Antigen Presentation Pathway Research Articles

T cell expressions of aberrant gene signatures and Co-inhibitory receptors (Co-IRs) as predictors of renal damage and lupus disease activity

BackgroundSystemic lupus erythematosus (SLE) is distinguished by an extensive range of clinical heterogeneity with unpredictable disease flares and organ damage. This research investigates the potential of aberrant signatures on T cell genes, soluble Co-IRs/ligands, and Co-IRs expression on T cells as biomarkers for lupus disease parameters.MethodsComparative transcriptome profiling analysis of non-renal and end-stage renal disease (ESRD) phenotypes of SLE was performed using CD4 + and CD8 + cDNA microarrays of sorted T cells. Comparing the expression of Co-IRs on T cells and serum soluble mediators among healthy and SLE phenotypes.ResultsSLE patients with ESRD were downregulated CD38, PLEK, interferon-γ, CX3CR1, FGFBP2, and SLCO4C1 transcripts on CD4 + and CD8 + T cells simultaneously and NKG7, FCRL6, GZMB/H, FcγRIII, ITGAM, Fas ligand, TBX21, LYN, granulysin, CCL4L1, CMKLR1, HLA-DRβ, KIR2DL3, and KLRD1 in CD8 T cells. Pathway enrichment and PPI network analyses revealed that the overwhelming majority of Differentially Expressed Genes (DEGs) have been affiliated with novel cytotoxic, antigen presentation, and chemokine-cell migration signature pathways. CD8 + GZMK + T cells that are varied in nature, including CD161 + Mucosal-associated invariant T (MAIT) cells and CD161- aged-associated T (Taa) cells and CD161-GZMK + GZMB + T cells might account for a higher level of GZMK in CD8 + T cells associated with ESRD. SLE patients have higher TIGIT + , PD1 + , and lower CD127 + cell percentages on CD4 + T cells, higher TIM3 + , TIGIT + , HLA-DR + cell frequency, and lower MFI expression of CD127, CD160 in CD8 T cells. Co-IRs expression in T cells was correlated with soluble PD-1, PDL-2, and TIM3 levels, as well as SLE disease activity, clinical phenotypes, and immune-therapy responses.ConclusionThe signature of dysfunctional pathways defines a distinct immunity pattern in LN ESRD patients. Expression levels of Co-IRs in peripheral blood T cells and serum levels of soluble PD1/PDL-2/TIM3 can serve as biomarkers for evaluating clinical parameters and therapeutic responses.

NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population.

Neoantigen vaccines make use of tumor-specific mutations to enable the patient's immune system to recognize and eliminate cancer. Selecting vaccine elements, however, is a complex task which needs to take into account not only the underlying antigen presentation pathway but also tumor heterogeneity. Here, we present NeoAgDT, a two-step approach consisting of: (i) simulating individual cancer cells to create a digital twin of the patient's tumor cell population and (ii) optimizing the vaccine composition by integer linear programming based on this digital twin. NeoAgDT shows improved selection of experimentally validated neoantigens over ranking-based approaches in a study of seven patients. The NeoAgDT code is published on Github: https://github.com/nec-research/neoagdt.

Investigation of the Protective Effect of Probiotic Lactobacillus plantarum Ep-M17 on the Hepatopancreas of Penaeus vannamei

Infection with the pathogenic bacterium Vibrio parahaemolyticus typically causes severe hepatopancreatic damage in Penaeus vannamei, often resulting in acute shrimp mortality. Therefore, protecting the shrimp’s hepatopancreas is crucial for enhancing their disease resistance. Previous research has demonstrated that the probiotic strain Lactobacillus plantarum Ep-M17 inhibits the growth of V. parahaemolyticus E1 in vitro. However, it remains uncertain whether Ep-M17 can provide protective benefits to the shrimp’s hepatopancreas. To address this knowledge gap, our present study investigated the histological changes, enzyme activity, gene transcription, and metabolite levels in the hepatopancreas of shrimp after a 4-week diet supplemented with Ep-M17. The results revealed that incorporating Ep-M17 into the shrimp’s diet alleviated the damage by V. parahaemolyticus E1 infection in hepatopancreatic cells. In addition, the inclusion of Ep-M17 notably boosted the effectiveness of immunodigestive enzymes such as SOD, AKP, and CAT. Furthermore, Ep-M17 stimulated gene transcription in crucial immune response-related signalling pathways like the mitogen-activated protein kinase signaling pathway and the antigen processing and presentation pathway. Moreover, the incorporation of Ep-M17 into shrimp diets increased the levels of β-alanine, and histidine in the hepatopancreas, enhancing anti-inflammatory capacity and improving the shrimp’s immune response. Overall, the results indicate that incorporating Ep-M17 into the diet can enhance shrimp disease resistance by bolstering both immune response and metabolic activity within the hepatopancreas. These results underscore the importance of probiotics in controlling aquatic animal diseases and highlight Ep-M17 as a promising dietary supplement for enhancing shrimp health and immunity in aquaculture.

