Zeng, Hu

Abstract Introduction The underlying immunopathogenesis of inflammatory arthritis (IA) immune-related adverse event (irAE) remains obscure. Unlike rheumatoid arthritis (RA), where autoantibodies and B cell dysfunction are central features, the contribution of humoral immunity to IA-irAE is unclear. Methods Here, we performed immunophenotyping of peripheral blood from IA-irAE patients, and compared them with seronegative RA patients, ICI-treated patients without irAE, and healthy controls. Results IA-irAE was marked with increased cytotoxic gene expression and metabolic activation in T cells, and reduced CXCR3 and CCR6 expression in CD4+ T cells. Contrary to seronegative RA, IA-irAE patients displayed no significant elevation in autoantibody levels or atypical CD11c+CD21⁻ B cells. IA-irAE was further characterized by elevated levels of IL-6, IL-12, and type I IFN, which correlated with the T cell activation phenotypes. Conclusion Altogether, our findings define IA-irAE as a disease with certain immunological features distinctive from RA, representing a potentially T cell driven, autoantibody-independent autoimmunity. These results offer insights into immune tolerance breakdown and therapeutic targeting in irAEs. Funding Source National Institute of Arthritis and Musculoskeletal and Skin Diseases Mark E. and Mary A. Davis Initiative in Rheumatoid Arthritis Research Mayo Foundation for Medical Education and Research Topic Categories Basic Autoimmunity (BA)

Objective We aim to identify risk factors to enable stratification of patients' susceptibility to inflammatory arthritis immune‐related adverse events (IA‐irAEs). This retrospective study mainly examines whether preexisting osteoarthritis (OA) increases the likelihood of de novo IA‐irAEs. Methods The prevalence of OA among immune checkpoint inhibitor (ICI)–treated patients who developed IA‐irAE, those who developed other types of irAEs but not IA (non‐IA irAEs), and those who did not develop any irAEs (non‐irAEs) were compared. Electronic medical records were reviewed to extract demographic, clinical, and laboratory data. Group comparisons and logistic regression analyses were performed. Results A total of 181 de novo IA‐irAE patients, 140 non‐IA irAE patients, and 170 non‐irAE patients were included. The prevalence of OA was significantly higher in the IA‐irAE group (69%) than in the non‐IA irAE group (48%) and the non‐irAE group (48%) (both P < 0.001). The IA‐irAE group demonstrated a higher frequency of multisite OA, with more predominant hand involvement (62%) than the non‐IA irAE with OA group (13%) and the non‐irAE with OA group (13%) (both P < 0.001). A family history of autoimmune disease (AID) (odds ratio [OR] 2.03, 95% confidence interval [CI] 1.02–4.05), preexisting OA (OR 2.88, 95% CI 1.85–4.52), and melanoma (OR 2.63, 95% CI 1.56–4.47) were identified as risk factors for the development of IA‐irAE. Conclusion OA was more prevalent among ICI‐treated patients developing IA‐irAE than those who were not. Hand OA was the most common OA pattern in IA‐irAE patients. Preexisting OA, melanoma, and a family history of AID were associated with IA‐irAE.

Abstract B cell activation and differentiation into antibody-secreting cells require extensive metabolic and epigenetic remodeling, yet the molecular mechanisms that integrate these programs remain incompletely understood. ATP-citrate lyase (ACLY) links glucose metabolism to acetyl-CoA production, supporting lipid biosynthesis and protein acetylation. However, its role in humoral immunity has not been fully defined. Here, using genetic and integrated multi-omics approaches, we show that B cell activation is accompanied by coordinated metabolic, transcriptional, and epigenetic reprograming. Although ACLY is dispensable for B cell development and homeostasis, it is required to establish chromatin accessibility programs in activated B cells, with a more pronounced impact on the epigenetic landscape than on transcriptional output. ACLY-deficient B cells exhibit profound defects in TLR and BCR elicited activation, survival and metabolic fitness ex vivo . In vivo , B cell-intrinsic loss of ACLY results in impaired antigen-specific antibody production, associated with reduced germinal center and plasmablast formation, but normal homeostatic proliferation. Deletion of ACLY after B cell activation reduces plasmablast generation in vivo , indicating a continued requirement for ACLY beyond the initial activation phase. Together, these findings identify ACLY as a central regulator that links metabolism to epigenetic programing that supports B cell activation and humoral immunity.

