Biology subjects

Raz, Y.

Publications and source records attributed to Raz, Y..

6 recordsLinked to original sources

bioRxiv2026

Spatially resolved transcriptional programs link fallopian tube precursor lesions to immune activation and stromal reorganization

Despite its name, high-grade serous ovarian carcinoma (HGSC) originates in the fallopian tube, not the ovary, arising from a morphologically recognizable precursor lesion, serous tubal intraepithelial carcinoma (STIC). Yet the early cellular and microenvironmental changes driving this transformation remain poorly understood, limiting progress in early detection, interception, and prevention. Here, we generated a Visium HD spatial transcriptomic atlas of fallopian tube carcinogenesis spanning histologically unremarkable fallopian tube epithelium (FTE), STIC, and invasive HGSC. This approach enabled unbiased, tissue-wide, whole-transcriptome mapping at single-cell-level resolution within preserved histologic architecture, providing spatial granularity beyond prior region-of-interest-based platforms. STIC lesions displayed a coordinated epithelial transformation program marked by proliferation, replication stress, DNA repair activation, chromatin remodeling, and induction of tumor-associated antigens, including PRAME and CLDN6, which are emerging targets for vaccine and antigen-directed therapeutic strategies. In contrast, histologically unremarkable FTE contained spatially restricted epithelial defense programs marked by SCGB1A1 and MUC6, suggesting localized protective states that may influence susceptibility to malignant transformation. Using distance- and density-aware spatial analyses, we found that precursor lesions were embedded within immune-enriched, stromal-depleted microenvironments characterized by interferon-dominant immune activation, attenuation of TNF/NF-{kappa}B signaling, macrophage and lymphoid remodeling, and extracellular matrix-associated fibroblast interactions. Computational pathology analysis of collagen architecture confirmed reduced collagen fiber density in STIC-adjacent stroma, linking transcriptomic evidence of stromal remodeling to structural extracellular matrix changes. Together, these data define early epithelial, immune, and stromal programs associated with STIC and identify tumor-associated antigens, epithelial defense states, and immune-stromal niches as candidate targets for HGSC prevention and early interception.

cancer biology↗

bioRxiv2026

Sustained exposure to CAR-T cell secretome impairs human Hematopoietic Stem Cell function and is reversible by dual TNFα-IFNγ blockade

Prolonged cytopenias are a frequent complication of chimeric antigen receptor (CAR) T-cell therapies and are associated with increased infection risk and non-relapse mortality. Although inflammatory cytokines released during CAR-T cell activation have been implicated in immune effector cell-associated hematotoxicity (ICAHT), their direct effects on human hematopoietic stem and progenitor cells (HSPCs) function remains incompletely understood. Here, we established a reductionist model of CAR-T-associated hematotoxicity using conditioned media (CM) derived from activated CD19 CAR-T cells. Sustained exposure of human HSPCs to CAR-T-derived inflammatory secretome impaired HSPC expansion and reduced long-term repopulating capacity in xenotransplantation assays. In contrast, short-term exposure did not abrogate HSPC function, indicating that brief inflammatory signals can initiate durable reprogramming events, with functional consequences emerging during subsequent proliferative expansion. Mechanistically, CAR-T CM induced IFN{gamma}- and TNF-responsive transcriptional programs in HSPCs and promoted inflammatory myeloid skewing without evidence of apoptosis-dependent stem cell loss. Combined inhibition of IFN{gamma} and TNF restored HSPC expansion, normalized lineage output, reversed inflammatory transcriptional signatures, and rescued in vivo repopulating capacity without impairing CAR-T cytotoxic activity. These findings demonstrate that CAR-T-derived inflammatory signaling can directly impair human HSC function and identify dual TNF/ IFN{gamma} blockade as a potential strategy to mitigate CAR-T-associated hematotoxicity while preserving antitumor efficacy.

cell biology↗

bioRxiv2023

Mesenchymal Stromal Cells regulate human Hematopoietic Stem Cell survival and regeneration via cAMP/PKA pathway

