T Cells Research Articles

BAP1 Deficiency Inflames the Tumor Immune Microenvironment and Is a Candidate Biomarker for Immunotherapy Response in Malignant Pleural Mesothelioma

IntroductionMalignant pleural mesothelioma (MPM) is a rare and universally lethal malignancy with limited treatment options. Immunotherapy with immune checkpoint inhibitors (ICIs) has recently been approved for unresectable MPM, but response to ICIs is heterogeneous, and reliable biomarkers for prospective selection of appropriate subpopulations likely to benefit from ICIs remain elusive. MethodsWe performed multiscale integrative analyses of published primary tumor data set from The Cancer Genome Atlas (TCGA) and the French cohort E-MTAB-1719 to unravel the tumor immune microenvironment of MPM deficient in BAP1, one of the most frequently mutated tumor suppressor genes (TSGs) in the disease. The molecular profiling results were validated in independent cohorts of patients with MPM using immunohistochemistry and multiplex immunohistochemistry. ResultsWe revealed that BAP1 deficiency enriches immune-associated pathways in MPM, leading to increased mRNA signatures of interferon alfa/gamma response, activating dendritic cells, immune checkpoint receptors, and T-cell inflammation. This finding was confirmed in independent patient cohorts, where MPM tumors with low BAP1 levels are associated with an inflammatory tumor immune microenvironment characterized by increased exhausted precursor T-cells and macrophages but decreased myeloid-derived suppressor cells (MDSCs). In addition, BAP1low MPM cells are in close proximity to T cells and therefore can potentially be targeted with ICIs. Finally, we revealed that BAP1-proficient MPM is associated with a hyperactive mitogen-activated protein kinase (MAPK) pathway and may benefit from treatment with MEK inhibitors (MEKis). ConclusionOur results suggest that BAP1 plays an immunomodulatory role in MPM and that BAP1-deficient MPM may benefit from immunotherapy, which merits further clinical investigation.

Analysis of the Effects of the Addition and Subtraction Therapy of Jianpi Jiedu Decoction on T-lymphocyte Subpopulations’ Changes in Colorectal Cancer Patients’ Clinical Symptoms

Objective: To investigate the clinical efficacy of applying the addition and subtraction of Jianpi Jiedu decoction (JPJD) in patients suffering from colorectal cancer and changes in their clinical symptoms. Methods: Seventy-two colorectal cancer cases were selected and randomly divided into the control group and the observation group, where both groups received the same comprehensive treatment and chemotherapy intervention after surgery. The observation group received the addition and subtraction therapy of JPJD based on the control group. The Chinese medicine (TCM) symptom scores, the intestinal bacterial flora, and the changes in the T-lymphocyte subsets of the two groups were compared. Results: The observation group had lower TCM evidence points, more Escherichia coli, less Bifidobacterium and Lactobacillus, and higher T-lymphocyte subpopulation levels than that of the control group after treatment (P < 0.05). Conclusion: The application of addition and subtraction therapy of JPJD in conjunction with postoperative radiotherapy for colorectal cancer patients further improved the patient's clinical symptoms and intestinal flora environment, and effectively enhanced their immunity. which is worthy of promotion.

The expression of CTLA-4 in hepatic alveolar echinococcosis patients and blocking CTLA-4 to reverse T cell exhaustion in Echinococcus multilocularis-infected mice.