Sulfonium-Stapled Peptides-Based Neoantigen Delivery System for Personalized Tumor Immunotherapy and Prevention.

Neoantigen peptides hold great potential as vaccine candidates for tumor immunotherapy. However, due to the limitation of antigen cellular uptake and cross-presentation, the progress with neoantigen peptide-based vaccines has obviously lagged in clinical trials. Here, a stapling peptide-based nano-vaccine is developed, comprising a self-assembly nanoparticle driven by the nucleic acid adjuvant-antigen conjugate. This nano-vaccine stimulates a strong tumor-specific T cell response by activating antigen presentation and toll-like receptor signaling pathways. By markedly improving the efficiency of antigen/adjuvant co-delivery to the draining lymph nodes, the nano-vaccine leads to 100% tumor prevention for up to 11 months and without tumor recurrence, heralding the generation of long-term anti-tumor memory. Moreover, the injection of nano-vaccine with signal neoantigen eliminates the established MC-38 tumor (a cell line of murine carcinoma of the colon without exogenous OVA protein expression) in 40% of the mice by inducing potent cytotoxic T lymphocyte infiltration in the tumor microenvironment without substantial systemic toxicity. These findings represent that stapling peptide-based nano-vaccine may serve as a facile, general, and safe strategy to stimulate a strong anti-tumor immune response for the neoantigen peptide-based personalized tumor immunotherapy.

Molecular patterns of resistance to immune checkpoint blockade in melanoma

Immune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB naïve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.

Abstract CT069: Targeting EpCAM via CAR T-cells is an effective treatment for gastric cancer patients and subsequent toll-like receptor signaling activation in CD36+ monocyte underlies the resulting cytokine release syndrome

Abstract EpCAM is highly expressed in various cancer types of the gastrointestinal system and at metastatic sites. It serves as a promising prognostic marker and therapeutic target. We conducted a first-in-human, open-label, single-arm, multicenter, phase 1 clinical trial following the classical "3+3" dose escalation design. The endpoints of this clinical trial are to assess the safety, efficacy, and pharmacokinetic (PK)/pharmacodynamic (PD) profile of EpCAM CAR-T. The trial is still ongoing, and our interim analysis results revealed a favorable safety profile of EpCAM CAR-T. No treatment-related deaths were observed within the 4-week follow-up period after infusion. 2 (12.5%) patients in high dose group (3*106) experienced dose-limiting toxicity (DLT) and 8 (50%) patients experienced grade 1-3 CRS. EpCAM CAR-T showed promising efficacy in gastric cancer. In gastric cancer group, the overall response rate (ORR) and disease control rate (DCR) reached 20.0% and 90.0%, respectively. However, the efficacy of EpCAM CAR-T in treating colorectal cancer was suboptimal, with an objective response rate (ORR) of 0% and disease control rate (DCR) of 50%. In our study, we observed that patients in gastric cancer (GC) group who developed cytokine release syndrome (CRS) had a weak response to CAR-T cell therapy, which is consistent with previous observations in animal models. We employed single-cell RNA sequencing (scRNA-seq) to analyze peripheral blood mononuclear cells (PBMCs) from GC group patients receiving EpCAM CAR-T treatment to explore the potential antagonism between CRS and treatment efficacy. Our findings underscore the significant role of monocytes in the regulation of CRS and treatment response. Specifically, we identified an increased abundance of Toll-like receptor (TLR)-dependent CD36+ monocytes in non-responders experiencing CRS. In a mouse model, we demonstrated that blocking TLR signaling in monocytes attenuated CRS induced by EpCAM CAR-T cells. Conversely, CD16+ monocytes were enriched in responders, displaying upregulated antigen presentation pathways and enhanced tumor infiltration capacity. In vivo, experiments revealed that blocking the antigen presentation pathway or inhibiting tumor infiltration of CD16+ monocytes resulted in reduced anti-tumor response of EpCAM CAR-T cells. Our findings highlight the critical role of intrinsic monocyte subpopulations as determinants of CAR-T efficacy and CRS. These insights may provide valuable strategies for predicting and enhancing the safety and efficacy of CAR-T cell therapy for solid tumors. Citation Format: TIanhang Luo, Zhengmao Lu, Zhongen Wu, Yuxuan Dong, Yuanyuan Zhu, Mei Feng, Shenglin Mei, Weijia Fang, Di Zhu. Targeting EpCAM via CAR T-cells is an effective treatment for gastric cancer patients and subsequent toll-like receptor signaling activation in CD36+ monocyte underlies the resulting cytokine release syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT069.

