Biology subjects

Keramati, F.

Publications and source records attributed to Keramati, F..

4 recordsLinked to original sources

bioRxiv2026

Platform-Imprinted Transcriptional and Clonal Remodeling of αβ and γδT Cells After Allogeneic Transplantation

Immune reconstitution after allogeneic hematopoietic stem cell transplantation is influenced by graft-composition and viral reactivation, but the combined long-term impact on {beta} and {gamma}{delta}T cells remains unclear. We analyzed a cohort of 213 patients receiving either {beta}T cell-depleted grafts (n=146; graft engineering that removes donor {beta}T cells) or T cell-replete grafts (n=67; containing donor T cells). Longitudinal immune phenotyping was integrated with bulk and single-cell TCR repertoire and transcriptomic profiling. CMV reactivation was associated with expansion of CD8+ {beta}T cells across both transplant types and with numerical dominance of V{delta}2- {gamma}{delta}T cells specifically in {beta}T cell-depleted recipients. V{delta}2- {gamma}{delta}T cells underwent early polyclonal expansion followed by repertoire focusing, independent of CMV, whereas {beta}T cells remained clonally restricted. Reduced early V{delta}2+ {gamma}{delta}TCR diversity was associated with EBV reactivation. Single-cell and TCR tracking analyses revealed long-term persistence of donor-derived V{delta}2+ {gamma}{delta}TCRs, whereas V{delta}1+ {gamma}{delta} and {beta}T cell repertoires were predominantly rebuilt de novo. Despite de novo rebuilding, {beta}TCR repertoire diversity diverged by platform at one year: {beta}T cell-depleted recipients exhibited marked (hyper)expansion of {beta}TCR clonotypes and lower diversity than T cell-replete recipients, indicating a durable imprint of graft engineering on {beta}TCR-clonality. Transcriptomic profiling showed that post-transplant T cells predominantly adopted effector programs, with platform-dependent polarization toward cytotoxic signatures in {beta}T cell-depleted recipients and toward AREG-associated tissue-repair signatures in T cell-replete recipients, consistent with wound-healing functions. In conclusion, transplantation platforms imprint durable clonal and transcriptional remodeling of {beta} and {gamma}{delta}T cells, while viral reactivation primarily amplifies expansion without fundamentally reshaping repertoire architecture. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/704768v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@88f136org.highwire.dtl.DTLVardef@944f13org.highwire.dtl.DTLVardef@d3835corg.highwire.dtl.DTLVardef@5548ef_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

De novo H3.3K27M-altered Diffuse Midline Glioma in human brainstem organoids to dissect GD2 CAR T cell function

Diffuse midline glioma (DMG) is a rare yet highly aggressive paediatric cancer primarily arising in the pontine region of the brainstem, necessitating the development of scalable patient-representative models for treatment advance1,2. Here, we developed an FGF4-driven human brainstem organoid model, with high representation of pontine glial lineages. By genetically engineering de novo H3.3K27M-altered DMG, we show that this brainstem glial specification is essential for driving DMG tumorigenesis, resulting in tumours that recapitulate the infiltrative nature and molecular heterogeneity of patient samples. By performing prolonged GD2 CAR T cell treatment in this model, we could mirror variable treatment outcomes as observed in the clinic3,4 and demonstrate a high level of CAR T cell transcriptional heterogeneity. From these CAR T cell functional states, we could identify the most potent effector population and validated NCAM1 as a selection marker for their enrichment. In contrast, NCAM1- cells were linked to a cellular stress response, previously associated to immunotherapy resistance5. Furthermore, incorporating the brain-resident myeloid compartment resulted in DMG-specific, largely immunosuppressive microglia subtypes6. These disease-representative microglia reduced GD2 CAR T cell treatment efficacy and we identified the functional profiles most susceptible to this microglia-dependent immune modulation. Thus, we present a scalable human DMG model with critical applications towards understanding CAR T cell functionality to aid therapy development for this detrimental disease.

cancer biology↗

bioRxiv2025

Functional γδT-omics pipeline reveals compartmentalization of Vδ1⁺ T cell migration, tumor-reactivity, and clonality in human colorectal cancer

{gamma}{delta}T cells play a pivotal role in cancer immune surveillance, yet the current knowledge of their function across the compartments in solid tumors is meager. To address this gap, we developed a comprehensive {gamma}{delta}T-omics platform that integrates functional screening, biomimetic migration assays, {gamma}{delta}TCR repertoire analysis, and transcriptomic profiling. Using matched samples from 31 patients with microsatellite-stable colorectal cancer (CRC), we analyzed {gamma}{delta}T cells from peripheral blood (PBLs{gamma}{delta}), adjacent colon (LPLs{gamma}{delta}), primary tumors (pTILs{gamma}{delta}), and liver metastases (mTILs{gamma}{delta}). This approach uncovered striking compartmentalization of {gamma}{delta}T cell phenotypes, clonality, and function. Tumor-reactive, clonally expanded V{delta}1 {gamma}{delta}T cells were enriched in primary tumors and shared transcriptional and functional features with lamina propria lymphocytes (LPLs). In contrast, V{delta}1 {gamma}{delta}T cells from liver metastases lacked tumor reactivity, exhibited distinct {gamma}{delta}TCR repertoires, and expressed transcriptional signatures associated with TGF-{beta}-mediated suppression and cellular quiescence, suggesting they are shaped by tissue-specific environmental cues. CXCL16 secretion by tumor cells initiated V{delta}1 LPLs{gamma}{delta} migration, which was further amplified by {gamma}{delta}TCR-mediated CCL5 induction from pTILs{gamma}{delta}, leading to CCR5 downregulation and subsequent entrapment of pTILs{gamma}{delta} within the tumor microenvironment. Accordingly, our clinical data from an independent second cohort of 69 patients showed that infiltration by pTILs{gamma}{delta}, but not mTILs{gamma}{delta}, is associated with a protective effect against CRC progression. In summary, our study offers a compartment-resolved perspective on {gamma}{delta}T cell behavior in CRC, revealing key trafficking and functional mechanisms, and enabling the identification of novel tumor-reactive {gamma}{delta}TCRs and migratory cues to inform immunotherapeutic strategies for both primary and metastatic CRC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/671055v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@ff3bborg.highwire.dtl.DTLVardef@14a7e1forg.highwire.dtl.DTLVardef@19e4de4org.highwire.dtl.DTLVardef@bc600_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids

Cellular immunotherapies are rapidly gaining clinical importance, yet predictive platforms for modeling their mode of action are lacking. Here, we developed a dynamic immuno-organoid 3D imaging-transcriptomics platform; BEHAV3D, to unravel the behavioral and underlying molecular mechanisms of solid tumor targeting. Applied to an emerging cancer metabolome-sensing immunotherapy: TEGs, we first demonstrate targeting of multiple breast cancer subtypes. Live-tracking of over 120,000 TEGs revealed a diverse behavioral landscape and identified a super engager cluster with serial killing capability. Inference of single-cell behavior with transcriptomics identified the gene signature of super engager killer TEGs, which contained 27 genes with no previously described T cell function. Furthermore, guided by a dynamic type 1 interferon (IFN-I) signaling module induced by high TEG-sensitive organoids, we show that IFN-I can prime resistant organoids for TEG-mediated killing. Thus, BEHAV3D characterizes behavioral-phenotypic heterogeneity of cellular immunotherapies and holds promise for improving solid tumor-targeting in a patient-specific manner.

cancer biology↗