Gene Activation In Cells Research Articles

IMMU-15. CD74/MIF SIGNALING AXIS DISRUPTION IN BONE MARROW-DERIVED MYELOID CELLS DELAYS MALIGNANT PROGRESSION IN A PRECLINICAL MODEL OF GLIOMA

Abstract INTRODUCTION CD74, a chaperone associated with the major histocompatibility complex class II (MHC-II), plays a crucial role in assembling and transporting MHC-II molecules on the cellular surface. Beyond its physiological function in antigen presentation, CD74 is a negative regulator of inflammation, and its dysregulation is associated with inflammatory disorders and cancer. Notably, tumor stem cells release macrophage migration inhibitory factor (MIF) to trigger CD74 immunosuppressive signaling in tumor-infiltrating immune cells, thereby abrogating CD8+ T cell activation and promoting angiogenesis. While CD74 expression is known in dendritic cells, macrophages and B cells, our recent findings reveal its upregulation in immunosuppressive macrophages within the low-grade glioma (LGG) tumor microenvironment, and its negative correlation with the survival of adolescent and young adult patients with LGG. HYPOTHESIS. We hypothesize that inhibiting CD74/MIF in immunosuppressive myeloid cells may affect tumor progression and prevent malignant transformation (MT) to high-grade glioma (HGG). METHODS To test our hypothesis, we isolated bone marrow cells from immunocompetent RCAS n/tv-a LGG bearing animals, differentiated them into bone marrow-derived myeloid cells (BMDMs), silenced CD74 expression, and co-cultured them with primary CD8+T cells. Moreover, we inhibited CD74/MIF signaling in vivo. RESULTS. Deconvolution analysis of tumor-infiltrating immune cells revealed upregulation of CD74 and its network in myeloid cells during LGG compared to HGG. Silencing CD74 in LGG BMDMs in vitro resulted in the downregulation of genes associated with migration, proliferation, and immunosuppression. The co-culture of LGG CD74KD-BMDMs with CD8+ T cells increased the expression of T cell activation genes. In vivo treatment of LGG mice with MIF inhibitors significantly decreased myeloid cell infiltration in the tumor microenvironment (TME) and prolonged survival. CONCLUSIONS These preclinical studies highlight a role for the CD74/MIF signaling axis in glioma and present a novel immunotherapeutic target to modulate the activity of immunosuppressive myeloid cells in order to delay MT.

IMMU-16. ANTI-VEGF TREATMENT EFFECT AGAINST GLIOMA IS IMMUNE DEPENDENT AND MEDIATED BY ENHANCED T CELL ACTIVITY

Abstract Immunotherapy trials in glioblastoma patients increasingly avoid immunosuppressive steroids and consider bevacizumab as alternative anti-edema treatment. Since VEGF is also a potent immunosuppressive factor, we explored the dimension and mechanisms of immune-mediated effects of anti-VEGF treatment. Murine glioma cells were injected intracerebrally into C57BL/6 wild-type mice or immunodeficient Pfp/Rag2 knockout mice and animals were treated with B20 (anti-murine VEGF) or dexamethasone. Immune cells were profiled by flow cytometry, and RNAseq was performed on sorted tumor and immune cells at different timepoints. B20 prolonged the survival of immunocompetent mice but not of Pfp/Rag2 knockout mice, indicating that the immune system is essential for its effect. At an early timepoint when controls became symptomatic, B20 “early” tumors (B20-ea) showed increased infiltration with T cells and myeloid cells, and decreased vascularization, whereas B20 tumors at the survival endpoint resembled IgG-controls. Gene expression in B20-ea tumor cells was dominated by hypoxia, neural development, invasion, TGF-β, Notch and Wnt signatures as well as concerted upregulation of Kmt2 H3K4 methyltransferases. In CD11b+ myeloid cells from B20-ea tumors, M1 hallmark genes and T cell activation genes were upregulated, while M2 genes were downregulated. Deconvolution revealed a transient shift towards pro-immune microglia/macrophages as well as increased NK cells and DCs. In CD8+ and CD4+ T cells, B20 increased the expression of S1pr1 and α/β TCR genes. The proportion of progenitor-like exhausted CD8+ cells, which are responsive to PD-1 blockade, was increased in B20-ea. In CD4+ cells, B20 caused skewing towards TFH, while dexamethasone increased TH2 cytokine expression. Depletion experiments demonstrated that CD8+ and CD4+ T cells but not NK cells were necessary for the survival-prolonging effect of B20. To conclude, anti-VEGF therapy has significant immunostimulatory effects which are, however, largely transient, so that an early treatment window of opportunity may exist during which it could actively support immunotherapy.

Possible involvement of Toll-like receptor 8-positive monocytes/macrophages in the pathogenesis of Sjögren's disease.