Abstract LB403: Suppression of antigen presentation in pediatric rhabdomyosarcoma

Abstract Background: Rhabdomyosarcoma (RMS) is an aggressive soft tissue sarcoma that is diagnosed based on the tumor cell's resemblance to embryonic or poorly differentiated skeletal muscle progenitors. Multiple immunotherapy clinical trials have found no evidence of immune reactivity against RMS, which has been attributed to the relatively low tumor mutation burden in these cancers. However, we made an unexpected observation that many patient RMS tumors had a near absence of MHC-I expression, a key requisite for anti-tumor CD8+ T lymphocytes and many immunotherapies. In this study, we explore the etiology of low antigen presentation in RMS and systematically evaluate therapeutic interventions that sensitize RMS to immunotherapy. Methods: Surface MHC-I expression was evaluated on pediatric tumor cell lines (n=65) from five major pediatric tumor types. RNA-seq, whole exome and genome sequencing data were analyzed from RMS tumors (total of n=247) and iPSC models of skeletal muscle development (PMID: 32011235). Epigentic drugs targeting DNA methylation (decitabine), EZH2 (tazemetostat), Class I/IV HDACs (mocetinostat), and LSD1 (GSK-LSD1) were used at sub-cytotoxic doses on RMS cell lines (n=10) and analyzed for surface MHC-I expression with flow cytometry and gene expression. T cell cytotoxicity assays were performed using engineered human T cells expressing an optimized TCR which recognizes an HLA*A2:01 restricted peptide from PRAME. Results: RMS cell line models exhibited a range of MHC-I expression with most having low or undetectable MHC-I expression, similar to that of a known MHC-I negative tumor type MYCN-amplified neuroblastoma. Exome sequencing of RMS tumors showed no evidence of loss-of-function alterations in essential antigen processing and presentation (APP) pathway genes. Gene expression profiling by RNAseq and western blotting, however, revealed an absence of core APP genes in many RMS tumors and cell lines. We uncovered that during a specific window of embryonic myogenesis, APP is suppressed and that RMS tumors mimicking this state of development show the deepest loss of APP. Multiple classes of epigenetic drugs were evaluated to rescue APP in RMS. Treatment of RMS using a DNA demethylating agent or HDAC inhibitor exhibited the strongest MHC-I restoration across RMS models with no changes observed using LSD1 or EZH2 inhibitors. As a proof-of-concept, we demonstrate that targeting the RMS antigen PRAME using TCR therapy is enhanced by the inclusion of epigenetic therapy. Conclusions and Significance: We revealed that epigenetic suppression of APP is a new hallmark of RMS and normal embryonic skeletal muscle development. Pharmacological reversal of APP pathway downregulation could be achieved using drugs targeting DNA methylation or class I/IV HDACs, and enhanced T cell cytotoxicity against RMS when used in combination. Overall, these findings may explain the historical lack of RMS responsiveness to immunotherapy and unlocks new immunotherapy strategies against RMS that rely on targeting MHC-I antigens. Citation Format: David Milewski, Hsien-Chao Chou, Vineela Gangalapudi, Meijie Tian, Yong Kim, Young Song, Jun Wei, Javed Khan. Suppression of antigen presentation in pediatric rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB403.

Abstract LB367: Effects of modulation of ERAP1 activity in antigen processing and presentation

Abstract ERAP1 is an enzyme that plays a key role in the antigen processing and presentation pathway as an editor of the peptide repertoire, allowing for the binding of neoantigens to MHC I. ERAP1 is polymorphic, with the different allelic variants showing various degrees of peptide trimming function expressed in humans. However, the trimming mechanism by which ERAP1 trims peptides is still not fully understood. The purpose of the study is to characterize the effect of the different ERAP1 variants and their inhibition on the peptide repertoire presented by tumor cells, enabling us to gain valuable insights into how this process works. This characterization will also enhance the pharmacological modulation of ERAP1, which has already been proven to promote T cell and NK-mediated anti-tumor cytotoxic response. By specifically targeting the activity levels of the ERAP1 variant expressed, we can adopt a personalized approach that maximizes the potential production of neoantigens, crucial for activating an anti-tumor immune response. We CRISPR knocked out the ERAP1 gene in the CT26 cell line and assessed the MHC I kinetics and stability by investigating the dissociation of pMHC complexes at the cell surface, using a Brefeldin-A decay assay and an acid-stripping test compared to wild-type. The assessment of MHC I assembly and cell surface expression kinetics showed higher MHC I in the ERAP1 KO cell line, highlighting that the lack of ERAP1 translated into a faster recovery time of peptide/MHC complexes at the cell surface. After assessing the kinetics, we re-expressed different human ERAP1 allotypes in CT26 ERAP1KO cell line through retroviral transduction and characterized MHC I expression levels through flow cytometry. Interestingly, MHC I expression levels varied across the transduced samples, with specific variants showing much higher expression levels indicating more peptide availability for loading onto the MHC molecules. Immunopeptidomic analysis comparing the WT, ERAP1 KO and the CT26 human ERAP1 transduced cell lines, showed distinct subsets of neoantigens presented in the KO cell line. ERAP1 plays a significant role in the assembly and recovery of peptide/MHC complexes. The reintroduction of different ERAP1 allelic variants greatly alters MHC I expression levels suggesting the formation of new peptide-MHC complexes responsible for the increase in MHC I expression. Modulation of ERAP1 activity significantly alters the presented peptide repertoire , uncovering neoantigens which are potentially immunogenic. Citation Format: Shami Alvarez Mourid, Edward James, Dario Guglietta, Emma Reeves. Effects of modulation of ERAP1 activity in antigen processing and presentation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB367.

