Zexian Zeng

Autoantibodies against type I IFNs can severely compromise antiviral defense, yet the mechanisms underlying their development remain elusive. Using high-throughput autoantigen profiling, we observed that a subgroup of severe COVID-19 patients exhibited strong binding to multiple type I IFNs. Integrated single-cell RNA and B cell receptor (BCR) sequencing with functional analysis identified B cell subsets/states enriched for IFN-α2–binding and –neutralizing antibodies in COVID-19. These findings were compared with those from patients with autoimmune polyendocrine syndrome type I, a rare genetic disease characterized by defective immune tolerance and persistent type I IFN autoimmunity. Competition surface plasmon resonance and AlphaFold 3 structural modeling identified three major functional epitope groups and seven predicted structural subclasses among neutralizing antibodies. Our results indicate that IFN-α2 autoreactivity is present in both naive and antigen-experienced B cell compartments, whereas functional IFN-neutralizing antibodies are predominantly associated with memory and atypical B cells, consistent with defective tolerance and affinity maturation-mediated selection of autoreactive B cell clones.

Spatial transcriptomics offers a glimpse into the immunology of tissues. However, limitations in spatial transcriptomics preclude the detection of highly diverse, low-abundance, and previously unknown sequences, including immune repertoires and microbiota. Here, we introduce Archimap, a spatial transcriptomic platform that simultaneously profiles spatial transcriptomes, immune repertoires, and microbiota from formalin-fixed paraffin-embedded (FFPE) tissues. Using Archimap, we profile the spatial localization of TCRs, BCRs, and the microbiota landscape in archived clinical tissues at single-cell resolution. Through comprehensive benchmarking, we validate Archimap's performance and fidelity. Archimap in situ assembles the immune complex and reconstructs the clonal evolution of antibodies. Together, Archimap shows the power of in situ discovery of functional immune repertoires for their antitumor immunity.

Advances in imaging- and sequencing-based spatial transcriptomics have increased molecular throughput and resolution, enabling the measurement and analysis of spatial transcriptomes at single-cell resolution. However, accurate cell segmentation remains challenging because cell morphology, tissue processing and staining methods vary across samples and platforms, limiting the accuracy and generalizability of existing algorithms. Here we show that DISSECT, a cell segmentation model integrating cytological images with spatial transcriptomic profiles, improves spatial single-cell transcriptome reconstruction. DISSECT uses a pretrained deep generative model to denoise multiscale image features, predicts cell instances with an instance-aware detection module and applies image- and transcriptome-derived gradient fields to refine segmentation masks. Benchmarking across multiple datasets showed that DISSECT achieved higher mean average precision than several existing segmentation tools. We further applied DISSECT to three pairs of gastric adenocarcinoma samples collected before and after anti-PD-1 treatment and profiled by Stereo-seq, illustrating its utility for downstream spatial biological interpretation.

Tumor-infiltrating T cell plasticity dictates the efficacy of immune checkpoint blockade. While interferon-imprinted (ISG15+) T cells frequently emerge within the tumor microenvironment, their biological fate—whether acting as terminally exhausted sinks or active precursors—remains controversial. Integrating a pan-cancer atlas of 2.3 million cells across 39 malignancies with epigenomic, spatial, and in vivo profiling, we redefine ISG15+ T cells as an epigenetically poised, transitional reservoir. These stress-adapted cells maintain open chromatin at both cytotoxic and exhaustion loci. Spatially sequestered in the tumor core, they physically juxtapose with proliferating epithelial cells, where LGALS9-CD44 signaling acts as a tether enforcing this stalled state. Crucially, clonal tracking and in vivo models demonstrate that ICB breaks this spatial tethering, driving massive lineage diversion of ISG15+ clones into active effector pools. Consequently, baseline ISG15+ abundance represents a "spring-loaded" reservoir whose initial presence—and subsequent post-treatment clearance—robustly predicts ICB success.

