Biology subjects

Warhadpande, S.

Publications and source records attributed to Warhadpande, S..

4 recordsLinked to original sources

bioRxiv2026

Hormone signaling and immune programs define differential endocrine responsiveness in high-risk breast tissue

Hormone therapies are frequently used to reduce breast cancer risk in individuals at increased risk for primary or subsequent disease; however, tissue-level responses to these therapies are heterogeneous and incompletely understood. Background parenchymal enhancement (BPE) on breast magnetic resonance imaging (MRI) provides a non-invasive radiologic readout of breast tissue features associated with endocrine responsiveness and cancer risk. Although BPE is associated with hormonal exposure, a subset of patients with BPE do not show a response to preventive endocrine therapy and therefore may remain at increased breast cancer risk. In this study, we integrated single-nucleus RNA sequencing and spatial transcriptomics to define the determinants of endocrine responsiveness in the setting of BPE. We identify hormone-driven epithelial cells with high levels of estrogen signaling and endocrine responsiveness, together with immune-associated epithelial programs characterized by diminished luminal identity and increased expression of immune-modulatory pathways, including major histocompatibility complex (MHC) class II and CD74. Functional organoid assays validate that these epithelial states exhibit differential sensitivity to tamoxifen and demonstrate that inflammatory signals can induce immune-modulatory epithelial programs. Together, our findings identify hormone signaling and immune programs as key determinants of endocrine responsiveness in breast tissue and provide a biological basis for interpreting radiologic markers relevant to cancer prevention.

cancer biology↗

bioRxiv2025

Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems

HER2 proteoforms promote therapeutic resistance and aggressiveness in HER2-positive breast cancer, yet their epigenetic consequences remain poorly defined. Here, we establish EpiBlot, a joint assay incorporating a customized plateATAC-seq workflow that minimizes sample inputs with single-cell western blotting to concurrently profile chromatin accessibility with protein and proteoform expression. We applied our method to engineered MCF7 cells expressing HER2 proteoforms - full-length p185HER2 or truncated 611-CTF -, where we evaluated the impact of such proteoforms on the epigenetic and protein profiles after lapatinib or doxorubicin exposure. Expression of 611-CTF elicits pervasive chromatin remodeling, whereas p185HER2 provokes only modest accessibility shifts under the same treatments. EpiBlot reveals that treatment with doxorubicin drives extensive genome-wide accessibility changes, while lapatinib treatment produces limited global effects but unmasks proteoform-specific responses. Concordance between chromatin accessibility and protein abundance is moderate, underscoring complex regulatory coupling. Extending this dual-modality approach to HER2-low patient-derived organoids uncovers distinct chromatin states and reveals a subpopulation of triple-negative breast-cancer cells expressing truncated HER2 proteoforms. We anticipate that EpiBlot will highlight the value of multimodal profiling with proteoform identification for dissecting tumor heterogeneity and therapeutic response in cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/678463v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@673263org.highwire.dtl.DTLVardef@11d28c5org.highwire.dtl.DTLVardef@15fa336org.highwire.dtl.DTLVardef@1d4426b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Organoid-evaluable clinical biomarkers predict drug responses and guide new breast cancer therapies

Poor therapeutic response in subsets of breast cancer (BC) patients poses an ongoing challenge. Here, we present a biomarker-guided characterization of 44 patient-derived BC organoids, with the aim of modeling resistant disease with greater fidelity and developing an in-vitro system grounded in clinical data for testing alternative treatment strategies. We utilized patient transcriptomic and outcome data from the I-SPY2 clinical trial to develop predictive models of response to a range of therapies, using only organoid-detectable biomarkers as input. A model predicting response to veliparib-platinum chemotherapy (VP) in triple-negative BC (TNBC) was validated in organoids, showing that in vitro drug responses matched predictions from the patient data-derived model. A drug screen in VP-resistant TNBC organoids identified combination treatments that overcame resistance to cisplatin, including pro-apoptotic therapies. This demonstrates that gene expression-based resistance models derived from patient data can be successfully modeled in organoids that can then be used for therapeutic evaluation.

cancer biology↗

bioRxiv2025

Fine needle aspiration biopsy of breast specimens effectively harvests cells for patient-derived organoids modeling breast ductal carcinoma in situ

BackgroundPatient-derived organoids (PDOs) generated from benign breast tissue and breast carcinomas have successfully recapitulated their respective in vivo counterparts. PDOs model tumorigenesis and allow for screening of novel therapeutics personalized to individual patients. However, acquiring cells to generate PDOs is cumbersome. We demonstrate the feasibility of fine needle aspiration biopsy (FNAB) for harvesting cells for PDOs modeling ductal carcinoma in situ (DCIS). MethodsSurgical specimens from patients with biopsy-proven DCIS were used for this study. Core needle biopsy (CNB) was performed on fresh specimens in the operating room, and tissue was mechanically dissociated before culture in basement membrane extract (BME) and organoid medium to generate PDOs. FNAB was performed in the gross room on fresh specimens, and the remaining aspirate was similarly submitted for PDO culture. ResultsPDOs were successfully generated in 15/18 specimens obtained by CNB and 7/11 specimens obtained by FNAB. The average time to initial organoid growth was 4 days for FNAB specimens compared to 19.3 days for CNB specimens. Tumor cells were seen on 7/11 FNAB smears and 16/18 CNB touch preps. Immunofluorescence staining confirmed the presence of both luminal and myoepithelial cells in derived PDOs. ConclusionsFNAB effectively obtains cells for PDOs modeling DCIS. CNB after mincing yielded PDOs with a high success rate, but they were slow to establish. Notably, the time to organoid growth was significantly shorter for FNAB specimens. Thus, FNAB offers an efficient alternative for breast PDO culture and can reduce the time and resources spent on generating PDO cultures.

cell biology↗