Alveolar echinococcosis (AE) is a zoonotic parasitic disease caused by the infection of Echinococcus multilocularis (E. multilocularis) larvae. Cytotoxic T-lymphocyte antigen 4 (CTLA-4) produces inhibitory signals and induces T cell exhaustion, thereby inhibiting the parasiticidal efficacy of the liver immune system. Therefore, the purpose of this study is to explore how T-cell exhaustion contributes to AE and whether blocking CTLA-4 could reverse T cell exhaustion. Here we discovered that the expression of CTLA-4 was increased in the infiltrating margin around the lesion of the liver from AE patients by using western blot and immunohistochemistry assay. Multiple fluorescence immunohistochemistry identified that CTLA-4 and CD4/CD8 molecules were co-localized. For in vitro experiments, it was found that the sustained stimulation of E. multilocularis antigen could induce T cell exhaustion, blocking CTLA-4-reversed T cell exhaustion. For in vivo experiments, the expression of CTLA-4 was increased in the liver of E. multilocularis-infected mice, and the CTLA-4 and CD4/CD8 molecules were co-localized. Flow cytometry analysis demonstrated that the percentages of both CD4+ T cells and CD8+ T cells in the liver and peripheral blood were significantly increased and induced T exhaustion. When the mice were treated with anti-CTLA-4 antibodies, the number and weight of the lesions decreased significantly. Meanwhile, the flow cytometry results suggested that blocking CTLA-4 could effectively reverse T cell exhaustion and reactivate immune function. Our work reveals that blocking CTLA-4 could effectively reverse the T cell exhaustion caused by E. multilocularis and could be used as a novel target for the treatment of AE.

Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning.

Exhausted T cells are a key component of immune cells that play a crucial role in the immune response against cancer and influence the efficacy of immunotherapy. Accurate assessment and measurement of T-cell exhaustion (TEX) are critical for understanding the heterogeneity of TEX in the tumor microenvironment (TME) and tailoring individualized immunotherapeutic strategies. In this study, we introduced DeepEpiTEX, a novel computational framework based on deep neural networks, for inferring the developmental hierarchy and functional states of exhausted T cells in the TME from epigenetic profiles. DeepEpiTEX was trained using various modalities of epigenetic data, including DNA methylation data, microRNA expression data, and long non-coding RNA expression data from 30 bulk solid cancer types in the TCGA pan-cancer cohort, and identified five optimal TEX subsets with significant survival differences across the majority of cancer types. The performance of DeepEpiTEX was further evaluated and validated in external multi-center and multi-type cancer cohorts, consistently demonstrating its generalizability and applicability in different experimental settings. In addition, we discovered the potential relationship between TEX subsets identified by DeepEpiTEX and the response to immune checkpoint blockade therapy, indicating that individuals with immune-favorable TEX subsets may experience the greatest benefits. In conclusion, our study sheds light on the role of epigenetic regulation in TEX and provides a powerful and promising tool for categorizing TEX in different disease settings.

FEATURES OF THE T-IMMUNE SYSTEM IN PATIENTS WITH GLOMERULONEPHRITISES WITH NEPHROTIC SYNDROME

The study of issues related to glomerulonephritises with nephrotic syndrome is one of the urgent problems of medicine due to their prevalence worldwide, mainly in the young age group. Medical workers distinguish primary (idiopathic) nephrotic syndrome, which occurs in 80–90% of cases, and secondary nephrotic syndrome, mainly associated with systemic autoimmune diseases, diabetes mellitus and neoplasms. Glomerulonephritises, manifested by nephrotic syndrome (membranous nephropathy, focal segmental glomerulosclerosis, nephropathy with minimal changes), are known to be autoimmune diseases. To date, the immunological mechanisms of the pathogenesis of glomerulonephritises with nephrotic syndrome associated with the T-system of adaptive immunity remain unexplored. The aim of the study was to study the role of the T–immune system in the pathogenesis of primary nephrotic syndrome based on the study of immunoregulatory, activated T-cell subsets in patients with this pathology. Material and methods. 136 patients with chronic glomerulonephritis with nephrotic syndrome were selected for the study. The assessment of the T-immune system included determination of the lymphocyte phenotype of immunoregulatory T-cell subsets (T-helper/inducers, cytotoxic T-lymphocytes), various subpopulations of activated T-cells (activated T-lymphocytes; activated T-lymphocytes expressing CD25–alpha chain of IL-2 receptor; activated cytotoxic T-lymphocytes expressing HLA-DR and CD38) and regulatory T-cells (Treg cells). Study results. In the patients of the examined cohort, an increase in the number of T-lymphocytes and T-helper cells, as well as activated T-lymphocytes expressing HLA-DR antigens, was found. At this, the content of cytotoxic T-cells and the number of activated T-cells expressing the IL-2 – CD25 receptor did not differ from similar indicators in healthy individuals. The levels of Treg cells and activated cytotoxic T-lymphocytes with the CD3+CD8brightCD38+ phenotype were reduced. The immunoregulatory index (T-helpers/cytotoxic T-lymphocytes) was increased, due to an increase in the number of T-helper cells against the background of an unchanged number of cytotoxic T-lymphocytes. Conclusions. The results of the study indicate that the main features of the T-system of the immune response in primary nephrotic syndrome are imbalance in the ratio of the content of immunoregulatory cells due to predominance of T-helper cells and a decrease in the number of Treg cells.