Abstract Chimeric antigen receptor (CAR) T-cell therapy achieves high response rates in relapsed/refractory aggressive B-cell non-Hodgkin lymphoma, yet only 40% of patients achieve durable remission. Identifying biological programs linked to long-term response remains critical. As metabolic fitness underlies T-cell persistence and effector function, we profiled metabolic pathways associated with clinical outcomes following commercial CD19 CAR T-cell therapy. Single-cell RNA sequencing of peripheral blood mononuclear cells collected at baseline (BL), peak CAR-T expansion (PK), and one-month post-infusion (M1) was analyzed using CellRanger v7.0.1, immunopipe. Seurat v4.3.0 was applied for unsupervised clustering to delineate cell subsets based on top differentially expressed genes. Patients were categorized as durable complete remission (CR ≥6 months; n = 16), primary refractory (PD1; n = 4), or relapse after initial response (PD2; n = 12). Gene-set enrichment analysis defined metabolic pathway activity across T-cell, monocyte, dendritic cell (DC), and natural killer (NK) subsets. Oxidative phosphorylation (OXPHOS) emerged as the dominant metabolic program distinguishing clinical outcomes. At BL and PK, OXPHOS was consistently enriched in PD1 relative to CR across T-cell, monocyte, and DC subsets, suggesting early oxidative activation in non-responders. By M1, this pattern inverted, with higher OXPHOS activity in CR. PD2 largely paralleled PD1, but several subsets including CD8 T central memory, classical monocytes TGFβ, intermediate monocytes CD38, monocytic myeloid-derived suppressor cell (mMDSC) HIF1A, and mMDSC SIRPA, showed OXPHOS enrichment in CR at BL and/or PK that persisted through M1. In contrast, DC and NK subsets exhibited the opposite pattern: OXPHOS was enriched in CR at PK (conventional DC 2 (cDC2), plasmacytoid DC (pDC), NK, proliferating NK), but shifted toward enrichment in PD2 at M1 (cDC2, NK, NK CD56bright). Glycolysis (GLY) followed a similar trajectory in monocytes and NK cells, with enrichment in PD1/PD2 at BL and PK, followed by enrichment in CR at M1. In T-cells, PD1 maintained GLY enrichment from BL through PK, with no significant differences observed at M1. The inositol-phosphate metabolism pathway showed a more static pattern and was consistently enriched in multiple PD2 effector and memory T-cell subsets without reversal at M1. Taken together, these data reveal distinct, lineage-specific metabolic signatures that differentiate durable remission from early and late progression. Dynamic OXPHOS and GLY programming, characterized by lower activity early and enhanced activity at M1 in CR, may reflect adaptive metabolic programming that supports sustained antitumor immunity. Immune-metabolic profiling may therefore serve as a biomarker of response and highlight actionable metabolic pathways to enhance CAR T-cell durability. Citation Format: Melinda S.Y. Tan, Panwen Wang, Patrizia Mondello, Jacqueline Turner, Andre de Menezes Silva Corraes, Chen Wu, Zuoyi Shao, Kevin Regan, Ma Audrey, Arushi Khurana, Nora N. Benanni, Yucai Wang, Paul Hampel, Jonas Paludo, Saad J. Kenderian, Urshila Durani, Patrick B. Johnston, Jose Caetano Villasboas, Stephen M. Ansell, Ying Li, Haidong Dong, Hu Zeng, Yi Lin. Metabolic pathway signatures defining response to CD19 CAR T-Cell therapy in aggressive B-cell non-hodgkin lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3278.

The underlying immunopathogenesis of inflammatory arthritis (IA) immune-related adverse event (irAE) remains obscure. Unlike rheumatoid arthritis (RA), where autoantibodies and B cell dysfunction are central features, the contribution of humoral immunity to IA-irAE is unclear. Here, we performed immunophenotyping of peripheral blood from patients with IA-irAE and compared them with patients with seronegative RA, immune checkpoint inhibition–treated patients without irAE, and healthy controls. IA-irAE was marked with increased cytotoxic gene expression and metabolic activation in T cells and reduced CXCR3 and CCR6 expression in CD4 + T cells. Contrary to seronegative RA, patients with IA-irAE displayed no substantial elevation in autoantibody levels or atypical CD11c + CD21 − B cells. IA-irAE was further characterized by elevated levels of interleukin-6 (IL-6), IL-12, and type I interferon, which correlated with the T cell activation phenotypes. Together, our findings define IA-irAE as a disease with certain immunological features distinctive from RA, representing a potentially T cell–driven, autoantibody-independent autoimmunity. These results offer insights into immune tolerance breakdown and therapeutic targeting in irAEs.