Sjögren's disease (SjD) is an autoimmune disease marked by lymphocytic infiltration of salivary and lacrimal glands, leading to glandular dysfunction, where CD4-positive helper T (Th) cells and their cytokines are crucial in the pathogenesis. Recent studies have demonstrated that Toll-like receptors (TLRs), particularly those recognizing immune complexes containing DNA and RNA, contribute to Th cell activation in various autoimmune diseases. This study explores the expression and function of these TLRs in SjD. DNA microarray analysis of salivary gland tissue from six SjD patients and real-time PCR (n = 32) was used to identify overexpressed TLRs. Single-cell RNA sequencing (scRNA-seq) was performed using tissue lesions and integrated with published scRNA-seq data from tissues and peripheral blood mononuclear cells to examine gene expression in macrophages and monocytes. Finally, multi-color immunofluorescence staining was conducted to confirm TLR8 expression and function in SjD lesions (n = 19). DNA microarray analysis revealed the up-regulation of TLR8, along with other TLRs and innate immune response genes in SjD. Real-time PCR showed significant up-regulation of TLR7 and TLR8. TLR8 up-regulated in both analyses. In scRNA-seq analysis, the TLR8-expressing cluster comprised macrophages and monocytes, which also produced T cell activation genes like CD86. TLR8-positive macrophages infiltrated inflammatory sites and frequently expressed CD86 in quantitative imaging approaches. These results suggest that infiltrating monocytes and macrophages may produce cytokines and chemokines through TLR8 stimulation, potentially enhancing B7 molecule expression, promoting the adaptive immune response, and contributing to SjD pathogenesis.

Abstract 114: Identification of the actionable target, LILRB4, through genetic linkage analysis of Diversity Outbred (DO) F1 mice expressing HER2(neu)

Abstract Our goal is to identify, in situ, the regulatory genes that dictate the onset age and growth rate of spontaneously arising tumors to implement new intervention strategies. For genetic linkage analysis, we crossed HER2(neu) Tg mice with Diversity Outbred (DO) mice, an outbred population comprised of 8 founding strains (A/J, C57BL/6J, 129S1/SvlmJ, NOD/ShiLtJ, NZO/HILtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) maintained by non-sibling crossing to ensure each mouse is genetically unique. Using R/QTL package, we linked Quantitative Trait Loci (QTL) in Chr 1 and X with tumor onset age, and a Chr 10 QTL with tumor growth rate. The Chr1 (=human Chr2) QTL was linked to human breast cancer diagnosis in 11 Genome-Wide Association Studies (GWAS; the human GWAS catalog, https://www.ebi.ac.uk/gwas/). Because human GWAS data is deficient in Chr X mapping and also does not assess tumor growth rate as a trait, the QTL loci identified in mouse Chr X and 10 were discoveries beyond the capacity of human GWAS. In total, we identified 26 candidate genes across the 3 QTL. For clinical validation, the genes were analyzed with CodeAI (Caris LS) which associated cancer patient clinical data with candidate gene expression. We found 21/26 genes significantly associated with the survival of patients with primary (n=3,533) and/or metastatic (n=4,870) breast cancers and 17/26 were associated with lung cancer (n=11,334) survival, with 13 overlapping genes between lung and breast cancer, indicating broad applicability of these candidate genes. We interrogated the immune status in BALB NeuT and (BALBxPWK)F1 NeuT mice because the F1 mice developed tumors around 9 wk, much earlier than the 14 wk observed in BALB NeuT mice. Surprisingly, (BALBxPWK)F1 mice responded to cancer vaccines more vigorously. Single cell RNA (scRNA) libraries from (BALBxPWK)F1 NeuT tumors showed an expanded lymphocyte cluster (12%), compared with BALB NeuT (2%) and an enrichment of T cell activation genes. These findings may reflect a deficiency in tumor cell recognition by the activated anti-tumor effectors and a window of opportunity for correction. Of the 21 candidate genes, LILRB4, a myeloid cell checkpoint molecule, was of particular interest. Expression of LILRB4 is predictive of patient survival in both breast and lung cancer. Using scRNA sequencing, we found this transmembrane receptor expressed primarily by tumor infiltrating myeloid cells. In a reported scRNA sequencing dataset (GSE161529), LILRB4 was expressed by infiltrating macrophages in human breast cancers, and is also correlated with reduced survival. In a PAN Cancer ATACseq dataset (Corces et al., 2018), promoter accessibility of LILRB4 was associated with reduced survival. Taken together, there are multiple immune regulatory mechanisms of tumor progression and LILRB4 is an important new actionable target. CA76340 (WZW), KCI TBM program (JBJ) and CCSG P30 CA022453 (GB). Citation Format: Jennifer B. Jacob, Wei-Zen Wei, Benjamin L. Kidder, Tolulope Adeyelu, Andrew Elliott, Gerold Bepler, Joyce D. Reyes. Identification of the actionable target, LILRB4, through genetic linkage analysis of Diversity Outbred (DO) F1 mice expressing HER2(neu) [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 114.

Serine and Arginine-Rich Splicing Factor 3 Promotes the Activation of Quiescent Mouse Neural Stem Cells.

The quiescence and activation of adult stem cells are regulated by many kinds of molecular mechanisms, and RNA alternative splicing participates in regulating many cellular processes. However, the relationship between stem cell quiescence and activation regulation and gene alternative splicing has yet to be studied. In this study, we aimed to elucidate the regulation of stem cell quiescence and activation by RNA alternative splicing. The upregulated genes in activated mouse neural stem cells (NSCs), muscle stem cells, and hematopoietic stem cells were collected for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The genes from three tissue stem cells underwent Venn analysis. The mouse NSCs were used for quiescence and reactivation induction. The immunostaining of cell-specific markers was performed to identify cell properties. The reverse transcription-polymerase chain reaction and western blotting were used to detect the gene expression and protein expression, respectively. We found that the upregulated genes in activated stem cells from three tissues were all enriched in RNA splicing-related biological processes; the upregulated RNA splicing-related genes in activated stem cells displayed tissue differences; mouse NSCs were successfully induced into quiescence and reactivation in vitro without losing differentiation potential; serine and arginine-rich splicing factor 3 (Srsf3) was highly expressed in the activated mouse NSCs, and the overexpression of SRSF3 protein promoted the activation of quiescent mouse NSCs and increased the neural cell production. Our data indicate that the alternative splicing change may underline the transition of quiescence and activation of stem cells. The manipulation of the splicing factor may benefit tissue repair by promoting the activation of quiescent stem cells.

