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Jeselsohn, R.

Publications and source records attributed to Jeselsohn, R..

10 recordsLinked to original sources

Dual HER2/HER3 Targeting with Antibody-Drug Conjugates Reveals a Novel Therapeutic Strategy for HER2-Mutant Lobular Breast Cancer

Activating HER2 mutations are significantly enriched in both primary and metastatic invasive lobular breast cancer (ILC), with large public datasets of primary breast tumors linking them to a worse prognosis in ILC. Despite their oncogenic role, no FDA-approved therapies currently target HER2-mutant breast cancers. While the HER2-directed antibody-drug conjugate (ADC) trastuzumab deruxtecan (T-DXd) has shown efficacy in HER2-mutant non-small cell lung cancer, its activity in HER2-mutant ILC remains unknown. Using the Caris real-world database, one of the largest cohorts with survival data in advanced breast cancers, we confirmed that HER2 mutations are more prevalent in advanced ILC than in invasive breast cancer of no special type (NST) tumors, are associated with worse survival in both histologies, yet predict improved response to T-DXd across subtypes, highlighting the need for mutation-directed, histology-informed therapies. Using endogenous HER2-mutant ILC cell lines (UACC3133-S310F, BCK4-L755S) and CRISPR-engineered isogenic ILC models with clinically relevant HER2 mutations (S310F, V777L), we found these mutations drive HER2/HER3 hyperactivation and downstream signaling, conferring increased sensitivity to HER2 tyrosine kinase inhibitors (TKIs) and T-DXd. Mechanistically, HER2 mutants showed enhanced receptor ubiquitination, internalization, and lysosomal degradation upon T-DXd treatment, explaining the observed drug sensitivity. While combining T-DXd with neratinib or the HSP90 inhibitor ganetespib yielded synergistic effects in long-term growth assays, accompanied by increased HER2 ubiquitination, the concurrent hyperactivation of HER3 in HER2-mutant cells suggested that co-targeting HER3 could provide an effective alternative strategy. Accordingly, HER2-mutant ILC exhibited enhanced sensitivity to the HER3-directed ADC patritumab deruxtecan (P-DXd) or LJM716, a HER3-targeting antibody. We further uncovered a previously unrecognized mechanism of P-DXd beyond HER3 ligand blockade and payload delivery: P-DXd promotes HER2/HER3 association, increases HER2 ubiquitination, and enhances T-DXd internalization, resulting in potent synergy with T-DXd. Mechanistically, we identified HER3 extracellular domains I and II as essential for P-DXd binding and for mediating P-DXd-induced HER2/HER3 association, establishing a structural basis for this activity. In vivo, both T-DXd and P-DXd suppressed UACC3133 and BCK4 xenograft growth, with combination therapy trending toward greater efficacy and prevented regrowth of tumors. Extending these findings beyond HER2-mutant ILC, combination treatment with T-DXd and P-DXd demonstrated synergistic activity across multiple breast cancer models, including (i) HER2-amplified NST patient-derived organoids (PDOs) harboring hotspot HER2 mutations, (ii) HER2-wild-type NST PDOs with clinically intrinsic or acquired T-DXd resistance, and (iii) isogenic HER2-mutant ILC PDOs with experimentally induced resistance after prolonged T-DXd exposure. Collectively, these findings support HER2 as an actionable target in HER2-mutant ILC and position T-DXd-based regimens, particularly in combination with HER3 inhibition, as a promising therapeutic strategy for this underserved patient population.

Cancer Biology↗

Circadian misalignment underlies immune escape in breast cancer

Circadian regulation shapes tissue physiology, yet how it organizes cellular and molecular dynamics within the tumor microenvironment (TME) and influences tumor immunity remains unclear. Using temporal single-nucleus multiomic profiling of mouse breast tumors, we uncovered extensive circadian programs that are both cell-type-specific and shared across the TME, governing proliferation and immune responses. Notably, cancer epithelial cells exhibited global acrophase misalignment relative to immune populations. This intercellular desynchrony manifests as temporal decoupling between tumor proliferation and immune activation, discordant antigen presentation and T cell recognition with intrinsic activation-exhaustion overlap in T cells, and asynchronous PD-1/PD-L1 oscillations that sustain checkpoint-mediated suppression. Similar patterns were observed in human triple-negative breast cancer (TNBC). Together, these findings establish intercellular circadian misalignment as a mechanism of tumor immune evasion and position the circadian architecture of the tumor-immune ecosystem as a previously underappreciated determinant of tumor development and therapeutic response. HIGHLIGHTSO_LISingle-cell multiomics maps circadian regulation of tumor-immune programs. C_LIO_LICircadian regulation in cancer epithelial cells is misaligned with immune cell populations. C_LIO_LITumor-immune temporal misalignment undermines antitumor immunity. C_LIO_LICircadian misalignment in human TNBC suggests relevance for immunotherapy timing. C_LI

