells. Finally, we identify PR+ basal cells in multiple proteomes, scRNAseq datasets and localize PR in clinical breast specimens. This forms a new foundation for comprehending hormone receptor patterning in the breast, not only based on lineage-identity but also the progenitor-progeny hierarchy. Our study shifts the current paradigm of breast biology with implications for breast cancer treatment given the growing interest in anti-progestin based primary prevention strategies.

cell biology↗

bioRxiv2023

FABP7 Progenitors are a Targetable Metabolic Root in the BRCA1 Breast

It has been nearly 3 decades since the discovery of the BRCA1/2 genes and their link to breast cancer risk, with prophylactic mastectomy remaining the primary management option for these high-risk mutation carriers. The current paucity of interception strategies is due to undefined, targetable cancer precursor populations in the high-risk breast. Despite known cellular alterations in the BRCA1 breast, epithelial populations at the root of unwarranted cell state transitions remain unresolved. Here, we identify a root progenitor population that is dysregulated in BRCA1 carriers stemming from the metabolic role of BRCA1. This fatty-acid binding protein 7 (FABP7) expressing luminal progenitor population is spatially confined to the mammary ducts, has enhanced clonogenic capacity, and is the predicted origin of mixed basal-luminal differentiation in the BRCA1 but not BRCA2 breast. We show global H3K27 acetylation is reduced within ductal FABP7 cells in BRCA1 carriers in situ, linking to a non-canonical metabolic role of BRCA1 in regulating acetyl-CoA pools and de novo fatty acid synthesis. We demonstrate FABP7 progenitor capacity is preferentially ablated in BRCA1 carriers through inhibition of fatty acid metabolism using an FDA-approved fatty acid synthase (FASN) inhibitor. This study lays the foundation for metabolic control of breast progenitor dynamics to mitigate breast cancer risk in the BRCA1 breast.

cell biology↗

bioRxiv2023

Droplet based low input proteomic platform for rare cell populations

Deep proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present DROPPS, an accessible low-input platform that generates high-fidelity proteomic profiles of 100 - 2,500 cells. By applying DROPPS within the mammary epithelium, we elucidated the connection between mitochondrial activity and clonogenicity, discovering and validating CD36 as a marker of progenitor capacity in the basal cell compartment. We anticipate DROPPS will accelerate biology-driven proteomic research for a multitude of rare cell populations.

biochemistry↗