Sustained store-operated calcium entry utilizing activated chromatin state leads to instability in iTregs.

Thymus-originated tTregs and in vitro induced iTregs are subsets of regulatory T cells. While they share the capacity of immune suppression, their stabilities are different, with iTregs losing their phenotype upon stimulation or under inflammatory milieu. Epigenetic differences, particularly methylation state of Foxp3 CNS2 region, provide an explanation for this shift. Whether additional regulations, including cellular signaling, could directly lead phenotypical instability requires further analysis. Here, we show that upon TCR (T cell receptor) triggering, SOCE (store-operated calcium entry) and NFAT (nuclear factor of activated T cells) nuclear translocation are blunted in tTregs, yet fully operational in iTregs, similar to Tconvs. On the other hand, tTregs show minimal changes in their chromatin accessibility upon activation, in contrast to iTregs that demonstrate an activated chromatin state with highly accessible T cell activation and inflammation related genes. Assisted by several cofactors, NFAT driven by strong SOCE signaling in iTregs preferentially binds to primed-opened T helper (TH) genes, resulting in their activation normally observed only in Tconv activation, ultimately leads to instability. Conversely, suppression of SOCE in iTregs can partially rescue their phenotype. Thus, our study adds two new layers, cellular signaling and chromatin accessibility, of understanding in Treg stability, and may provide a path for better clinical applications of Treg cell therapy.

Baseline Immune State and T Cell Clonal Kinetics Are Associated with Response to CAR-T Therapy in Large B-Cell Lymphoma

Engineered adoptive cellular therapy with CD19-targeting chimeric antigen receptor T-cells (CART) has revolutionized the treatment landscape for patients with relapsed/refractory (R/R) large B cell lymphoma (LBCL); however, failure rates remain high. Thus, improved molecular understanding of patient and treatment characteristics linked to response are urgently needed to define the basis for achieving sustained remission. Single cell technologies have the power to evaluate heterogenous populations and provide unprecedented ability to track T cell clonal kinetics. Here we focused on patients with R/R LBCL treated with axicabtagene ciloleucel (axi-cel), from whom we collected serial peripheral blood mononuclear cell (PBMC) samples from Day -30 to +28 relative to CAR-T infusion, as well as bag washings from infusion products (IPs). We evaluated 308,357 single cell transcriptomes (10x Genomics) from serial PBMCs and IPs from 29 patients (16 responders [R], 13 non-responders [NR], R defined as complete [CR] or partial response [PR] at 1 year, NR defined as progressive disease [PD] by 1 year), of which 220,653 originated from 19 patients in a previously reported cohort generated from our center (Haradhvala et al., Nat Med, 2022) and 87,704 newly generated from 10 of 50 patients (29 R, 21 NR) from an extension cohort on whom flow cytometry and mass cytometry (CyTOF) were also generated. With this expanded power, we systematically evaluated baseline and immediate post-treatment samples for features associated with durable response. While we observed no quantitative differences in post-infusion circulating immune subsets in R versus NR, scRNA-seq analysis yielded two notable findings at baseline (Day -30). First, the proportion of B cells (mostly naïve B cells) was increased in R (n=12) compared to NR (n=7) (p=0.012). Protein expression by flow cytometry in the full extension cohort (of whom 20 [13 R, 7 NR] had available PBMC data at baseline) revealed a trend towards increased B cells in R (p=0.16), dominated by four exceptional outliers in whom B cells comprised 2-30% of total PBMCs, all of whom were CR. Resegregating these 20 patients to 11 CR vs 9 non-CR confirmed higher frequency of circulating B cells (median CR 0.18% vs non-CR 0.011%, p=0.0057). Patients with B cells had longer time from anti-CD20 therapy (60, 41, 22, and 10 months) whereas patients without B cells had median 1 month since last anti-CD20 therapy. Second, lymphocyte to monocyte ratio [ALC/AMC] by scRNA-seq trended higher in R (n=12) compared to NR (n=7) (median 1.36 vs 1.02, p=0.22). This was confirmed in the larger flow cytometry cohort (median 2.38 vs 0.69, p=0.0013) and supported by both increased percent of total lymphocytes in R (n=13) vs NR (n=7) (median 31% vs 9.4%, p=0.011) as well as decreased percent of monocytes in R vs NR (median 68% vs 91%, p=0.019). As validation, we detected an elevated ALC/AMC upon evaluation of our entire cohort of patients treated with commercial axi-cel at DFCI from 2019-2022 (n=157 R, 123 NR) based on complete blood count and differential on Day -30 (median 1.31 for R vs 0.97 for NR, p=0.0034). Since we detected evidence of immunologic differences at baseline between R and NR, we asked whether differences in IPs contributed to therapy outcome. By scRNA-seq, IP cells demonstrated increased proportion of CD8 T cells in R (62% vs 32%, p=0.024, Fig 1A) with a trend toward higher proportion of a T effector memory (T EM) expression profile (median 45% vs 21%, p=0.079). By scTCR-seq analysis, we observed greater clonal expansion of CD8 T EM cells in R vs NR, whereas non-clonally expanded cells tended towards a T CM profile (median ratio of clonal TEM to clonal TCM 2.61 for R vs 0.71 for NR, p=0.042, Fig 1B). Differential gene expression of clonally expanded vs nonclonally expanded CD8 T cells revealed increased expression of T cell activation genes ( GZMH, IFNG, TNF, KLRD1, B3GAT1, HLA-class II genes) among clonally expanded cells. These data implicate clonal expansion and T cell activation at infusion as key indicators of CAR-T response. Our results suggest that baseline patient immunologic state affects likelihood of response to CART through modulation of the T cell apheresis product composition and promoting a more favorable circulating immune compartment prior to therapy. These features, detectable by highly accessible clinical measures, could be leveraged for improved patient selection and enhanced CAR-T manufacturing.