Investigating peripheral blood monocyte and T-cell subsets as non-invasive biomarkers for asymptomatic hepatic steatosis: results from the Multi-Ethnic Study of Atherosclerosis.

Circulating immune cells have gained interest as biomarkers of hepatic steatosis. Data on the relationships between immune cell subsets and early-stage steatosis in population-based cohorts are limited. This study included 1,944 asymptomatic participants of the Multi-Ethnic Study of Atherosclerosis (MESA) with immune cell phenotyping and computed tomography measures of liver fat. Participants with heavy alcohol use were excluded. A liver-to-spleen ratio Hounsfield units (HU) <1.0 and liver attenuation <40 HU were used to diagnose liver fat presence and >30% liver fat content, respectively. Logistic regression estimated cross-sectional associations of immune cell subsets with liver fat parameters adjusted for risk factors. We hypothesized that higher proportions of non-classical monocytes, Th1, Th17, and memory CD4+ T cells, and lower proportions of classical monocytes and naive CD4+ T cells, were associated with liver fat. Exploratory analyses evaluated additional immune cell phenotypes (n = 19). None of the hypothesized cells were associated with presence of liver fat. Higher memory CD4+ T cells were associated with >30% liver fat content, but this was not significant after correction for multiple hypothesis testing (odds ratio (OR): 1.31, 95% confidence interval (CI): 1.03, 1.66). In exploratory analyses unadjusted for multiple testing, higher proportions of CD8+CD57+ T cells were associated with liver fat presence (OR: 1.21, 95% CI: 1.02, 1.44) and >30% liver fat content (OR: 1.34, 95% CI: 1.07, 1.69). Higher circulating memory CD4+ T cells may reflect liver fat severity. CD8+CD57+ cells were associated with liver fat presence and severity, but replication of findings is required.

Characterisation of choroid plexus-infiltrating T cells reveals novel therapeutic targets in murine neuropsychiatric lupus

ObjectiveDiffuse central nervous system manifestations, referred to as neuropsychiatric lupus (NPSLE), are observed in 20–40% of lupus patients and involve complex mechanisms that have not yet been adequately elucidated. In...

PD-L1 Expression in Colorectal Carcinoma Correlates with the Immune Microenvironment.

Colorectal carcinoma (CRC) is a common malignancy, with its diverse clinical, pathological, and molecular features. The immune microenvironment of a tumor comprises of interplay between various cells and molecules, and has a significant role in deciding the tumor behavior and overall prognosis. PD-L1 (programmed cell death ligand-1) has been implicated in the regulation of the tumor immune microenvironment (TIME). There is limited data regarding the correlation of PD-L1 expression with immune cell profile in CRCs, especially in the Indian setting. The study aimed to assess the PD-L1 expression in CRC tumor cells and its association with TIME, mismatch repair (MMR), and various other clinicopathological parameters. This is a hospital-based, cross-sectional observational study. PD-L1 expression was assessed at the protein level by immunohistochemistry and mRNA level by qRT-PCR. Immune cell markers (CD4, CD8, CD20, FOXP3, and CD163) were interpreted using the ImageJ Fiji platform. Of the 104 cases, 21% were PD-L1 positive and were more common in right-sided CRCs. PD-L1 positive cases showed significantly higher concentrations of all T-cell subsets (CD4+ , CD8+ , and FOXP3+), CD20+ B-cells, and CD163+ macrophages were noted. No statistical significance was seen between PD-L1 expression with clinical profile, pathological subtype, grade or stage, mismatch repair status (proficient vs deficient), and survival. The present study showed a relatively lower frequency of PD-L1 in CRC from the Eastern Indian cohort. The immune cell concentration in the present study was calculated using image analysis-based objectivised methods. Significant correlation of PD-L1 expression in tumor cells with the tumor-infiltrating immune cells indicated its crucial role in the pathobiology of CRC especially by regulating the TIME. Considering the therapeutic implication of PD-L1 in various malignancies, it may be one of the crucial therapeutic targets in a proportion of cases.

RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell-mediated Rejection.

Delineation of T-cell genes, gene sets, pathways, and T-cell subtypes associated with acute T cell-mediated rejection (TCMR) may improve its management. We performed bulk RNA-sequencing of 34 kidney allograft biopsies (16 Banff TCMR and 18 no rejection [NR] biopsies) from 34 adult recipients of human kidneys. Computational analysis was performed to determine the differential intragraft expression of T-cell genes at the level of single-gene, gene set, and pathways. T-cell signaling pathway gene sets for plenary T-cell activation were overrepresented in TCMR biopsies compared with NR biopsies. Heightened expression of T-cell signaling genes was validated using external TCMR biopsies. Pro- and anti-inflammatory immune gene sets were enriched, and metabolism gene sets were depleted in TCMR biopsies compared with NR biopsies. Gene signatures of regulatory T cells, Th1 cells, Th2 cells, Th17 cells, T follicular helper cells, CD4 tissue-resident memory T cells, and CD8 tissue-resident memory T cells were enriched in TCMR biopsies compared with NR biopsies. T-cell exhaustion and anergy were also molecular attributes of TCMR. Gene sets associated with antigen processing and presentation, and leukocyte transendothelial migration were overexpressed in TCMR biopsies compared with NR biopsies. Cellular deconvolution of graft infiltrating cells by gene expression patterns identified CD8 T cell to be the most abundant T-cell subtype infiltrating the allograft during TCMR. Our delineation of intragraft T-cell gene expression patterns, in addition to yielding new biological insights, may help prioritize T-cell genes and T-cell subtypes for therapeutic targeting.

Abstract 33: Revitalizing CAR-T cells for TNBC: Targeting phosphorylation of TCF7 to overcome T cell exhaustion

Abstract Breast cancer stands as the second leading cause of cancer-related deaths among women in the United States, with triple-negative breast cancer (TNBC) representing the most aggressive subtype. Although immune checkpoint inhibitors (ICI) demonstrated durable response in some TNBC patients, the added benefit of current FDA-approved ICI in combination with chemotherapy is estimated to be only around 10%. Fortunately, TNBC displays the highest number of tumor-infiltrating lymphocytes (TILs), compared to other BC subtypes, indicating an optimal context for the survival of T cells. Therefore, CAR-T therapy emerges as a promising therapeutic option for TNBC patients. Expanding the application of CAR-T therapies to solid tumors, including breast cancer, remains challenging. One of the key hurdles lies in the immunosuppressive tumor microenvironment, where the T cell receptor experiences long-term exposure to tumor antigens, leading to T cell exhaustion. This state impedes the T cells' capacity to efficiently target and eliminate cancer cells. Identifying key regulatory mechanisms downstream of the T cell receptor holds the potential to revolutionize existing immunotherapeutic strategies. In our study, we discovered that the presence of the master transcriptional factor of T cell stemness, TCF1, in CD8+ T cells, is essential for controlling TNBC tumors. TCF1 undergoes phosphorylation by LCK, a crucial component of initiating T cell receptor signaling, upon T cell activation. We found this phosphorylation site is indispensable for TCF1's transcriptional activities, inhibiting the downstream program of T-cell persistence and causing T-cell exhaustion. Reversing this process, either through LCK inhibition or introducing a non-phosphorylated form of TCF1, results in a more sustained CAR-T cell-mediated anti-tumor response. Our findings reveal the significance of TCF1 post-translational modification in the development and longevity of stem-like CD8+ T cells, bridging the gap between TCR signaling and transcriptional and epigenetic programs of stem-like CD8+ T cells. This insight contributes to a potential cure for TNBC by maintaining T cell persistence. Citation Format: Zhou Jiang, Yu-Yi Chu, Heng-Huan Lee, Mien-Chie Hung, Liuqing Yang, Chunru Lin. Revitalizing CAR-T cells for TNBC: Targeting phosphorylation of TCF7 to overcome T cell exhaustion [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 33.