cancer biology↗

PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses

Single-cell RNA sequencing profiles cellular heterogeneity but captures only static snapshots, limiting inference of gene expression dynamics. We developed PROFET (Particle-based Reconstruction Of generative Force-matched Expression Trajectories), a framework that reconstructs continuous, nonlinear single-cell trajectories from sparsely sampled scRNA-seq time series. PROFET combines a particle-based gradient-flow algorithm with simulation-free force matching to accurately infer cellular dynamics. Across mouse and human in vitro datasets and an in vivo axolotl regeneration dataset, PROFET achieved 2.6-12.5X lower prediction error than ten state-of-the-art trajectory inference methods. Applying PROFET to newly generated scRNA-seq data from a palbociclib-treated MCF7 cell line and three published breast cancer patient datasets, we reconstructed treatment-response trajectories and identified a resistant cell subpopulation exhibiting large phenotypic shifts and enrichment of the surface markers UNC5B, TLR3, PCDH19, PROCR, SLITRK6, and SEMA6B. PROFET provides a biologically grounded framework for reconstructing cell-state dynamics from static single-cell data across development, regeneration, and therapeutic response.

bioinformatics↗

Super-resolution microscopy reveals distinct epigenetic states regulated by estrogen receptor activity

Changes in gene expression regulated by ligand-dependent transcription factors such as estrogen receptor- (ER) involves the recruitment of coactivators including p300 that acetylates histone H3 at lysine 27 (H3K27ac). While H3K27ac marks active enhancers, the detailed chromatin architecture of enhancers remains unclear. Using super-resolution microscopy, we reveal distinct structural states of H3K27ac modified chromatin in response to ER activation. In estradiol (E2)-treated cells, H3K27ac modified chromatin adopts open, elongated structures, while ER inhibition induces compact, spherical H3K27ac modified chromatin conformations. Using MED1, a core subunit of the Mediator complex that bridges transcription factors with RNA polymerase II (Pol II), we demonstrate that larger H3K27ac structures are preferentially associated with active enhancers, whereas more compact structures show reduced MED1 association, consistent with a less active or inactive state. A constitutively active ER mutation linked to endocrine therapy resistance in breast cancer maintains open chromatin states independent of ligand, suggesting sustained transcriptional activity. Our findings provide the first direct visualization of H3K27ac associated chromatin structural dynamics, challenging the assumption that H3K27ac modification alone is sufficient to lead to enhancer activation. By demonstrating that H3K27ac architecture is dynamically regulated by ER, we establish a new paradigm for understanding epigenetic regulation and highlight potential therapeutic targets for endocrine therapy resistant cancers.

cancer biology↗

An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer

T cells are generally sparse in hormone receptor-positive (HR+) breast cancer, potentially due to limited antigen presentation, but the driving mechanisms of low T cell abundance remains unclear. Therefore, we defined and investigated programs ( gene modules), related to estrogen receptor signaling (ERS) and immune signaling using bulk and single-cell transcriptome and multiplexed immunofluorescence of breast cancer tissues from multiple clinical sources and human cell lines. The ERS gene module, dominantly expressed in cancer cells, was negatively associated with immune-related gene modules TNF/NF-{kappa}B signaling and type-I interferon (IFN-I) response, which were expressed in distinct stromal and immune cell types, but also, in part, expressed and preserved as a cancer cell-intrinsic mechanisms. Spatial analysis revealed that ERS strongly correlated with reduced T cell infiltration, potentially due to its association with suppression of TNF/NF-{kappa}B-induced angiogenesis and IFN-I-induced HLA expression in macrophages. Preoperative endocrine therapy in ER+/HER2-breast cancer patients produced better responses in ERS-high patients, with TNF/NF-{kappa}B expression associated with reduced ERS. Targeting these pathways may enhance T cell infiltration in HR+ breast cancer patients. Statement of SignificanceThis study elucidates the immunosuppressive role of ER signaling in breast cancer, highlighting a complex interplay between cancer, stromal, and immune cells and reveals potential approaches to enhance immunogenicity in HR+ breast cancer. These findings offer crucial insights into immune evasion in breast cancer and identify strategies to enhance T cell abundance.