Single-Cell Analysis of Immune Recognition in Chronic Myeloid Leukemia Patients Following Tyrosine Kinase Inhibitor Discontinuation

Background: Modern treatment goal for patients with chronic myeloid leukemia (CML) is to maintain treatment-free remission (TFR) following tyrosine kinase inhibitor (TKI) discontinuation. The control of residual leukemia cells may occur with immunological mechanisms as several studies have shown that a higher proportion of CD56 dim NK cells before TKI discontinuation is associated with a better probability of TFR. In addition, CD8+ T cell abundances and phenotypes have been associated with responses to TKIs. However, the more detailed phenotypes and mechanisms and how to translate these findings to increased TFR rates have remained unknown. Methods: We analyzed 55 single-cell RNA and T cell receptor (TCR) sequenced (scRNA+TCRαβ-seq) samples from patients with CML ( n=13, N=25), other cancers (AML n=11, CLL n=13, solid tumors n=4), and healthy ( n=7). Additionally, we profiled 90 CML and 786 healthy TCRβ-seq samples, and sorted T cells specific to leukemia-associated antigen PR1 and matched these back to the scRNA+TCRαβ-seq and TCRβ-seq data. To validate and refine our findings, we performed co-culture of primary and expanded NK cells with CML cell lines (K562 and LAMA84) with a multiplexed scRNA-seq readout. Results: In the pan-cancer scRNA+TCRαβ-seq comparison of >250,000 cells, CML was separated from other cancers and healthy by the high number and active phenotype NK cells. The other phenotype more pronounced in CML was CD8+ T EM/T EMRA phenotype. Most NK cells in CML had an active CD56 dim phenotype with high expression of GZMA/B, PRF1, CCL3/4 and IFNG. In the off-TKI samples from patients with TFR, these NK cells upregulated NK cell activation genes such as TNFRSF4/OX40, TNFRSF9/4-1BB, and TNFRSF18/GITR. The most important predicted interactions between NK cells and CD34+ leukemic cells were inhibitory LGALS9- TIM3 and PVR- TIGIT interactions. Following TKI discontinuation, the inhibitory markers HAVCR2/TIM3 and TIGIT decreased in patients with TFR, which was not seen in patients with relapse following TFR. Accordingly, in our co-culture data of NK cells with CML cell lines, we noted activation of NK cells to a similar phenotype as noted in ex vivo off-TKI samples. In co-culture with CML target cells, NK cells gained an activation by upregulation of genes like TNFRSF4/OX40, TNFRSF9/4-1BB, TNFRSF18/GITR and the inhibitory markers HAVCR2/TIM3 and TIGIT. In co-culture with NK cells, CML target cells upregulated the IFN-γ response pathway including elevated HLA-expression and accordingly, upregulation of LGALS9 and PVR. The CD8+ T EM/EMRA cells that were expanded in CML diagnosis were suppressed following TKI treatment and decreased following TKI discontinuation. To track anti-CML T cells, we created a classifier to identify TCRs targeting leukemia-associated antigen PR1 from the TCRb-sequenced samples. As a validation of our classifier, we noticed that anti-PR1 T cells were more prevalent in CML than in healthy ( P adj<0.0001) or melanoma ( P adj<0.0001), more expanded than similar anti-viral T cells ( P adj<0.0001) and enriched in bone marrow samples compared to peripheral blood ( P adj<0.0001). From different TKIs, dasatinib expanded anti-PR1 T cells the most ( P adj<0.01). In the scRNA+TCRαβ-seq data, anti-PR1 T cells were enriched in the mature, cytotoxic CD8+ T EMRA phenotype ( P adj<0.0001). In a patient maintaining TFR, anti-PR1 T cells had a highly cytotoxic profile ( GZMB, PRF1) throughout the therapy with upregulated NK receptors like FCGR3A/CD16 and KIR2DL2, even more so than T cells targeting other targets e.g., different viruses. In comparison, the anti-PR1 T cells in a patient with early relapse had an exhausted profile with upregulation of memory marker GZMK and exhaustion markers like LAG3 and HAVCR2/TIM3. Conclusions: With our in-depth analysis of cellular and molecular immune responses in CML, we identified the active NK cells and anti-PR1 T cells that could help maintain TFR in patients discontinuing TKI treatment. Different immune-checkpoint blockade therapies such as anti-TIM3 could be considered as future strategies to improve the TFR rates.