Birinapant Reshapes the Tumor Immunopeptidome and Enhances Antigen Presentation.

Birinapant, an antagonist of the inhibitor of apoptosis proteins, upregulates MHCs in tumor cells and displays a better tumoricidal effect when used in combination with immune checkpoint inhibitors, indicating that Birinapant may affect the antigen presentation pathway; however, the mechanism remains elusive. Based on high-resolution mass spectrometry and in vitro and in vivo models, we adopted integrated genomics, proteomics, and immunopeptidomics strategies to study the mechanism underlying the regulation of tumor immunity by Birinapant from the perspective of antigen presentation. Firstly, in HT29 and MCF7 cells, Birinapant increased the number and abundance of immunopeptides and source proteins. Secondly, a greater number of cancer/testis antigen peptides with increased abundance and more neoantigens were identified following Birinapant treatment. Moreover, we demonstrate the existence and immunogenicity of a neoantigen derived from insertion/deletion mutation. Thirdly, in HT29 cell-derived xenograft models, Birinapant administration also reshaped the immunopeptidome, and the tumor exhibited better immunogenicity. These data suggest that Birinapant can reshape the tumor immunopeptidome with respect to quality and quantity, which improves the presentation of CTA peptides and neoantigens, thus enhancing the immunogenicity of tumor cells. Such changes may be vital to the effectiveness of combination therapy, which can be further transferred to the clinic or aid in the development of new immunotherapeutic strategies to improve the anti-tumor immune response.

Hippo-signaling-controlled MHC class I antigen processing and presentation pathway potentiates antitumor immunity

The major histocompatibility complex class I (MHC class I)-mediated tumor antigen processing and presentation (APP) pathway is essential for the recruitment and activation of cytotoxic CD8+ T lymphocytes (CD8+ CTLs). However, this pathway is frequently dysregulated in many cancers, thus leading to a failure of immunotherapy. Here, we report that activation of the tumor-intrinsic Hippo pathway positively correlates with the expression of MHC class I APP genes and the abundance of CD8+ CTLs in mouse tumors and patients. Blocking the Hippo pathway effector Yes-associated protein/transcriptional enhanced associate domain (YAP/TEAD) potently improves antitumor immunity. Mechanistically, the YAP/TEAD complex cooperates with the nucleosome remodeling and deacetylase complex to repress NLRC5 transcription. The upregulation of NLRC5 by YAP/TEAD depletion or pharmacological inhibition increases the expression of MHC class I APP genes and enhances CD8+ CTL-mediated killing of cancer cells. Collectively, our results suggest a crucial tumor-promoting function of YAP depending on NLRC5 to impair the MHC class I APP pathway and provide a rationale for inhibiting YAP activity in immunotherapy for cancer.

Immune Cytolytic Activity and Strategies for Therapeutic Treatment.

Intratumoral immune cytolytic activity (CYT), calculated as the geometric mean of granzyme-A (GZMA) and perforin-1 (PRF1) expression, has emerged as a critical factor in cancer immunotherapy, with significant implications for patient prognosis and treatment outcomes. Immune checkpoint pathways, the composition of the tumor microenvironment (TME), antigen presentation, and metabolic pathways regulate CYT. Here, we describe the various methods with which we can assess CYT. The detection and analysis of tumor-infiltrating lymphocytes (TILs) using flow cytometry or immunohistochemistry provide important information about immune cell populations within the TME. Gene expression profiling and spatial analysis techniques, such as multiplex immunofluorescence and imaging mass cytometry allow the study of CYT in the context of the TME. We discuss the significant clinical implications that CYT has, as its increased levels are associated with positive clinical outcomes and a favorable prognosis. Moreover, CYT can be used as a prognostic biomarker and aid in patient stratification. Altering CYT through the different methods targeting it, offers promising paths for improving treatment responses. Overall, understanding and modulating CYT is critical for improving cancer immunotherapy. Research into CYT and the factors that influence it has the potential to transform cancer treatment and improve patient outcomes.

