Differentially expressed genes (adjusted P <0.01 ) in STAG2/LMO2 subtype compared to other T-ALL cases.

Differentially expressed genes (adjusted P <0.05) in three TLX3 subtypes (TLX3 γδ, TLX3 immature, TLX3 DP-like) compared to other T-ALL cases.

T cell receptors (TCRs) recognize peptides presented by polymorphic human leukocyte antigen (HLA) molecules, but HLA genotype data are often missing from TCR repertoire sequencing studies. To address this, we developed TCR2HLA, an open-source tool that infers HLA genotypes from TCRβ repertoires. Expanding on work linking public TRBV-CDR3 sequences to HLA genotypes, we incorporated "quasi-public" metaclonotypes - composed of rarer TCRβ sequences with shared amino acid features - enriched by HLA genotypes. Using four TCRβseq datasets from 3,150 individuals, we applied TRBV gene partitioning and locality-sensitive hashing to identify ~96,000 TCRβ features strongly associated with specific HLA alleles from 71M input TCRs. Binary HLA classifiers built with these features achieved high balanced accuracy (>0.9) across common HLA-A (9/12), B (9/12), C (6/13), DRB1 (11/11) alleles and prevalent DPA1/DPB1 (6/10), DQA1/DQB1 (8/17) heterodimers. We also introduced a high-sensitivity calibration to support predictions in samples with as few as 5,000 unique clonotypes. Calibrated predictions with confidence filtering improved reliability. Beyond genotype imputation, TCR2HLA enables the discovery of novel HLA- and exposure-associated TCRs, as shown by the identification of SARS-CoV-2 related TCRs in a large COVID-19 dataset lacking HLA data. TCR2HLA provides a scalable framework for bridging the gap between TCRseq data and HLA genotype for biomarker discovery.

The gene expression profiles of γδ T-ALL.

Compounds used in single-dose (10uM) drug screening.

Nearly all chimeric antigen receptors (CARs) signal in the absence of antigen, referred to as ‘tonic signaling’. Tonic signaling of CARs containing 41BB domains enhances T cell fitness and function, in contrast to the exhaustion driven by CD28-containing CARs. Here we show that 41BB induces BACH2, a transcriptional regulator that directs stem and memory programs. Overexpression of BACH2 successfully prevented exhaustion but locked CAR T cells in a quiescent state. We linked BACH2 to a degradation domain to tune BACH2, enabling us to prevent exhaustion while enabling potent effector function that broadly enhanced the long-term efficacy of CAR T cells targeting liquid and solid tumors. Through interrogation of clinical CAR products, we further found an association between BACH2 activity and clinical outcomes in patients with leukemia. These data identify a central function for BACH2 in regulating CAR T cell efficacy. One of three back-to-back papers to show that dosage of BACH2 can modulate T cell differentiation and function and how we might apply this to enhance CAR T cell therapies for cancer.

Abstract Sonic Hedgehog (SHH) signaling functions in temporal- and context-dependent manners to pattern diverse tissues during embryogenesis. The signal transducer Smoothened (SMO) is induced by sterols, oxysterols, and arachidonic acid (AA) through binding pockets in its extracellular cysteine-rich domain (CRD) and 7-transmembrane (7TM) bundle. In vitro analyses suggest SMO signaling is allosterically enhanced by combinatorial ligand binding to these pockets, but in vivo evidence of SMO allostery is lacking. Herein, we map an AA binding pocket at the top of the 7TM bundle and show that its disruption attenuates SHH- and sterol-stimulated SMO induction. A knock-in mouse model of compromised AA binding reveals that homozygous mutant mice are cyanotic, exhibit perinatal lethality, and display congenital heart disease. Surviving mutants demonstrate pulmonary maldevelopment and fail to thrive. Neurodevelopment is unaltered in these mice, suggesting that context-specific allosteric regulation of SMO signaling allows for precise tuning of pathway activity during cardiopulmonary development.

Objectives:CD4+ T cells play key roles in regulating immune responses during pregnancy; therefore, we aimed to understand the CD4+ T-cell surface proteome and transcriptome during pregnancy. Methods:CD4+ T cells were analysed in blood and decidua from term pregnancies (> 37 weeks) and non-pregnant blood. > 350 surface proteins were screened via flow cytometry, and transcriptomes were analysed using single-cell RNA sequencing with > 130 CITE-seq barcoded antibodies. Results:Surface protein screening identified changes to ILT4/CD85d, CD9, IFN-γ receptor β-chain, CX3CR1 and CCR5 in the pregnant blood and decidual CD4+ T cells. CX3CR1 and CCR5 had the highest expression on the effector-memory T-cell (TEM) subset in the blood, with expression consistent across subsets in decidua. CD126/IL-6R was lower in pregnant blood and decidual CD4+ T cells, while scRNAseq identified enrichment in the IL-6R signalling pathway in naive CD4+ T cells in pregnant blood. Both sIL-6R and IL-6 concentrations were increased in plasma during pregnancy, suggesting perturbations to the IL-6/IL-6R signalling axis. Meanwhile, decidual CD4+ T cells had increased expression of transcription factor RUNX3 in the CD69+ tissue-resident-like subset. Conclusions:Our findings demonstrate altered molecular expression in CD4+ T cells during pregnancy. This provides important mechanistic insight of their adaptation and regulation during placental development, which may drive placental dysfunction or pregnancy complications, including preeclampsia, fetal growth restriction and stillbirth. These new data may inform future studies that focus on determining the significance of differentially expressed immune features in pregnancy to identify potential targets for immune modulation to treat pregnancy complications and infections.

Differential peaks of H3K27ac and differentially expressed genes in gene-edited PF382 model.

The list of drugs for the patient-derived xenografts (PDX) cell screening.

Comparison of clinical characteristics and outcomes between gamma delta T-ALL and non-gamma delta T-ALL.

Lists of T-ALL related genes for filtering tumor-only and RNAseq samples.

Patient characteristics of 24 cases of STAG2/LMO2 subtype T-ALL that were performed genomic analysis.

The clinical features of γδ T-ALL.

Patient characteristics of 76 γδ T-ALL cases performed genomic analysis.

Up-regulated pathways in STAG2/LMO2 subtype compared to other T-ALL cases for mouse leukemia initiating cells (LIC) signatures analyzed by gene-set enrichment analysis (GSEA).

Abstract Transgenic mouse models expressing predefined T-cell receptors (TCRs) have been instrumental in advancing our understanding of T-cell biology. However, these traditional models rely on random genomic insertion of large constructs, require labor-intensive embryo manipulation, and frequently result in aberrant TCR expression and phenotypes. These limitations render traditional models insufficient to meet the mounting demands for rapid and precise model systems to evaluate TCR specificities. In this study, we developed a streamlined method that uses adeno-associated virus (AAV) and CRISPR/Cas9-mediated genome editing to precisely integrate pre-rearranged TCRα/β sequences into the mouse TCRβ (Trb) locus, enabling the rapid generation of TCR knock-in mice with physiological TCR expression and functional T-cell differentiation upon antigenic challenge. This approach bypasses the need for screening multiple founders for faithful TCR expression, enhancing the versatility and utility of monoclonal TCR mice in basic immunology and preclinical research, such as in the fields of cancer immunotherapy and vaccine development.

Models for examining the effects of STAG2 inactivation.

Differentially expressed genes (adjusted P <0.01 ) of LMO2 γδ-like subtype vs other T-ALL.