Abstract 1689: CRISPR functional genetic screening for immune enhancers of inhibitor receptors in human primary CD8 T cells

Abstract The restrained efficacy of T cell therapies in cancer treatment is associated with T cell exhaustion (TEX), an impaired effector function state that is marked by distinct epigenetic landscape. These unique epigenetic features promoted the progression of TEX, hindered reinvigoration of TEX state and controlled the abnormal expression of inhibitor receptors (IRs), which could serve as target sites in cancer treatment. Thus, deciphering the regulatory elements in primary human T cells will deeply reveal the mechanism controlling TEX and provide novel therapeutic strategies to promote clinical response. However, how enhancers can be effectively applied in anti-cancer treatment is still poorly understood because high throughput identifying the functional enhancers of inhibitor receptors at scale is technically limited in human T cells. Here, we first developed a pooled screening platform that employs a compact CRISPRi system and enabled efficient one-step delivery of pooled screening libraries to primary human T cells. Leveraging this platform, we screened large genomic regions (~300kb) at saturation around key TEX genes, two IRs—PDCD1, HAVCR2 and one transcription factor (TF)—TBX21 to interrogate functional enhancers in human primary CD8 T cells. We identified two enhancers for PDCD1, three enhancers for HAVCR2 and three enhancers for TBX21, all of which are located over 12kb away from each gene’s transcription start sites. Then, to parse the essential sequences that fulfill enhancer function, we employed Cas9-based in-situ saturation mutagenesis screening to the identified enhancers of PDCD1 and HAVCR2. We found disrupt essential sequences impaired the entire enhancer function, quantitatively phenocopied the effect of targeting the entire enhancer with CRISPRi. Transcription factor motifs analyses of these sequences revealed potential regulation of ZFX for controlling PDCD1 expression and STAT for HAVCR2 expression. Finally, we explored the functional consequences of applying enhancers to anti-cancer treatment. Indeed, targeting the identified enhancers of PDCD1 and HAVCR2 in CAR T cells lead to enhanced cancer cell killing efficiency in vitro. Together, our study provides a platform and paradigm to interrogate functional enhancers in human T cells, illuminated the great potential of manipulating enhancers in T cell therapies. Citation Format: Ping Wang, Josephine R. Giles, Hua Huang, Junwei Shi, E.John Wherry. CRISPR functional genetic screening for immune enhancers of inhibitor receptors in human primary CD8 T cells [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 1689.

Abstract 580: APP as a novel immune checkpoint: Expression in T cells and its clinical implications for immuno-oncology drug refractory

Abstract Amyloid precursor protein (APP) is a type I transmembrane protein expressed in various cell types and tissues. We previously confirmed that APP expressed in T cells is a binding partner protein of a novel immune checkpoint contactin 4 (CNTN4), and APP is a central molecule for conveying the immunosuppressive signal of CNTN4 to T cells. We further profiled an expression of APP in tumor-infiltrating T cells from tumors of NSCLC patients who received anti-PD-1 as a neoadjuvant treatment combined with chemotherapy using single-cell RNA analysis. As a result, the proportion of APP-expressing CD4+ Teff or CD8+ Teff cells was higher in stable disease (SD) patients than in partial response (PR) patients. In contrast, we observed higher PDCD1-expressing CD4+ Tnaïve and CD4+ Teff cell proportions in PR patients than in SD patients. When we performed a Differential Expression Gene analysis between the PR and SD patients within Teff cells, we observed that the PR patients’ CD8+ Teff cells manifested a higher IFNG and PDCD1, while the SD patients’ CD8+ Teff cells predominantly exhibited elevated APP levels. Subsequent pathway analysis also suggested a negative relationship between immune-related pathways and APP expression in CD8+ Teff cells. Such findings imply that the predominant presence of APP in T cells is associated with I/O refractory. From a biological view, we demonstrated increased APP expression in T cells by stimulation with an anti-CD3 antibody or antigen-presenting cell. We also identified that upon stimulation with an anti-CD3 antibody, transcription factors for T-cell activation bind to the proximal promoter of APP and increase its expression. Furthermore, it was confirmed that APP in T cells not only increases its expression upon anti-CD3 antibody stimulation but also translocates from the cytoplasm to the membrane through the Golgi apparatus. When anti-CD3 antibody stimulation of T cells persists, the membrane expression of APP increases for 14 to 24 h, then gradually decreases when the stimulation disappears and becomes the same as before stimulation at 48 h. T cells differentiate into various subsets and play an essential role in adaptive immunological responses to foreign substances. In particular, CD4+ (helper) T cells differentiate into different T-cell subsets, such as Th1, Th2, Th17, Th19, Th22, Tfh, and Treg, to govern the overall immune response by producing cytokines that can recruit other cells of the immune system. So, we investigated whether APP is expressed on T cell subsets including naïve, effector, memory, and exhausted T-cells. We identified that APP is expressed in various CD4+ and CD8+ T cell subsets upon stimulation with anti-CD3 antibody. Taken together, our results suggest that APP is expressed on multiple functional T cells and that increased expression of APP on T cells in TIL may increase resistance to immunotherapy. Citation Format: Mi Young Cha, Bu-Nam Jeon, Gihyeon Kim, Areum Jeong, Sang-Moo Park, Kyung Mi Park, Hansoo Park. APP as a novel immune checkpoint: Expression in T cells and its clinical implications for immuno-oncology drug refractory [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 580.