Abstract 542: Development of novel syngeneic tumor models with intrinsic or extrinsic resistance mechanisms to PD-1 blockade

Abstract Programmed cell death-1 (PD-1) blockade has demonstrated remarkable clinical efficacy across various tumor types. However, the current PD-1 blockade monotherapy benefits only a small proportion of patients, and primary or acquired resistance can ultimately lead to cancer progression in clinical settings. Understanding the underlying mechanisms of resistance is both necessary and urgent to enhance clinical outcomes. Increasing evidence suggests that resistance to PD-1 therapy can arise from both tumor-cell-intrinsic and tumor-cell-extrinsic factors. Loss-of-function mutations in the antigen presentation pathway and downstream elements represent intrinsic mechanisms, while tumor-infiltrating immunosuppressive cells such as regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and tumor-associated macrophages (TAMs) contribute to immune tolerance as extrinsic factors. Currently, the rational design of combination therapies based on these resistance mechanisms remains to be achieved. In this study, we developed two types of anti-PD-1 antibody-resistant models based on the intrinsic anti-PD-1 treatment-sensitive MC38 models. These models include genetically engineered resistant models with B2M or STK11 knockout (KO) and induced resistant models through in vivo progressive drug selection. STK11 KO mutations resulted in reduced expression of PD-L1 on tumor cells and a lower infiltration of CD8+ cytotoxic T lymphocytes in the tumor microenvironment, while B2M KO led to a lack of antigen presentation on the tumor cell surface, blocking the binding of the anti-PD-1 antibody. In terms of the induced anti-PD-1 resistant models, a higher proportion of immunosuppressive cells, including Tregs, MDSCs, and TAMs, were observed in the tumor microenvironment compared to the parental counterparts, contributing to immune escape from PD-1 blockade. These models simulate extrinsic and intrinsic mechanism-based anti-PD-1 resistance, allowing for the identification of combination therapies to overcome resistance to anti-PD-1. Our study enhances our understanding of the biological basis of anti-PD-1 resistance and supports the discovery of mechanistically-designed combination therapies to overcome resistance to anti-PD-1 therapy, potentially broadening its clinical applicability. Citation Format: Xiaomin Wang, Ziwei Zhang, Longzhou Liu, Xue Zhang, Dong Wang, Nengwei Xu, Xiangnan Qiang, Qingyang Gu, Jian Xiang, Zhixiang Zhang. Development of novel syngeneic tumor models with intrinsic or extrinsic resistance mechanisms to PD-1 blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 542.

Abstract 6400: Tislelizumab combined with XELOX as a neoadjuvant therapy for locally advanced gastric and gastroesophageal junction adenocarcinomas: A prospective, phase II trial

Abstract Background: Combing anti-PD-(L)1 antibody with chemotherapy in neoadjuvant therapy of gastric/gastroesophageal junction (G/GEJ) adenocarcinomas is a promising strategy, but clinical data are remain insufficient. Whether immunotherapy biomarkers in previous studies (TMB, MSI, PD-L1, etc.) have equivalent predictive value for G/GEJ remains to be verified. In this phase II clinical trial of tislelizumab in combination with chemotherapy, potential therapy-related biomarkers in tumor samples, and changes in the tumor microenvironment during treatment were analyzed, and a predictive model for efficacy was developed. Methods: This was a prospective, single-center, single-arm, phase II trial. Patients with G/GEJ adenocarcinomas (stage cT3-4aN+M0) were treated with PD-1 inhibitor tislelizumab in combination with oxaliplatin plus capecitabine (XELOX) as neoadjuvant treatment for 2 or 3 cycles. The primary endpoint was the major pathological response (MPR). The secondary endpoints included pathological complete response (pCR) rate, R0 resection rate, and safety. Tumor samples underwent RNA-sequencing (Amoy Diagnostics Co Ltd, Xiamen, China), to identify potential biomarkers, and a predictive model was developed to explore factors influencing tumor response and survival. Results: 28 patients were enrolled; mean age was 59.5 years (SD = 8.2), 19 (67.9%) patients were male; 14 (50.0%) patients with primary tumor location in the stomach, and 14 (50.0%) patients with primary tumor location in the GEJ. All patients were EB virus negative. Except one patient with PMS2 loss, 27 patients were pMMR. Nine (32.1%) patients achieved MPR after treatment, with four (14.3%) of them achieved pCR. The R0 resection rate was 96.4%, with 14 (50.0%) patients achieved objective response. No serious adverse events were reported. The most common grade 2 TRAEs during neoadjuvant treatment were anemia (5 of 28, 17.86%) and nausea (3 of 28, 10.71%). Analysis of differentially expressed genes revealed enrichment of the antigen processing and presentation pathway in the MPR group, while the TGF-β signaling pathway was enriched in the non-MPR group. Notably, the differential immune microenvironment analysis also uncovered significant differences in the TGF-β signature between the MPR and non-MPR groups. Additionally, a therapeutic response prediction model (HT score) was developed with an AUC of 0.98 (0.932-1) in the training set, and its performance was validated in publicly available datasets. Conclusion: Tislelizumab combined with XELOX holds promise as a neoadjuvant therapy for resectable G/GEJ adenocarcinomas, especially for EBV- and pMMR population, offering a well-tolerated safety profile. Moreover, the HT score has the potential to predict treatment efficacy in this regimen. Trial registration numbers: NCT05507658 and NCT05508399. Citation Format: Haikun Zhou, Tao Han, Lei Tuo, Qingchuan Yang, Ruiqi Gao, Pengfei Yu, Jiangpeng Wei, Changbin Zhu, Jin Wang, Peng Cheng, Xiang Kang, Sihui Pi, Hui Liu, Xiaoxi Pan, Xiaohua Li, Gang Ji. Tislelizumab combined with XELOX as a neoadjuvant therapy for locally advanced gastric and gastroesophageal junction adenocarcinomas: A prospective, phase II trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6400.