ABSTRACT Objective Identifying risk factors enables stratification of patients’ susceptibility to inflammatory arthritis immune-related adverse events (IA-irAE). This retrospective study examines whether preexisting osteoarthritis (OA) increases the likelihood of de novo IA in patients treated with immune checkpoint inhibitors (ICIs). Methods The prevalence of OA among ICI–treated patients who developed IA-irAE, those who developed other types of irAEs but not IA (non-IA irAE), and those who did not develop any irAEs (non-irAE) were compared. Electronic medical records were reviewed to extract demographic, clinical and laboratory data. Group comparisons and logistic regression analyses were performed. Results 181 de novo IA-irAE patients, 140 non-IA irAE patients and 170 non-irAE patients were included. The prevalence of OA was significantly higher in the IA-irAE group (69%) than the non-IA irAE group (48%) and the non-irAE group (48%) (both p < 0.001). The IA-irAE group demonstrated a higher frequency of multisite OA, with predominant hand involvement (62%) than the non-IA irAE with OA group (13%) and the non-irAE with OA group (13%) (both p < 0.001). A family history of autoimmune disease (AID) (OR 2.03, 95% CI 1.02–4.05), preexisting OA (OR 2.88, 95% CI 1.85–4.52) and melanoma (OR 2.63, 95% CI 1.56–4.47) were identified as risk factors for the development of IA-irAE. Conclusions OA was more prevalent among ICI-treated patients developing IA-irAE than those who did not. Hand OA was the most common OA pattern in IA-irAE patients. Preexisting OA, melanoma and a family history of AID were risk factors for IA-irAE.

Abstract Chimeric antigen receptor (CAR) T-cell therapy has demonstrated remarkable response rates in relapsed/refractory aggressive B-cell non-Hodgkin's lymphoma. However, durable remissions occur in only 40% of treated patients, highlighting mechanisms of therapeutic resistance and immune escape. While cytotoxicity is principally executed by CAR T-cells, monocytes shape CAR-T cell efficacy and orchestrate cytokine-driven immunity. In this study, we defined distinct metabolic profiles of T-cell and monocyte subsets based on clinical response. Single-cell RNA sequencing (scRNA-seq) and T-cell receptor sequencing (scTCR-seq) were performed on peripheral blood mononuclear cells at three timepoints: before lymphodepletion (BL), at peak CAR-T expansion (PK), and one-month post-infusion (M1). Data were processed with CellRanger v7.0.1 and analyzed with the immunopipe pipeline (Wang et al., 2025). Seurat v4.3.0 was utilized for unsupervised hierarchical clustering analysis; subsets identified included classical monocytes (CM), intermediate monocytes (IM), non-classical monocytes (NM), and monocytic myeloid derived suppressor cells (mMDSC). Metabolic profiles were compared across patients achieving ≥6-month complete remission (CR, n=16), primary refractory disease (PD1, n=4), or relapsed after a prior response (PD2, n=12). A total of 107035 T cells and 129981 monocytes from 77 serial samples in 32 patients were analyzed. CR patients had a higher T-cell:monocyte ratio than PD1/PD2 at all time points, especially at BL and PK (BL 1.2 vs 0.4, p=0.011; PK 1.3 vs 0.3, p=0.027). Clinical responses were compared with metabolic pathway analysis and identified oxidative phosphorylation (OXPHOS) as the dominant pathway. OXPHOS was consistently enriched in PD cohorts across T-cell subsets, particularly in PD1 vs CR at BL (mucosal-associated invariant T-cell (MAIT) and T peripheral memory (Tpm)), and at PK (CD4/CD8 memory precursor effector cells (MPEC) and activated MPECs (MPECa), CD4 T-helper 1 proliferating (Th1p), CD4 Th2 activated (Th2a), regulatory T-cell (Treg), CD8 naive senescent (CD8NS), CD8 T effector memory (Tem) tumor recirculating (TR), CD8 Tpm, CD8 T resident memory (Trm) TR and MAIT Tpm). By M1, OXPHOS enrichment in CD4/CD8MPECa, CD4Th2a, CD8NS, CD8TemTR reversed, now predominant in CR although CD8Tpm and CD8TrmTR remained enriched in PD1. In the monocyte subsets at BL, PD2 showed OXPHOS enrichment in CD163+ monocytes (mono), IM IL1, mMDSC SIRPA, mMDSC TGFβ, and CM IL6 subsets compared to PD1 and CR, while PD1 showed OXPHOS enrichment in IM CD38, CM TGFβ, and mMDSC HIF1A vs CR and PD2. This persisted at PK. By M1, the pattern reversed and mirrored that of T-cells, with CR patients showing OXPHOS enrichment in CD163+mono, CM IL6, CM TGFβ, IM CD38, mMDSC HIF1A, mMDSC SIRPA and mMDSC TGFβ, and additionally in CM EMT, CM p53, NM, NM CD36 vs PD1/PD2. Glycolysis/gluconeogenesis (GLY) was also enriched across subsets. In T-cells, PD1 vs CR showed GLY enrichment in CD4Th2a, CD8Tpm, CD8Tpm proliferating and MAIT Tpm at PK. In monocytes, GLY was enriched in PD1/2 vs CR at BL (CD163+mono, CM IL6) and PK (CD163+mono, IM CD18, mMDSC SIRPA). By M1, GLY metabolism was enriched in CR vs PD1/PD2 in CD163+mono, CM IL6, mMDSC SIRPA. Additional GLY enriched subsets at CR vs PD1 included CM, CM p53, EMT, IM CD38, IM IL1, mMDSC HIF1A, NM, NM CD36. Inositol phosphate metabolism (IP) was predominantly enriched in PD2 vs CR at BL (CD8NS, CD8Tcm, CD8Tpm activated), PK (CD4Th2, CD8NS, CD8Tem TR, CD8Tpm proliferating, γδT Tem) and M1 (CD4/CD8 MPECa, CD4 Th1/Th2, CD8NS, CD8Tpm, CD8 Tpm proliferating, Treg and MAIT Tpm). Notably, Treg was the only T-cell subset enriched for IP at PK in CR vs PD1/PD2. Additionally, the TCA cycle was enriched in PD1 Tregs and Th2 cells at BL and PK vs CR/PD2. A higher T-cell:monocyte ratio in CR vs PD1/PD2 supports prior evidence that elevated pre-lymphodepletion lymphocyte:monocyte ratios predict better outcomes. We identified distinct metabolic signatures in T-cells and monocytes between CR and PD1/PD2. OXPHOS enrichment in T-cells and monocytes at M1 in CR patients may reflect oxidative programming as a hallmark of sustained anti-tumor immunity. Conversely, GLY enrichment in PD1 T-cells at PK may reflect short-lived effector states lacking persistence. Overall, these findings highlight metabolic profiling as a promising predictive biomarker and therapeutic programming target to enhance CAR T-cell outcomes.