Abstract 1522: Tumor-associated fibrosis leads to an increase in T-cell exhaustion and impairs tumor control in non-small cell lung cancer

Abstract Lung cancer is the leading cause of cancer-related mortality with non-small cell lung cancer (NSCLC) being the most predominant type. Recent studies have shown the efficacy of anti-PD1 inhibitors which improved overall survival. However, this efficacy is limited to a subset of patients due to the intrinsic tumor resistance to immune checkpoint inhibitors. Our group recently demonstrated that tumor-associated fibrosis negatively correlates with T cell-mediated immune response in lung cancer. This is largely dependent on Col13a1-expressing cancer-associated fibroblasts (CAFs), which result in recruiting the immunosuppressive macrophages and regulatory T cells while limiting dendritic cells and CD8 T cell infiltration. Here, we characterize the effect of fibrosis on the TME including TILs and macrophages using an orthotopic KRAS and P53-driven murine NSCLC model (KPL86-mCher model) with FITC-induced fibrosis.Fibrosis significantly increased the number of cancer-associated fibroblasts and collagen density in KPL86-mCher lung tumors. Following carboplatin + pemetrexed and Anti-PD1 treatment, we observed no increase in tumor-infiltrating CD4+ and CD8+ T cells or decrease in tumor burden when compared with the non-fibrotic tumors. Rather, we observed a significant increase in exhausted T cells marked by high Tim3, PD1, and TOX in fibrotic KPL86-mCher tumors. Corresponding to these impaired T-cell responses, we found an increase in tumor-infiltrating alveolar macrophages with immunosuppressive phenotype under fibrotic tumor conditions. Our data suggests that tumor-associated fibrosis leads to an increase in CD8+ T cell exhaustion as well as immunosuppressive macrophage infiltration in our spontaneously derived murine model on NSCLC. Overall, this indicates that targeting tumor fibrosis may significantly improve the efficacy of immunotherapy which would have translational implications for patients with immunotherapy-resistant NSCLC. Citation Format: Usman Y. Panni, Varun Shenoy, Brett Knolhoff, Faiz Ahmed, Brett Herzog, William G. Hawkins, John A. Olson, David G. DeNardo. Tumor-associated fibrosis leads to an increase in T-cell exhaustion and impairs tumor control in non-small cell lung cancer [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 1522.