Abstract 73: Spatial profiling of pediatric rhabdomyosarcoma to elucidate their immunosuppressive tumor microenvironment

Abstract Background: Pediatric rhabdomyosarcoma (RMS) is a mesenchymal soft tissue malignancy. Despite intensive chemotherapy regimens, there is currently a gap in improving treatment outcomes for RMS. Chemotherapy can modulate the tumor microenvironment (TME) by altering the immune cell composition or their functions. However, the impact of chemotherapy in pediatric RMS TME is unclear. RMS tumors are also considered as “cold” tumors due to low immune infiltration, which could be a determinant of why immunotherapy is unlikely to work. Additional investigations are required to determine the reasons of why RMS is “cold” and whether a combined immunotherapy and chemotherapy approach should be administered for this hard-to-cure cancer. Methods We conducted for the first time spatial GeoMx whole transcriptome atlas and 51-plex Akoya CODEX profiling for a tissue microarray (TMA) from a cohort of pediatric RMS patients (n = 12) with pre-chemotherapy (n = 5) and post-chemotherapy (n = 5) samples. Regions of interest (ROIs) were selected based on tumor areas with immune cell infiltration, with the lymphocytes, tumor cells, and nuclei visualized using fluorescent morphological markers CD45, Desmin, and DAPI. ROIs were segmented into tumor stroma compartments and immune cell compartments. Computational analyses were conducted on the transcriptomics data using R package standR including quality control, normalization, differential expression analysis, gene set enrichment analysis, and cell type deconvolution. For CODEX data, we preformed cell segmentation, followed by further quality control, cell phenotyping, cellular neighborhood and cellular interaction analysis. Results: From differential expression analysis of the immune compartment, we have identified type I interferon-related genes (DTX3L, ADAP2, RNF135) and reactive oxygen species (ROS)-induced gene (NCF1) are upregulated, and an antioxidant enzyme gene (PRDX2) is downregulated in post-chemotherapy samples compared to pre-chemotherapy samples. Gene set enrichment analysis of the immune compartment revealed an enriched antigen presentation pathway in post-chemotherapy samples. In the tumor stroma compartment, we identified increased TGF-β binding pathway in post-chemotherapy samples. Cellular deconvolution revealed a higher proportion of endothelial cells in post-chemotherapy samples, which is validated via CODEX imaging analysis. Cellular neighborhoods and cell-cell interaction analysis for CODEX data also reveal how chemotherapy affect functional units and cellular interactions in RMS TME with spatial context preserved. Conclusion: By applying spatial transcriptomic and multiplexed imaging to RMS samples, we have revealed key genes, pathways and cell types involved in chemotherapy-induced alterations in the TME. This will provide a new perspective for developing novel chemoimmunotherapy for RMS patients. Citation Format: Cui Tu, Chin Wee Tan, Ning Liu, Arutha Kulasinghe, Fernando Souza-Fonseca-Guimaraes. Spatial profiling of pediatric rhabdomyosarcoma to elucidate their immunosuppressive tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 73.

Abstract 3766: Utilizing whole-transcriptome digital spatial profiling for glioblastoma clinical biomarker discovery