Abstract Description During the humoral immune response, B cells undergo rapid metabolic reprogramming with a high demand for nutrients, which are vital to sustain the formation of the germinal centers (GCs). Rag-GTPases sense amino acid availability to modulate the mechanistic target of rapamycin complex 1 (mTORC1) pathway and suppress transcription factor EB (TFEB) and transcription factor enhancer 3 (TFE3). However, how Rag-GTPases coordinate amino acid sensing, mTORC1 activation, and TFEB/TFE3 activity in humoral immunity remains undefined. Here, we show that B cell-intrinsic Rag-GTPases are critical for the development and activation of B cells. RagA/RagB deficient B cells fail to form GCs, produce antibodies, and generate plasmablasts in both T-dependent (TD) and T-independent (TI) humoral immune responses. Deletion of RagA/RagB in GC B cells leads to abnormal dark zone (DZ) to light zone (LZ) ratio and reduced affinity maturation. Mechanistically, the Rag-GTPase complex constrains TFEB/TFE3 activity to prevent mitophagy dysregulation and maintain mitochondrial fitness in B cells, which are independent of canonical mTORC1 activation. TFEB/TFE3 deletion restores B cell development, GC formation in Peyer’s patches and TI humoral immunity, but not TD humoral immunity in the absence of Rag-GTPases. Collectively, our data establish Rag-GTPase-TFEB/TFE3 pathway as an mTORC1 independent mechanism to coordinating nutrient sensing and mitochondrial metabolism in B cells. Funding Sources National Institute of Allergy and Infectious Diseases (NIAID) - AI162678 National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) - AR077518 Topic Categories Immune Response Regulation: Molecular Mechanisms (IRM)

Abstract Single-cell sequencing technologies provide us with information at the level of individual cells. Combining single-cell RNA-seq and single-cell TCR-seq profiling enables the exploration of cell heterogeneity and T-cell receptor repertoires simultaneously. Integrating both types of data can play a crucial role in enhancing our understanding of T-cell-mediated immunity and, in turn, facilitate the advancement of immunotherapy. Here, we present immunopipe, a comprehensive and flexible pipeline to perform integrated analysis of scRNA-seq and scTCR-seq data. In addition to the command line tool, we provide a user-friendly web interface for pipeline configuration and execution monitoring, benefiting researchers without extensive programming experience. With its comprehensive functionality and ease of use, immunopipe empowers researchers to uncover valuable insights from scRNA-seq and scTCR-seq data, ultimately advancing the understanding of immune responses and immunotherapy development.