IMMU-03. UTILIZING IN SILICO SINGLE-CELL TRANSCRIPTOMIC AND TCR PROFILING FOR THE IDENTIFICATION AND ISOLATION OF TUMOR-REACTIVE TCR CLONOTYPES IN RECURRENT GLIOBLASTOMA PATIENTS

Abstract BACKGROUND Glioblastoma (GBM) is the most aggressive form of primary brain cancer with no current cure. Immunotherapies, such as checkpoint blockade and adoptive T cell therapy, have effectively treated other cancers, but in GBM, these therapies have shown limited efficacy. This may be partially due to a lack of infiltrating tumor-reactive T cell populations capable of eliminating the tumor. METHODS & RESULTS We used single-cell RNA and TCRsequencing to examine the transcriptome and TCR repertoire of tumor-infiltrating T cells from a cohort of 32 recurrent GBM patients, 18 of whom had received neoadjuvant anti-PD-1 therapy. After dimensional reduction, we found that the cluster defined by T cell activation and exhaustion gene expression had the greatest number of expanded T cell clones and a transcriptomic profile similar to a previously published signature of tumor-reactive T cells. Focusing on a patient treated with neoadjuvant anti-PD-1 and a EGFRvIII Bispecific T cell engager therapy, we selected TCRs from T cells within the activated and exhausted cluster. Utilizing the PathFinder DNA Assembly technology developed by Rootpath, we generated a TCR library containing the selected TCRs and transduced the library into a fluorescent-reporter Jurkat line that measures T cell activation. We co-cultured the transduced Jurkats with the patient-derived gliomasphere, FACs sorted for activated Jurkats and performed TCR sequencing on the sorted cells. Six TCRs within the sorted population were over-represented relative to sorted T cells from control co-cultures, indicating their tumor reactivity. CONCLUSIONS In this study we provide a proof-of-concept framework for how incorporating silico single-cell analysis of a T cell’s transcriptome and TCR can be used to identity tumor-reactive T cells for potential downstream adoptive T cell therapies for patients with recurrent GBM.

Regulation of dermal fibroblasts by human neutrophil peptides

Human neutrophil peptides (HNPs) can induce cell proliferation and activation so their growth promoting activities may have potential clinical benefit. This study investigated the effects of HNPs on human dermal fibroblasts. Differential gene expression in HNP-treated cells and genes involved in regulating intracellular pathways were explored. Dermal fibroblasts were isolated from healthy neonatal foreskin and treated with HNPs in 2D and 3D cell culture systems. The expression of cell proliferation (Ki-67) gene and cell activation (COL1A1) gene plus their proteins was measured. Differential gene expression was determined using RNA-seq, and upregulated and downregulated genes were mapped onto intracellular pathways by KEGG analysis and Gene Ontology databases. HNPs significantly increased cell proliferation without cytotoxicity whilst HNP1 enhanced expression of COL1A1 and type I collagen production in 2D cells and 3D spheroids. RNA-sequencing analysis showed gene clustering with clear separation between HNP1-treated and control groups. A heatmap of top 50 differentially expressed genes was consistent among HNP1-treated samples. Most upregulated genes were associated with cell proliferation and activation as mapped into intracellular pathways whilst most downregulated genes belonged to steroid/arachidonic acid metabolism and inflammatory signaling pathways. HNP1 increased cell proliferation and activation but reduced lipid metabolism and inflammation.

Larval T Cells Are Functionally Distinct from Adult T Cells in Xenopus laevis.

The amphibian Xenopus laevis tadpole provides a unique comparative experimental organism for investigating the roles of innate-like T (iT) cells in tolerogenic immunity during early development. Unlike mammals and adult frogs, where conventional T cells are dominant, tadpoles rely mostly on several prominent distinct subsets of iT cells interacting with cognate nonpolymorphic MHC class I-like molecules. In the present study, to investigate whole T cell responsiveness ontogenesis in X. laevis, we determined in tadpoles and adult frogs the capacity of splenic T cells to proliferate invivo upon infection with two different pathogens, ranavirus FV3 and Mycobacterium marinum, as well as invitro upon PHA stimulation using the thymidine analogous 5-ethynyl-2'-deoxyuridine and flow cytometry. We also analyzed by RT-quantitative PCR T cell responsiveness upon PHA stimulation. In vivo tadpole splenic T cells showed limited capacity to proliferate, whereas the invitro proliferation rate was higher than adult T cells. Gene markers for T cell activation and immediate-early genes induced upon TCR activation were upregulated with similar kinetics in tadpole and adult splenocytes. However, the tadpole T cell signature included a lower amplitude in the TCR signaling, which is a hallmark of mammalian memory-like T cells and iT or "preset" T cells. This study suggests that reminiscent of mammalian neonatal T cells, tadpole T cells are functionally different from their adult counterpart.

A first-in-human study of the fibroblast activation protein-targeted, 4-1BB agonist RO7122290 in patients with advanced solid tumors.