Abstract Objective: IDH-wildtype glioblastoma (GBM) is the most aggressive brain tumor in adults. Notable for substantial inter- and intra-tumoral heterogeneity, GBM is highly resistant to standard-of-care treatment. Emerging spatial omics technologies, such as GeoMx Digital Spatial Profiling (DSP), offer novel approaches to interrogate the molecular features of regionally defined cellular ecosystems in cancer. Here, we leverage DSP to study whole-transcriptome gene expression signatures in a spatially defined manner across five IDH-wildtype GBMs. Methods: Formalin-fixed paraffin-embedded tumors were assessed histologically and three spatially distinct areas from each tumor were used to construct a custom “spatial” tissue microarray. From each set of three areas, we identified nine spatially distinct regions of interest (ROIs) for bulk transcriptomic analysis according to two histopathological features: distribution (cellular tumor core or tumor periphery) and vascular proximity (near or far). We evaluated normalized target expression data statistically using linear mixed modeling (LMM) with Benjamini-Hochberg correction. Results: 44 profiled ROIs and 8531 transcriptomic targets were analyzed following quality control trimming. 3D principal component analysis and unsupervised hierarchical clustering analysis showed clustering according to tumor specimen as well as distribution (core versus periphery), thereby substantiating the presence of inter- and intra-tumoral transcriptional heterogeneity. LMM-based differential gene expression analysis identified distinct molecular signatures when comparing core and periphery. Specifically, we observed elevated log2-transformed expression of migration and proliferation markers including LAMC1 (p=0.00297) and FABP7 (p=0.00434) in core ROIs and neurodevelopmental markers including NTRK2 (p=0.00734) and DAAM2 (p=0.00263) in periphery ROIs. Additionally, reactome analysis demonstrated considerable enrichment for the aberrant programmed cell death pathway (R-HSA-9645723, coverage=71.84%) in core ROIs and the MHC class II antigen presentation pathway (R-HSA-2132295, coverage=69.11%) in periphery ROIs. Interestingly, differential gene expression analysis did not reveal any biologically significant targets when subsetting for vascular proximity within cellular tumor core ROIs. However, reactome analysis of this regional subset demonstrated upregulation of various cellular proliferation pathways (G2/M transition, APC/C activity, DNA synthesis, etc.) within vessel-near ROIs when compared with vessel-far ROIs. Conclusions: We preliminarily characterize the molecular heterogeneity of GBM using a spatially guided approach. Ongoing analyses are focused on dataset validation, mixed cell deconvolution, further regional genotyping, and potential biomarkers. Citation Format: Adam Luo, Kelly Casella, Shivang Sharma, Ezra Baraban, Calixto-Hope Lucas, Eugene Shenderov. Utilizing whole-transcriptome digital spatial profiling for glioblastoma clinical biomarker discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3766.

The balance between nuclear import and export of NLRC5 regulates MHC class I transactivation

MHC (major histocompatibility complex) class I molecules play an essential role in regulating the adaptive immune system by presenting antigens to CD8 T cells. CITA (MHC class I transactivator), also known as NLRC5 (NLR family, CARD domain-containing 5), regulates the expression of MHC class I and essential components involved in the MHC class I antigen presentation pathway. While the critical role of the nuclear distribution of NLRC5 in its transactivation activity has been known, the regulatory mechanism to determine the nuclear localization of NLRC5 remains poorly understood. In this study, a comprehensive analysis of all domains in NLRC5 revealed that the regulatory mechanisms for nuclear import and export of NLRC5 coexist and counterbalance each other. Moreover, GCN5 (general control non-repressed 5 protein), a member of HATs (histone acetyltransferases), was found to be a key player to retain NLRC5 in the nucleus, thereby contributing to the expression of MHC class I. Therefore, the balance between import and export of NLRC5 has emerged as an additional regulatory mechanism for MHC class I transactivation, which would be a potential therapeutic target for the treatment of cancer and virus-infected diseases.

Multi-Omics Analysis of Gut Microbiota and Host Transcriptomics Reveal Dysregulated Immune Response and Metabolism in Young Adults with Irritable Bowel Syndrome.

The integrated dysbiosis of gut microbiota and altered host transcriptomics in irritable bowel syndrome (IBS) is yet to be known. This study investigated the associations among gut microbiota and host transcriptomics in young adults with IBS. Stool and peripheral blood samples from 20 IBS subjects and 21 healthy controls (HCs) collected at the baseline visit of an RCT were sequenced to depict the gut microbiota and transcriptomic profiles, respectively. The diversities, composition, and predicted metabolic pathways of gut microbiota significantly differed between IBS subjects and HCs. Nine genera were significantly abundant in IBS stool samples, including Akkermansia, Blautia, Coprococcus, Granulicatella, Holdemania, Oribacterium, Oscillospira, Parabacteroides, and Sutterella. There were 2264 DEGs found between IBS subjects and HCs; 768 were upregulated, and 1496 were downregulated in IBS participants compared with HCs. The enriched gene ontology included the immune system process and immune response. The pathway of antigen processing and presentation (hsa04612) in gut microbiota was also significantly different in the RNA-seq data. Akkermansia, Blautia, Holdemania, and Sutterella were significantly correlated with ANXA2P2 (upregulated, positive correlations), PCSK1N (downregulated, negative correlations), and GLTPD2 (downregulated, negative correlations). This study identified the dysregulated immune response and metabolism in IBS participants revealed by the altered gut microbiota and transcriptomic profiles.

