Biology subjects

Jaffe, M.

Publications and source records attributed to Jaffe, M..

4 recordsLinked to original sources

bioRxiv2026

Early Epigenetic and Metabolic Responses to the Adipocyte Secretome Reveal Stress-Adaptive States in Triple-Negative Breast Cancer

Obesity is a well-established risk factor for triple-negative breast cancer (TNBC), yet how adipocyte-derived signals reprogram cancer cell metabolism and chromatin states remains poorly defined. Here, we investigate how adipocyte-driven lipogenesis reshapes metabolic-epigenetic coupling to support stress-adaptive cell states and functional changes in epithelial TNBC cells. Using an integrated multi-omic approach, we combine RNA sequencing (RNA-seq), chromatin accessibility (ATAC-seq), metabolic flux modeling, and functional metabolic assays in lipogenic BT-549 cells. Computational modeling trained on RNA-seq predicts shifts in metabolic pathway usage, including enhanced NAD-linked metabolism. RNA-seq reveals a predominance of gene activation, consistent with ATAC-seq data showing a strong bias toward increased accessibility. Regions of increased accessibility are enriched for stress-adaptive and antioxidant pathways, including superoxide dismutase 2 (SOD2) and metallothioneins (MT1F, MT1E, MT2A). Functionally, lipogenic cells exhibit increased spare respiratory capacity, altered ATP-linked respiration, elevated extracellular acidification, and reduced reactive oxygen species (ROS) accumulation, consistent with a bioenergetically flexible, stress-adaptive metabolic state. Together, these findings reveal that adipocyte-driven metabolic rewiring promotes selective chromatin opening and activation of stress-adaptive gene programs, enabling TNBC cells to buffer oxidative pressure for enhanced proliferation and survival after exposure to the adipocyte secretome.

cancer biology↗

bioRxiv2024

Tet Transgene Activation is Disrupted in Lipogenic Triple Negative Breast Cancer Cells

An important challenge for mammalian cell engineering is the unexpected response of transgenes to native transcriptional regulation pathways. One transgene can show different levels of expression at different genomic sites, in different cell types, and under different growth conditions. Collisions between transcription and DNA replication, heterochromatin encroachment, and viral defense have been linked to transgene silencing. In this study we identify fatty acid metabolism as another mediator of transgene behavior. Adipocyte secretome-induced lipogenesis in epithelial breast cancer cells was accompanied by the loss of expression from a Tet-TA regulated pCMV-AmCyan fluorescent protein (CFP) transgene. Transcription profiling verified the activation of lipid droplet biosynthesis genes, and revealed repression of loci at every chromosome, consistent with the idea that lipogenesis affects the availability of substrates and cofactors for global chromatin remodeling. Pre-induction of pCMV prevented full transgene silencing during lipogenesis. Our results provide new insights into the influence of the lipogenic epigenetic state on transgene behavior.

synthetic biology↗

bioRxiv2024

The T-cell niche tunes immune function through modulation of the cytoskeleton and TCR-antigen forces

Obesity is a major public health crisis given its rampant growth and association with an increased risk for cancer. Interestingly, patients with obesity tend to have an increased tumor burden and decreased T-cell function. It remains unclear how obesity compromises T-cell mediated immunity. To address this question, we modeled the adipocyte niche using the secretome released from adipocytes as well as the niche of stromal cells and investigated how these factors modulated T-cell function. We found that the secretomes altered antigen-specific T-cell receptor (TCR) triggering and activation. RNA-sequencing analysis identified thousands of gene targets modulated by the secretome including those associated with cytoskeletal regulation and actin polymerization. We next used molecular force probes to show that T-cells exposed to the adipocyte niche display dampened force transmission to the TCR-antigen complex and conversely, stromal cell secreted factors lead to significantly enhanced TCR forces. These results were then validated in diet-induced obese mice. Importantly, secretome-mediated TCR force modulation mirrored the changes in T-cell functional responses in human T-cells using the FDA-approved immunotherapy, blinatumomab. Thus, this work shows that the adipocyte niche contributes to T-cell dysfunction through cytoskeletal modulation and reduces TCR triggering by dampening TCR forces consistent with the mechanosensor model of T-cell activation.

bioengineering↗

bioRxiv2023

PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion

Scientists have used small molecule inhibitors and genetic knockdown of gene-silencing polycomb repressive complexes (PRC1/2) to determine if restoring the expression of tumor suppressor genes can block proliferation and invasion of cancer cells. A major limitation of this approach is that inhibitors can not restore key transcriptional activators that are mutated in many cancers, such as p53 and members of the BRAF SWI/SNF complex. Furthermore, small molecule inhibitors can alter the activity of, rather than inhibit, the polycomb enzyme EZH2. While chromatin has been shown to play a major role in gene regulation in cancer, poor clinical results for polycomb chromatin-targeting therapies for diseases like triple-negative breast cancer (TNBC) could discourage further development of this emerging avenue for treatment. To overcome the limitations of inhibiting polycomb to study epigenetic regulation, we developed an engineered chromatin protein to manipulate transcription. The synthetic reader-actuator (SRA) is a fusion protein that directly binds a target chromatin modification and regulates gene expression. Here, we report the activity of an SRA built from polycomb chromodomain and VP64 modules that bind H3K27me3 and subunits of the Mediator complex, respectively. In SRA-expressing BT-549 cells, we identified 122 upregulated differentially expressed genes (UpDEGs, [≥] 2-fold activation, adjusted p < 0.05). On-target epigenetic regulation was determined by identifying UpDEGs at H3K27me3-enriched, closed chromatin. SRA activity induced activation of genes involved in cell death, cell cycle arrest, and the inhibition of migration and invasion. SRA-expressing BT-549 cells showed reduced spheroid size in Matrigel over time, loss of invasion, and activation of apoptosis. These results show that Mediator-recruiting regulators broadly targeted to silenced chromatin activate silenced tumor suppressor genes and stimulate anti-cancer phenotypes. Therefore further development of gene-activating epigenetic therapies might benefit TNBC patients.

synthetic biology↗