This first-in-human study evaluated RO7122290, a bispecific fusion protein carrying a split trimeric 4-1BB (CD137) ligand and a fibroblast activation protein α (FAP) binding site that costimulates T cells for improved tumor cell killing in FAP-expressing tumors. Patients with advanced or metastatic solid tumors received escalating weekly intravenous doses of RO7122290 as a single agent (n = 65) or in combination with a 1200-milligram fixed dose of the anti-programmed death-ligand 1 (anti-PD-L1) antibody atezolizumab given every 3 weeks (n = 50), across a tested RO7122290 dose range of 5 to 2000 milligrams and 45 to 2000 milligrams, respectively. Three dose-limiting toxicities were reported, two at different RO7122290 single-agent doses (grade 3 febrile neutropenia and grade 3 cytokine release syndrome) and one for the combination (grade 3 pneumonitis). No maximum tolerated dose was identified. The pharmacokinetic profile of RO7122290 suggested nonlinearity in elimination. The observed changes in peripheral and tissue pharmacodynamic (PD) biomarkers were consistent with the postulated mechanism of action. Treatment-induced PD changes included an increase in proliferating and activated T cells in peripheral blood both in the single-agent and combination arms. Increased infiltration of intratumoral CD8+ and Ki67+CD8+ T cells was observed for both treatment regimens, accompanied by the up-regulation of T cell activation genes and gene signatures. Eleven patients experienced a complete or partial response, six of whom were confirmed to be immune checkpoint inhibitor naive. These results support further evaluation of RO7122290 in combination with atezolizumab or other immune-oncology agents for the treatment of solid tumors.

Alterations in germinal center formation and B cell activation during severe Orientia tsutsugamushi infection in mice.

Scrub typhus is a poorly studied but life-threatening disease caused by the intracellular bacterium Orientia tsutsugamushi (Ot). Cellular and humoral immunity in Ot-infected patients is not long-lasting, waning as early as one-year post-infection; however, its underlying mechanisms remain unclear. To date, no studies have examined germinal center (GC) or B cell responses in Ot-infected humans or experimental animals. This study was aimed at evaluating humoral immune responses at acute stages of severe Ot infection and possible mechanisms underlying B cell dysfunction. Following inoculation with Ot Karp, a clinically dominant strain known to cause lethal infection in C57BL/6 mice, we measured antigen-specific antibody titers, revealing IgG2c as the dominant isotype induced by infection. Splenic GC responses were evaluated by immunohistology, co-staining for B cells (B220), T cells (CD3), and GCs (GL-7). Organized GCs were evident at day 4 post-infection (D4), but they were nearly absent at D8, accompanied by scattered T cells throughout splenic tissues. Flow cytometry revealed comparable numbers of GC B cells and T follicular helper (Tfh) cells at D4 and D8, indicating that GC collapse was not due to excessive death of these cell subtypes at D8. B cell RNAseq analysis revealed significant differences in expression of genes associated with B cell adhesion and co-stimulation at D8 versus D4. The significant downregulation of S1PR2 (a GC-specific adhesion gene) was most evident at D8, correlating with disrupted GC formation. Signaling pathway analysis uncovered downregulation of 71% of B cell activation genes at D8, suggesting attenuation of B cell activation during severe infection. This is the first study showing the disruption of B/T cell microenvironment and dysregulation of B cell responses during Ot infection, which may help understand the transient immunity associated with scrub typhus.

Alterations in Germinal Center (GC) Formation and B Cell Activation during Severe Orientia tsutsugamushiInfection in Mice

Abstract Scrub typhus is a poorly studied, but life-threatening, disease caused by the bacterium Orientia tsutsugamushi (Ot). Humoral immunity in scrub typhus patients wanes as early as one-year post-infection; yet its underlying mechanisms remain unclear. The objective of this study is to delineate mechanisms underlying humoral immune dysregulation and B cell dysfunction during acute Ot infection. Using a lethal scrub typhus C57BL/6 murine model, we evaluated splenic GC responses by immunofluorescent staining. Splenic germinal centers (GL-7 +cells) were formed at D4, but were nearly absent at D8, accompanied by randomly scattered T cells. Both infection days had comparable numbers of GC B cells and T follicular helper (Tfh) cells, indicating that GC loss at D8 was less likely due to cell death, but rather dysregulation in GC formation. To confirm this hypothesis, we performed RNAseq analysis of purified B220 +B cells and revealed a set of differentially expressed genes associated with B cell adhesion (S1PR1, ICAM1, GPR183) and co-stimulation (CD40, ICOS-L, SLAMF1) at D8. Notably, the downregulation of S1PR2 (a GC-specific adhesion gene) was most evident at D8, correlating to disrupted GC formation. Furthermore, transcriptomic data revealed significant downregulation of 71% B cell activation genes on D8, suggesting attenuation of B cell activation. Additional studies with low- and high-virulence Ot strains and comparative flow cytometry revealed significant differences in both B cell subsets (plasmablasts, marginal zone B cells) and T cell subsets (Tfh and Tfr cells). This is the first study showing marked dysregulation of B cell responses during Ot infection, which helps understand the transient immunity associated with scrub typhus. Supported by grants from NIH (R01 AI132674, R21 AI156536, R21 AI153586, R01 EY028773, T32 AI007526), Department of Defense Threat Reduction Agency grant (HDTRA1-19-1-0043), UTMB IHII Data Acquisition (CIRWH&IHII Pilot/ Phase II Research grant) and UTMB Center for Biodefense and Emerging Infectious Diseases (Pilot grant)

ATG9B Is a Poor Prognostic Marker Associated With Immune Evasion in Colon Adenocarcinoma.