Background & Aims: Radiofrequency ablation (RFA) is becoming a standard treatment for early-stage hepatocellular carcinoma (HCC). However, high rates of postoperative recurrence, particularly following insufficient RFA (iRFA), remains a clinical obstacle. iRFA contributes to the formation of an immunosuppressive tumor microenvironment and facilitates tumor progression, though the molecular mechanisms driving these processes are not fully elucidated. This study seeks to comprehensively characterize the spatial architecture and cellular interactions within iRFA HCC, and to identify key transcriptional mechanisms through which sublethal heat stress promotes immune evasion and recurrence. Approach & Results: We integrated high-definition spatial transcriptomics (Visium HD) with single-cell RNA sequencing data to map the cellular heterogeneity and communication networks in samples from 6 HCC patients who underwent surgical resection after iRFA. Functional validation was performed using in vitro heat stress models, co-cultured assays, and orthotopic mouse models. We provided a high-resolution spatial atlas of iRFA HCC and the ablation zone, identifying a subpopulation of tumor cells exhibiting activation of the transcription factor CEBPD in response to sublethal heat stress. CEBPD directly bound to the promoter of CXCL2 and drove its expression. Up-regulation of CXCL2 diminished immune checkpoint inhibitors response in iRFA HCC through promoting SPP1+ TAM accumulation via the CXCL2/STAT3/SPP1 axis, and enhanced tumor cell invasion through autocrine signaling. Conclusions: Our study provides a comprehensive spatial characterization of HCC following iRFA, identifies the heat stress-CEBPD-CXCL2 axis as a key driver of tumor progression post-RFA, and demonstrating the therapeutic potential of CXCR2 inhibition for preventing tumor recurrence following RFA. Export

Uncontrolled hemorrhage in trauma, surgical, organ-related, and endoscopic settings, particularly in patients receiving antiplatelet therapy, remains difficult to manage clinically. Here, we introduce a high phosphatidylserine (PS)–exposed procoagulant platelet (hPPL) derivative reprogrammed from isolated platelets via calcium ionophore A23187–induced apoptosis, enriched in surface PS and capable of driving rapid hemostasis. Retaining a protein profile akin to resting platelets, hPPLs robustly promoted platelet activation and aggregation in human- and rat-derived plasma and whole blood in vitro and demonstrated superior hemostatic efficacy compared with clinical thrombin and commercial hemostatic materials [microporous polysaccharide hemispheres (MPH) and FIBRILLAR] in murine liver injury and porcine gastric ulcer bleeding models, even under antiplatelet treatment. Mechanistically, hPPLs up-regulated prostaglandin E synthase (PTGES), thereby increasing prostaglandin E2 (PGE ₂ ) production and its receptor 3 (EP3)–mediated platelet activation, which reinforced PS-mediated clot formation. Our findings identified an apoptosis-driven PTGES-PGE ₂ -EP3 signaling axis that augmented PS-mediated coagulation in murine and porcine hemorrhage models and established the hPPL derivative as a topical hemostatic agent with translational potential for organ-related bleeding and distinct advantages in managing complex endoscopic hemorrhages under both physiological and coagulopathic conditions.

Microsatellite-stable/proficient mismatch repair (MSS/pMMR) colorectal cancer (CRC) is characterized by a cold tumor microenvironment, with limited CD8⁺ T cell infiltration and poor responsiveness to immune checkpoint inhibitors (ICIs). Here, using an in vivo CRISPR/Cas9 screen in a CMT93 cell-derived murine tumor model, we identify Arid3b as a key negative regulator of CD8⁺ T cell infiltration and antitumor activity. Genetic ablation of Arid3b in CD8⁺ T cells significantly enhances their intratumoral accumulation and promotes robust tumor control. Mechanistically, Arid3b deficiency upregulates Runx3 , driving a tissue-resident memory-like phenotype and effector function. Notably, the benefits conferred by Arid3b deficiency are abrogated upon Runx3 deletion, indicating a RUNX3-dependent mechanism. Together, targeting ARID3B could offer a promising strategy to reshape the tumor microenvironment and sensitize MSS CRC to immunotherapy.

Background: Although HLA-II molecules are classically associated with professional antigen-presenting cells, their expression by cancer cells has been recognized for several decades. It has been linked to immune infiltration, responses to immune checkpoint blockade, and clinical outcomes. However, the regulatory mechanisms governing tumor-associated HLA-II expression remain incompletely understood. Methods: Genome-wide CRISPR-Cas9 screening was employed to identify candidate regulators of HLA-II expression in human melanoma cells. Key candidates were functionally validated through genetic and pharmacological perturbation approaches. Integrated transcriptomic and epigenomic analyses were conducted to characterize regulatory mechanisms. Retrospective clinical analyses were performed using publicly available The Cancer Genome Atlas (TCGA) datasets to assess associations with immune infiltration, immunotherapy response, and survival. Results: We identified the aryl hydrocarbon receptor (AHR) and its dimerization partner ARNT as critical, FICZ-responsive, positive regulators of HLA-II expression. AHR-ARNT promoted transcription of CIITA through direct binding to its promoter II (pII), in the absence of IFN-γ signaling. Clinically, an AHR-ARNT loss-of-function signature correlated with reduced immune infiltration, poorer response to immunotherapy, and inferior survival across cancer types. Conclusions: These findings reveal a previously unrecognized regulatory axis controlling HLA-II expression on cancer cells, suggesting that targeting the AHR-ARNT pathway may enhance tumor immunogenicity and improve immunotherapy efficacy.