Biology subjects

Reich-Zeliger, S.

Publications and source records attributed to Reich-Zeliger, S..

9 recordsLinked to original sources

bioRxiv2026

A stress-function tradeoff organizes epithelial heterogeneity across spatial scales in the human thyroid

Many organs are organized into repeating anatomical units, yet how cellular heterogeneity is structured within and between these units remains poorly understood. Here we use spatial transcriptomics to dissect multiscale heterogeneity in the human thyroid gland, a tissue composed of hormone-producing follicles. Across human thyroid samples spanning non-inflamed to inflamed states, we develop a follicle-aware analytical framework that separates intra-follicular from inter-follicular variability. We find that heterogeneity among thyrocytes is not dominated by differences in hormone synthesis but instead by two opposing transcriptional programs: an active hormone-producing state and a damage-response thyrocyte (DRT) state enriched for stress, immune, and damage-response pathways. DRTs are spatially clustered, associated with DNA damage markers, and are enriched near immune niches. Notably, the balance between active and damage-response programs constitutes a major axis of variability across cells, follicles, and patients. Our findings highlight a damage-response epithelial thyrocyte state that may be fundamental to follicular function in the human thyroid and provide a general framework for studying heterogeneity in tissues composed of repeating anatomical units.

systems biology↗

bioRxiv2025

An open CAR-T single-cell atlas to enable in-depth characterization and rational engineering of CAR-T products

BRIEF ABSTRACTWe built a CAR-T cell functional atlas from over one million cells across 13 studies, integrating data from patients and healthy donors. The atlas captures 11 phenotypes, links infusion product composition with clinical response, and reveals sex- and age-dependent effects, metabolic signatures, and rare ICANS-associated cells. This open-access resource provides a foundation to understand CAR-T cell function and guide the design of next-generation therapies.

bioinformatics↗

bioRxiv2024

TGFβ determines morphology and key cellular processes of activated CD4+ T cells

During an immune response, cells are simultaneously exposed to multiple cytokine signals that collectively determine their phenotype. Transforming growth factor {beta} (TGF{beta}) is a pleiotropic cytokine acting as a key regulator of T-cell differentiation with activating and suppressive effects on their immune function. Here, we systematically analyze the cellular responses of CD4+ T cells to TGF{beta} across diverse cytokine environments in the presence or absence of TGF{beta}. We found that TGF{beta} had a profound dominant effect independent of the presence of other cytokines, modulating the expression of more than 4,000 genes. In the presence of TGF{beta}, cells exhibit lower expression of translation-related and apoptosis-related genes, accompanied by increased survival of activated T cells. Notably, cells cultured in the presence of TGF{beta} were smaller in size while preserving their proliferative ability. Accordingly, we identified a dense network of transcription factors that were modulated by TGF{beta}, suggesting a core gene set connecting TGF{beta} signaling to the regulation of T-cell size. We found N-Myc to be at the center of this network, and we directly show that TGF{beta} regulates its gene expression level, protein level, and nuclear localization. Our work provides a system to study cell size control and demonstrate the profound effect of TGF{beta} in the modulation and regulation of T-cell properties, expanding its role beyond guiding their phenotype. Significance StatementTGF{beta} is a key determinant of CD4+ T-cell differentiation; however, understanding its effect on additional aspects of T-cell state is lacking. Here, we systematically studied the role of TGF{beta} in regulating T-cell physiology. Exposing cells to diverse combinations of cytokines enabled us to distill the core effect of TGF{beta}. We found TGF{beta} to have a profound effect on multiple cellular processes critical to T-cell function. Significantly, TGF{beta} induced smaller T-cells both in vitro and in vivo, suggesting that TGF{beta} could skew the population towards tissue infiltration and residency. Furthermore, TGF{beta} can be used to fine-tune T-cell size, providing a system for studying cell size control. Overall, our findings demonstrate the profound effect of TGF{beta} in the regulation of T-cell physiology.

immunology↗

bioRxiv2024

Molecular mechanisms underlying the modulation of T-cell proliferation and cytotoxicity by immobilized CCL21 and ICAM1

BackgroundAdoptive cancer immunotherapy, using engineered T-cells, expressing chimeric antigen receptor (CARs) or autologous tumor infiltrating lymphocytes (TILs) became, in recent years, a major therapeutic approach for diverse types of cancer. However, despite the transformative potential of adoptive cancer immunotherapy, this field still faces a major challenge manifested by the complex interplay between the proliferation rate and cytotoxic capacity of effector CD8+ T cells. MethodsWe performed integrated analysis of specific differentiation markers via flow cytometry, together with gene expression profiling to explore the molecular mechanisms through which a "synthetic immune niche" (SIN), composed of immobilized CCL21 and ICAM1, modulates the interplay between the proliferation and cytotoxic potency of effector CD8+ T cells. ResultsOn day 3, the transcriptomic effect induced by the SIN was largely similar for both DC/OVA and anti CD3/CD28-activated cells. Cell proliferation increased and the cells exhibited high killing capacity. On day 4 and on, the proliferation/cytotoxicity phenotypes were radically "activation-specific"; The DC/OVA-activated cells lost their cytotoxic activity, which, in turn, was rescued by the SIN treatment. Upon longer incubation, the cytotoxic activity further declined, and on day7, could not be rescued by the SIN. SIN stimulation following activation with antiCD3/CD28 beads resulted in a highly proliferative phenotype with low cytotoxicity, yet the cells regained killing activity on day 7. Potential molecular regulations of the SIN effects were identified, based on transcriptomic and multispectral imaging profiling. ConclusionsThese data indicate that cell proliferation and cytotoxicity are negatively correlated, and the interplay between them is differentially regulated by the mode of initial activation. The SIN stimulation greatly enhanced the cell expansion, following both activation modes, while maintaining high cytotoxic potency, suggesting that it could reinforce adoptive cancer immunotherapy.

immunology↗

bioRxiv2022

Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.