Autophagy-related genes (ATGs) are involved in autophagy activation, which has a pleiotropic role in cancer development. However, the potential value of ATG expression levels in colon adenocarcinoma (COAD) is unclear. This study aimed to examine the modulation of ATG expression levels and their association with clinical and molecular aspects of COAD. We used the clinical and molecular phenotypes and RNA sequencing datasets of the cancer genome atlas (TCGA)-COAD project using TCGAbiolinks and cBioPortal. Comparisons of ATG expression levels between tumor and normal tissues were performed using DESeq2 within R. Gene expression and immune cell infiltration levels were analyzed by TIMER. ATG9B had the highest expression levels among ATGs in COAD tissues compared to normal tissues and was related to advanced stage and poor prognosis in COAD. In addition, ATG9B expression was positively associated with the consensus molecular subtype 4 and chromosomal instability but negatively correlated with tumor mutation burden. Furthermore, high ATG9B expression levels were associated with low immune cell infiltration and decreased expression of natural killer cell activation genes. ATG9B is a poor prognostic biomarker driving immune evasion of COAD through negative correlation with immune cell infiltration.

Abstract 6537: Single cell transcriptomics uncovers cellular and molecular differences in PBMCs of responders and non-responders to the MUC1 cancer vaccine given in the preventative setting

Abstract Introduction: A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial (NCT02134925) were conducted in patients with newly diagnosed advanced colonic adenomas to test the safety and immunogenicity of the MUC1 antigen vaccine and its potential to prevent new adenoma formation. These are the first trials of a non-viral cancer vaccine administered in the absence of cancer. In both trials, the vaccine was safe and strongly immunogenic in 43% and 25% of participants (Responders), respectively. The lack of robust response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to regulatory influences that, in the case of the vaccine, determine who does and who does not respond. We hypothesized that there could be molecular and cellular differences in the immune competence between vaccine responders and non-responders, and that they could be identified by studying their pre-vaccination peripheral blood mononuclear cells (PBMCs). Methods: The two MUC1 vaccine trials are described in https://doi.org/10.1101/2022.10.05.22280474 and https://doi.org/10.1158%2F1940-6207.CAPR-12-0275. We performed single cell RNA-sequencing (scRNAseq) on banked pre-vaccination PBMCs from 16 Responders and 16 Non-Responders, determined by anti-MUC1 IgG response. Using differential gene expression (DGE), pathway enrichment, and network estimation analyses, we identified specific cell types, genes, and pathways that differ between responders and non-responders. Results: Pre-vaccination PBMCs from Responders contained a significantly higher percentage of CD4+ naive T cells, while Non-Responders showed significantly higher percentage of CD8+ T effector memory (TEM) cells and a higher percentage of CD16+ monocytes. DGE and gene interaction network analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in the CD4+ naive T cells in Responders. Further network analysis showed that these genes were directly connected to response. We also found pre-vaccination specific gene ontology (GO) pathways for translational and transcriptional activity enriched in all cell types in Responders compared to Non-Responders. Conclusion: Our analyses identified candidate biomarkers that are predictive of a preventative cancer vaccine response. Thus, our results can be used for patient selection for vaccine administration. Furthermore, we identified cell type differences and transcriptional pathways that provide information of possible mechanisms of vaccine response. Citation Format: Daniel Y. Yuan, Michelle L. McKeague, Matthew T. Dracz, Olivera J. Finn, Panayiotis V. Benos. Single cell transcriptomics uncovers cellular and molecular differences in PBMCs of responders and non-responders to the MUC1 cancer vaccine given in the preventative setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6537.

373 Identification of potential targets for immunotherapy in a cynomolgus macaque model of Ebola virus disease

OBJECTIVES/GOALS: Ebola virus infection causes severe disease and liver injury in humans. Macrophages contribute to inflammatory signaling and are prevalent in the liver. We assessed the activation status, including therapeutic target expression, of hepatic macrophages. METHODS/STUDY POPULATION: We compared formalin-fixed, paraffin-embedded liver tissue from terminal Ebola virus-infected and uninfected control cynomolgus macaques, a gold-standard model for human disease. We characterized region-specific protein and whole transcriptome expression in these tissues using GeoMx Digital Spatial Profiling. Macrophage (CD68+) and leukocyte (CD45+) accumulation in liver tissue was quantified by immunofluorescence image analysis using digital pathology software. RESULTS/ANTICIPATED RESULTS: Macrophage-specific (CD68+) regions in the liver of Ebola virus-infected macaques demonstrated a shift towards an inflammatory gene expression profile, as compared to those from healthy control tissue. These regions showed differential expression of monocyte/macrophage differentiation, antigen presentation, and T cell activation gene sets, which were associated with decreased MHC-II allele expression. Moreover, macrophage-specific regions in the infected macaques showed enriched expression of genes or proteins associated with known immunomodulatory therapeutics, including S100A9, IDO1, and CTLA-4. DISCUSSION/SIGNIFICANCE: These data demonstrate that hepatic macrophages express an inflammatory phenotype, that their ability to present antigens to the adaptive immune system may be impaired, and that they express therapeutically targetable markers for immunomodulation of these cells during Ebola virus infection.