Ionizing radiation (IR) and chemotherapies severely impair hematopoietic stem and progenitor cell (HSPC) function, causing bone marrow failure and secondary malignancies. Mesenchymal stromal cells (MSCs) within the hematopoietic niche support HSPC survival and regeneration, but the underlying pro-survival mechanisms remain incompletely understood. Here, we show that MSCs suppress IR-induced apoptosis in human HSPCs and preserve their regenerative capacity. Transcriptomic analyses identified a robust induction of CREB target genes in HSPCs upon MSC contact, driven by MSC-secreted prostaglandin E2 (PGE2) via cAMP signaling. While MSC-derived PGE2 predominantly protected quiescent HSPCs from IR-induced apoptosis, direct pharmacological elevation of cAMP with Forskolin/IBMX (FSKN/IBMX) effectively shielded both quiescent and cycling HSPCs, significantly enhancing their engraftment and self-renewal. Mechanistically, cAMP pathway activation reduced pro-apoptotic ASPP1 and PUMA expression, elevated p21, and stabilized anti-apoptotic MCL1 and BCL-XL proteins. Collectively, our study uncovers an MSC-driven PGE2/CREB signaling pathway critical for human HSPC regeneration, highlighting pharmacological modulation of this axis as a promising strategy to mitigate DNA damage-induced myelosuppression and improve transplantation outcomes.

cell biology↗

bioRxiv2021

A combined lifestyle intervention induces a sensitization of the blood transcriptomic response to a nutrient challenge

The global population is growing older. As age is a primary risk factor of (multi)morbidity, there is a need for novel indicators to predict, track, treat and prevent the development of disease. Lifestyle interventions have shown promising results in improving the health of participants and reducing the risk for disease, but in the elderly population, such interventions often show less reliable or subtle effects on health outcomes. This is further complicated by a poor understanding of the homeodynamics and the molecular effects of lifestyle interventions, by which their effects of a lifestyle intervention remain obscured. In the Growing Old Together (GOTO) study, we examined the responses of 164 healthy, elderly men and women to a 13-week combined physical and dietary lifestyle intervention. In addition to collecting blood samples at a fasted state, we sampled blood also 30 minutes following a standardized meal. This allows us to investigate an intervention response not only in the traditional fasted state, but also in the blood metabolic and cellular responses to a nutrient challenge. We investigated the transcriptomic and metabolomic responses to this nutrient challenge, how these responses relate to each other, and how this response is affected by the lifestyle intervention. We find that the intervention has very little effect on the fasted blood transcriptome, but that the nutrient challenge induces a large translational inhibition, and an innate immune activation, which together comprise a cellular stress response that is stimulated by the intervention. A sex-specific analysis reveals that although the same set of genes respond in the same direction in both males and females, the magnitude of these effects differ, and are modulated differently by the intervention. On the other hand, the metabolomic response to the nutrient challenge is largely unaffected by the intervention, and the correlation between the metabolomic nutrient response and transcriptomic modules indicates that the change in transcriptomic response to the nutrient challenge is independent from a change in cellular metabolomic environment. This work constitutes a glance at the acute transcriptomic stress response to nutrient intake in blood, and how a lifestyle intervention affects this response in healthy elderly, and may lead to the development of novel biomarkers to capture the phenotypic flexibility of health.

molecular biology↗

bioRxiv2019

Evolution of metastases-associated fibroblasts in the lung microenvironment is driven by stage-specific transcriptional plasticity

Mortality from breast cancer is almost exclusively a result of tumor metastasis, and lungs are one of the main metastatic sites. Cancer-associated fibroblasts (CAFs) are prominent players in the microenvironment of breast cancer. However, their role in the metastatic niche is largely unknown. In this study, we profiled the transcriptional co-evolution of lung fibroblasts isolated from transgenic mice at defined stage-specific time points of metastases formation. Employing multiple knowledge-based platforms of data analysis provided powerful insights on functional and temporal regulation of the transcriptome of fibroblasts. We demonstrate that fibroblasts in lung metastases are transcriptionally dynamic and plastic, and reveal stage-specific gene signatures that imply functional tasks, including extracellular matrix remodeling, stress response and shaping the inflammatory microenvironment. Furthermore, we identified Myc as a central regulator of fibroblast rewiring and found that stromal upregulation of Myc transcriptional networks is associated with worse survival in human breast cancer.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cancer biology↗

bioRxiv2018

High-throughput data-driven analysis of myofiber composition reveals muscle-specific disease and age-associated patterns

Contractile properties of myofibers are dictated by the abundance of myosin heavy chain (MyHC) isoforms. MyHC composition designates muscle function and its alterations could unravel differential muscle involvement in muscular dystrophies and aging. Current analyses are limited to visual assessments in which myofibers expressing multiple MyHC isoforms are prone to misclassifications. As a result, complex patterns and subtle alterations are unidentified. We developed a high-throughput data-driven myofiber analysis to quantitatively describe the variations in myofibers across the muscle. We investigated alterations in myofiber composition between genotypes, two muscles and two age groups. We show that this analysis facilitates the discovery of complex myofiber compositions and its dependency on age, muscle type and genetic conditions.\n\nNonstandard abbreviations

bioinformatics↗