Comparative Transcriptome Analysis Reveals the Light Spectra Affect the Growth and Molting of Scylla paramamosain by Changing the Chitin Metabolism.

Light is an essential ecological factor that has been demonstrated to affect aquatic animals' behavior, growth performance, and energy metabolism. Our previous study found that the full-spectrum light and cyan light could promote growth performance and molting frequency of Scylla paramamosain while it was suppressed by violet light. Hence, the purpose of this study is to investigate the underlying molecular mechanism that influences light spectral composition on the growth performance and molting of S. paramamosain. RNA-seq analysis and qPCR were employed to assess the differentially expressed genes (DEGs) of eyestalks from S. paramamosain reared under full-spectrum light (FL), violet light (VL), and cyan light (CL) conditions after 8weeks trial. The results showed that there are 5024 DEGs in FL vs. VL, 3398 DEGs in FL vs. CL, and 3559 DEGs in VL vs. CL observed. GO analysis showed that the DEGs enriched in the molecular function category involved in chitin binding, structural molecular activity, and structural constituent of cuticle. In addition, the DEGs in FL vs. VL were mainly enriched in the ribosome, amino sugar and nucleotide sugar metabolism, lysosome, apoptosis, and antigen processing and presentation pathways by KEGG pathway analysis. Similarly, ribosome, lysosome, and antigen processing and presentation pathways were major terms that enriched in FL vs. CL group. However, only the ribosome pathway was significantly enriched in up-regulated DEGs in VL vs. CL group. Furthermore, five genes were randomly selected from DEGs for qPCR analysis to validate the RNA-seq data, and the result showed that there was high consistency between the RNA-seq and qPCR. Taken together, violet light exposure may affect the growth performance of S. paramamosain by reducing the ability of immunity and protein biosynthesis, and chitin metabolism.

Dandruff lesional scalp skin exhibits epidermal T cell infiltration and a weakened hair follicle immune privilege.

Dandruff is characterised by the presence of perivascular leukocytes and mild inflammation; however, the immune microenvironment of dandruff-affected scalp skin and the potential changes to the hair follicle's (HF) physiological immune privilege (HF IP) remain unknown. Here, we characterised the HF immune microenvironment and immune privilege status in dandruff-affected scalp skin. We assessed relevant key parameters in healthy versus dandruff-affected human scalp biopsies using quantitative immunohistomorphometry, laser capture microdissection, and RNA sequencing. The number of epidermal CD4+ and CD8+ T cells was increased in lesional dandruff scalp skin, while the number of MHC class II+/CD1a+ Langerhans cells was decreased in the infundibulum. The number of intrafollicular and perifollicular CD4+ T cells and CD8+ T cells, perifollicular CD68+ macrophages, and tryptase+ mast cells remained unchanged. Interestingly, MHC class Ia and ß2-microglobulin protein expression were significantly increased specifically in the suprabulbar outer root sheath (ORS) compartment of dandruff-associated HFs. RNAseq analysis of laser capture micro-dissected suprabulbar ORS compartment revealed antigen presentation pathway as the top regulated canonical pathway, along with the upregulation of HF-IP genes such as HLA-C, HLA-DP, and TAP1, which are normally down-regulated in healthy HFs. Intrafollicular protein expression of known HF IP guardians (CD200 and α-MSH) and 'danger signals' (MICA and CXCL10) remained unaltered at the IP sites of dandruff lesional HFs compared to non-lesional and healthy HFs. Instead, the expression of macrophage migration inhibiting factor (MIF), another HF IP guardian, was reduced. Together, this work shows that dandruff is associated with epidermal T-cell infiltration and a weakened HF IP in the suprabulbar ORS of HFs in dandruff lesional scalp.

The immune cell transcriptome is modulated by vitamin D3 supplementation in people with a first demyelinating event participating in a randomized placebo-controlled trial

Vitamin D deficiency is a risk factor for developing multiple sclerosis. The PrevANZ trial was conducted to determine if vitamin D3 supplementation can prevent recurrent disease activity in people with a first demyelinating event. As a sub-study of this trial, we investigated the effect of supplementation on peripheral immune cell gene expression. Participants were randomized to 1000, 5000 or 10,000 international units daily of vitamin D3 or placebo. Peripheral blood was collected at baseline and 12 weeks and sent for ribonucleic acid sequencing. Datasets from 55 participants were included. Gene expression was modulated by high dose supplementation. Antigen presentation and viral response pathways were upregulated. Oxidative phosphorylation and immune signaling pathways, including tumor necrosis factor-alpha and interleukin-17 signaling, were downregulated. Overall, vitamin D3 supplementation for 12 weeks modulated the peripheral immune cell transcriptome with induction of anti-inflammatory gene expression profiles. Our results support a dose-dependent effect of vitamin D3 supplementation on immune gene expression.