Analysis of gene expression profile for identification of novel gene signatures during dengue infection

BackgroundDengue is a major arthropod-borne viral disease spreading rapidly across the globe. The absence of vaccines and inadequate vector control measures leads to further expansion of dengue in many regions globally. Hence, the identification of genes involved in the pathogenesis of dengue will help to understand the molecular basis of the disease and the genes responsible for the disease progression. MethodsIn the present study, a meta-analysis was carried out using dengue gene expression data obtained from Gene Expression Omnibus repository. The differentially expressed genes such as CCNB1 and CCNB2 (G2/mitotic-specific cyclin-B2 and B1) were upregulated in dengue fever to control (DF-CO) and severe dengue (dengue hemorrhagic fever [DHF]) to control (DHF-CO) were identified as key genes for controlling the major pathways (cell cycle, oocyte meiosis, p53 signaling pathway, cellular senescence and progesterone-mediated oocyte maturation). Similarly, interferon alpha-inducible (IFI27) genes, type-I and type-III interferon (IFN) signaling genes (STAT1 and STAT2), B cell activation and survival genes (TNFSF13B, TNFRSF17) and toll like receptor (TLR7) genes were differentially up activated during DF-CO and DHF-CO. Followed by, Cytoscape was used to identify the immune system process and topological analysis. ResultsThe results showed that the top differentially expressed genes under the statistical significance p <0.001, which is majorly involved in Kyoto Encyclopedia of Genes and Genomes orthology K05868 and K21770 with gene names CCNB1 and CCNB2. In addition to this, the immune system profile showed up-regulation of IL12A, CXCR3, TNFSF13B, IFI27, TNFRSF17, STAT, STAT2, and TLR7 genes in DF-CO and DHF-CO act as immunological signatures for inducing the immune response towards dengue infection. ConclusionsThe current study could aid in understanding of molecular pathogenesis, genes and corresponding pathway upon dengue infection, and could facilitate for identification of novel drug targets and prognostic markers.

Single-cell transcriptome analysis reveals functional changes in tumour-infiltrating B lymphocytes after chemotherapy in oesophageal squamous cell carcinoma.

Tumour immune microenvironment is related with carcinogenesis and efficacy of immunotherapy. B cells play major roles in humoral immunity, but detailed functions of tumour-infiltrating B lymphocytes (TIL-Bs) are unknown. Therefore, our aim was to investigate the functional heterogeneity of TIL-Bs in oesophageal squamous cell carcinoma (ESCC) and lymph nodes (LNs) during chemotherapy. Single-cell transcriptome analysis was performed on 23 specimens. We also performed immunohistochemical analysis of immunoglobulin κ C (IGKC), an antibody-secreting cell (ASC) marker, in 166 ESCC samples and evaluated the implication of IGKC in 2-year recurrence free survival (RFS) and 3-year overall survival (OS). A total of 81,246 cells were grouped into 24 clusters. We extracted B cell clusters based on canonical markers and identified 12 TIL-B subtypes in ESCC. We found that several functions, such as co-stimulation and CD40 signalling, were enhanced in TIL-Bs after chemotherapy. The proportion of naive B cells (NBCs) decreased and B cell activation genes were up-regulated in NBCs after chemotherapy. The proportion of ASCs in tumours increased with the loss of migratory abilities and antibody production in ASCs was promoted after chemotherapy. Differentially expressed genes up-regulated with chemotherapy in ASCs correlated with prolonged survival with oesophageal cancer (p=.028). In a metastatic LN, the ASC proportion increased and B cell differentiation was enhanced. In immunohistochemical analysis, RFS and OS of high IGKC expression cases were significantly better than those of low IGKC expression cases (RFS: p<.0001, OS: p<.0001). And in multivariable analysis, the expression of IGKC was an independent favourable prognostic factor for RFS (hazard ratio (HR): 0.23, 95% confidence interval (CI): 0.12-0.45, p<.0001) and OS (HR: 0.20, 95% CI: 0.086-0.47, p=.0002) in ESCC. Our findings provide novel insights for the heterogeneity of TIL-Bs during chemotherapy and will be useful to understand the clinical importance of TIL-Bs.

Dynamic alterations of immunosenescence-related genes in older women with breast cancer receiving chemotherapy: A prospective study

BackgroundThe exact impact of chemotherapy on the immune system of older patients with breast cancer is not well known. A longitudinal study was performed investigating the evolution of the blood immune profile during and after chemotherapy in this population. Patients and MethodsThe study included 39 patients receiving adjuvant chemotherapy (chemotherapy group, CTG) and 32 patients receiving only hormone therapy (control group, CG). A 10-gene panel associated with immunosenescence was measured in peripheral blood mononuclear cells (PBMC) before (T1), at 3 months (T2) and at 12 months (T3) after initiation of adjuvant therapy. Nutrition status was assessed by using a mini nutritional assessment scale. Linear mixed model analyses were performed for trajectory evolution, with or without adjusting for age, tumor stage, breast cancer phenotype, and/or corresponding baseline gene levels. ResultsSix genes relating to T cell activation (CD28, CD27, CD86, LCK, GRAP, LRRN3), and two genes relating to oxidative stress (PRDX6, HMOX1) exhibited a significant group-by-time effect, even after adjusting covariates(p≤ 0.01). In CTG, the T cell activation genes substantially declined from T1 to T2 and bounced back to a level higher than baseline at T3 (p<0.03), which was not observed in CG (p>0.26). Patients with malnutrition detected at T1 experienced more pronounced perturbation regarding CD27, LCK, CD69, VAMP5, and LRRN3 (p<0.05). ConclusionChemotherapy leads to transient perturbation of immune-related gene expression and potentially stimulates immunity in the long term. Well-nourished patients experience less impact of chemotherapy on immune-related gene expression profiles.