We analyzed the dynamics of the earliest T cell response to SARS-COV-2. A wave of TCRs strongly but transiently expand during infection, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Most epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains, but not with circulating human coronaviruses. Many expanding CDR3s were also present at high precursor frequency in pre-pandemic TCR repertoires. A similar set of early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the pre-infection naive repertoire. High frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection. One-Sentence SummaryHigh frequency naive precursors underly the rapid T cell response during the crucial early phases of acute viral infection.

immunology↗

bioRxiv2022

RORc expressing immune cells support pro-tumorigenic functions of tertiary lymphoid structures

Tertiary lymphoid structures (TLSs) are formed in many cancer types and have been correlated with better prognosis and response to immunotherapy. In liver cancer, TLSs have been reported to be pro-tumorigenic as they harbor tumor progenitor cells and nurture their growth. The processes involved in TLS development and the acquisition of a pro- or anti-tumorigenic phenotype in cancer are largely unknown. RORc expressing immune cells have been previously implicated in TLS formation, however we find that they are not necessary for TLS neogenesis in the context of inflammation-associated liver cancer. On the contrary, RORc expressing cells negatively regulate TLS formation, since in their absence TLSs form in excess. CD4 cells are essential for liver TLS formation whereas B cells are required for TLS formation specifically in the absence of RORc expressing cells. Importantly, in chronically inflamed livers lacking RORc expressing cells, TLSs become anti-tumorigenic, resulting in reduced tumor load. Comparing liver pro- and anti-tumorigenic TLSs by transcriptional, proteomic and immunohistochemical analyses, revealed enrichment of exhausted CD8 cells that retained effector functions as well as germinal center B cells and plasma cells in anti-tumorigenic TLSs. Cell depletion experiments revealed a role mainly for B cells in limiting tumor development, possibly via tumor directed antibodies. Thus, RORc expressing cells negatively regulate B cell responses, and facilitate the pro-tumorigenic functions of hepatic TLSs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/498540v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@385067org.highwire.dtl.DTLVardef@126c45corg.highwire.dtl.DTLVardef@25ad06org.highwire.dtl.DTLVardef@1829326_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

From pseudotime to true dynamics: reconstructing a real-time axis for T cells differentiation

Numerous methods have recently emerged for ordering single cells along developmental trajectories. However, accurate depiction of developmental dynamics can only be achieved after rescaling the trajectory according to the relative time spent at each developmental point. We formulate a model which estimates local cell densities and fluxes, and incorporates cell division and apoptosis rates, to infer the real time dimension of the developmental trajectory. We validate the model using mathematical simulations, and apply it on experimental high dimensional cytometry data obtained from the mouse thymus to construct the true time-profile of the thymocyte developmental process. Our method can easily be implemented in any of the existing tools for trajectory inference.

systems biology↗

bioRxiv2022

Population based selection shapes the T cell receptor repertoire during thymic development

One of the feats of adaptive immunity is its ability to recognize foreign pathogens while sparing the self. During maturation in the thymus, T cells are selected through the binding properties of their antigen-specific T-cell receptor (TCR), through the elimination of both weakly (positive selection) and strongly (negative selection) self-reactive receptors. However, the impact of thymic selection on the TCR repertoire is poorly understood. Here, we use transgenic Nur77-mice expressing a T-cell activation reporter to study the repertoires of thymic T cells at various stages of their development, including cells that do not pass selection. We combine high-throughput repertoire sequencing with statistical inference techniques to charactarize the selection of the TCR in these distinct subsets. We find small but significant differences in the TCR repertoire parameters between the maturation stages, which recapitulate known differentiation pathways leading to the CD4+ and CD8+ subtypes. These differences can be simulated by simple models of selection acting linearly on the sequence features. We find no evidence of specific sequences or sequence motifs or features that are suppressed by negative selection. These results are consistent with a collective or statistical model for T-cell specificity, where negative selection biases the repertoire away from self recognition, rather than ensuring lack of self-reactivity at the single-cell level.

immunology↗

bioRxiv2021

Antigen experience relaxes the organisational structure of the T cell receptor repertoire

The creation and evolution of the T cell receptor repertoire within an individual combines stochastic and deterministic processes. We systematically examine the structure of the repertoire in different T cell subsets in young, adult and LCMV infected mice, from the perspective of variable gene usage, nucleotide sequences and amino acid motifs. Young individuals share a high level of organization, especially in the frequency distribution of variable genes and amino acid motifs. In adult mice, this structure relaxes and is replaced by idiotypic evolution of the effector and regulatory repertoire. The repertoire of CD4+ regulatory T cells was more similar to naive cells in young mice, but became more similar to effectors with age. Finally, we observed a dramatic restructuring of the repertoire following infection with LCMV. We hypothesize that the stochastic process of recombination and thymic selection initially impose a strong structure to the repertoire, which gradually relaxes following asynchronous responses to different antigens during life.

immunology↗