cancer biology↗

A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer

Most invasive lobular breast cancers (ILC) are of the luminal A subtype and strongly hormone receptor positive. Yet, they are relatively resistant to tamoxifen and are associated with inferior long-term outcomes compared to invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. Through a comprehensive analysis of the epigenome of ILC in pre-clinical models and clinical samples we found that compared to IDC, ILC has a distinct chromatin state that is linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This results in an ILC-unique FOXA1-estrogen receptor (ER) axis that promotes the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1-ER axis leads to retained ER chromatin binding after tamoxifen treatment thereby facilitating tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the auto-induction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC. In summary, we show that ILC is characterized by a unique cell state and FOXA1-ER axis that dictate tumor progression and offer a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC to optimize endocrine treatments in this breast cancer subtype.

cancer biology↗

Temporal and spatial topography of cell proliferation in cancer

Proliferation is a fundamental trait of cancer cells but is poorly characterized in tumors by classical histologic methods. We use multiplexed tissue imaging to quantify the abundance of multiple cell cycle regulating proteins at single-cell level and develop robust multivariate proliferation metrics. Across cancers, the proliferative architecture is organized at two distinct spatial scales: large domains, and local niches enriched for specific immune lineages. A subset of tumor cells express cell cycle regulators in canonical patterns consistent with unrestrained proliferation, a phenomenon we refer to as "cell cycle coherence". By contrast, the cell cycles of other tumor cell populations are skewed toward a specific phase or characterized by non-canonical (incoherent) marker combinations. Coherence varies across space, with changes in oncogene activity, and with therapeutic intervention, and is associated with aggressive behavior. Multivariate measures capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.

systems biology↗

CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis

ChIP-seq and ATAC-seq have become essential technologies used as effective methods of measuring protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates correct normalization between samples, adjustment of copy number variations, and integration of new downstream analysis tools. Here we present CoBRA, a modularized computational workflow which quantifies ChIP and ATAC-seq peak regions and performs unsupervised and supervised analysis. CoBRA provides a comprehensive state-of-the-art ChIP and ATAC-seq analysis pipeline that is usable by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference DB and pathway analysis. Code availability: https://bitbucket.org/cfce/cobra

bioinformatics↗

GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers

Synthetic lethal interactions, where the simultaneous but not individual inactivation of two genes is lethal to the cell, have been successfully exploited to treat cancer. GATA3 is frequently mutated in estrogen receptor (ER)-positive breast cancers and its deficiency defines a subset of patients with poor response to hormonal therapy and poor prognosis. However, GATA3 is not targetable. Here we show that GATA3 and MDM2 are synthetically lethal in ER-positive breast cancer. Depletion and pharmacological inhibition of MDM2 induce apoptosis in GATA3-deficient models in vitro, in vivo and in patient-derived organoids (PDOs) harboring GATA3 somatic mutation. The synthetic lethality requires p53 and acts via the PI3K/Akt/mTOR pathway. Our results present MDM2 as a novel therapeutic target in the substantial cohort of ER-positive, GATA3-mutant breast cancer patients. With MDM2 inhibitors widely available, our findings can be rapidly translated into clinical trials to evaluate in-patient efficacy.

cancer biology↗

The SERM/SERD Bazedoxifene Disrupts ESR1 Helix 12 to Overcome Acquired Hormone Resistance in Breast Cancer Cells

Acquired resistance to endocrine therapy remains a significant clinical burden for breast cancer patients. Somatic mutations in the ESR1 (estrogen receptor alpha (ER) gene ligand-binding domain (LBD) represent a recognized mechanism of acquired resistance. Antiestrogens with improved efficacy versus tamoxifen might overcome the resistant phenotype in ER+ breast cancers. Bazedoxifene (BZA) is a potent antiestrogen that is clinically approved for use in hormone replacement therapies. We find BZA possesses improved inhibitory potency against the Y537S and D538G ER mutants compared to tamoxifen and has additional inhibitory activity in combination with the CDK4/6 inhibitor palbociclib. In addition, comprehensive biophysical and structural biology studies show that BZAs selective estrogen receptor degrading (SERD) properties that override the stabilizing effects of the Y537S and D538G ER mutations.\n\nSignificanceBazedoxifene (BZA) is a potent orally available antiestrogen that is clinically approved for use in hormone replacement therapy (DUAVEE). We explore the efficacy of BZA to inhibit activating somatic mutants of ER that can arise in metastatic breast cancers after prolonged exposure to aromatase inhibitors or tamoxifen therapy. Breast cancer cell line, biophysical, and structural data show that BZA disrupts helix 12 of the ER ligand binding domain to achieve improved potency against Y537S and D538G somatic mutants compared to 4-hydroxytamoxifen.

cancer biology↗