Abstract 1365: INB03: a new immune checkpoint inhibitor that reprograms macrophage polarization, boosts ADCP and reverts T-cell exhaustion markers

Abstract Trastuzumab resistance is an important clinical issue in HER2+ breast cancer (BC), and few actionable targets are available. We demonstrated that soluble TNF (sTNF) upregulates mucin 4 (MUC4) expression, which shields trastuzumab epitope on HER2 hindering its therapeutic effect, and that sTNF blockade with INB03 decreases MUC4 expression which, together with trastuzumab, triggers an effective antitumor immune response based on antitumoral macrophage-NK cell collaboration. Because immune checkpoint molecules (ICP) and T cell exhaustion foster tumor immune escape, we addressed whether INB03 could modulate macrophage polarization, T cell exhaustion, and ICP expression in both populations to boost an antitumor immune response. For in vitro assays, human monocytes and T cells were isolated from buffy coats and enriched with specific RosetteSep. Macrophages (Mϕ) were differentiated for 6 days with M-CSF (10 ng/ml) to M0, and polarized for 48h to the M1-like subtype with LPS (50 ng/ml)+IFNγ (20 ng/ml), or to the M2-like subtype with IL-4 (20 ng/ml)+IL-10 (20 ng/ml). Then, INB03 was added (10 μg/ml) for 96h with corresponding cytokines to already-polarized Mϕ to test its ability to revert polarization. Also, Mϕ antibody-dependent cellular phagocytosis (ADCP) against human HER2+ breast cancer cell line JIMT-1 was assessed. T cells were activated with CD3/CD28 beads and cultured for 7 or 14 days. INB03 was added at those times for 48h to test its ability to modulate ICP and exhaustion markers. For in vivo assays, tumor-free mice or bearing the HER2+ C4HD tumor were treated with vehicle or INB03 (10 mg/kg, i.p.) for 21 days. Polarization, exhaustion and ICP markers were studied in Mϕ and T cells from spleen and tumor. Adding INB03 to already-polarized human Mϕ enhanced polarization towards M1-like (CD86+CD206−). Polarized Mϕ exposed to INB03 showed decreased PD1 and PDL-1 expression. Also, the expression of ADCP-inhibitory markers B7H4 and SIRPα was diminished when INB03 was present. These Mϕ exhibited increased ADCP against JIMT-1 cells treated with INB03, which showed downregulation of the inhibitory signal CD47. Murine Mϕ from tumor-bearing mice treated with INB03 showed increased polarization to the M1-like phenotype. Human CD8+ T cells showed decreased expression of PD1, PD-L1, LAG3, TIM3 and TIGIT. However, only TIM3 and PD1 were downregulated in murine CD8+ T cells of tumor-bearing mice treated with INB03. In all, sTNF blockade skews Mϕ to the M1-like phenotype and reprograms already-polarized pro-tumoral M2-like Mϕ to antitumoral ones. INB03 can tailor the tumor microenvironment by promoting Mϕ ADCP against tumor cells and by acting as an ICP inhibitor for CD8+ T cells, possibly relieving their exhaustion. HER2+MUC4+ BC patients could benefit from the administration of INB03 to boost targeted therapy efficacy and overcome tumor-induced macrophage and T-cell immune escape. Citation Format: Sofia Bruni, Maria F. Mercogliano, Roxana Schillaci. INB03: a new immune checkpoint inhibitor that reprograms macrophage polarization, boosts ADCP and reverts T-cell exhaustion markers [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 1365.

Abstract 7517: Integrating in situ proximity ligation assay for PD1-PDL1 interaction with multiplexed immunofluorescence imaging

Abstract Background: Programmed cell death protein 1 (PD1) and its ligand PD-L1 are pivotal components of the immune checkpoint machinery, playing a crucial role in the regulation of immune responses in cancer. The interaction between PD1 and PD-L1 is a significant therapeutic target in oncology, as its inhibitors have shown improved outcomes across a variety of malignancies. However, the treatment response to immunotherapies such as pembrolizumab has shown a modest response (~30%) in previous studies. This could be explained by the lack of molecular insight pertaining to the interaction of PD1 on T-cells and PD-L1 in the tumor cells in malignant tissues at the time of clinical diagnosis. The recent development of in situ Proximity Ligation Assay (isPLA), marks a significant advancement in the field. This method allows for the visualization of direct protein interactions within tissues, for example between PD1 and PD-L1. This adds an important layer of information compared to multiplexed immunofluorescence, which is useful for deep phenotyping of cell types in a tissue but lacks the ability to detect direct interactions between specific cells. Methods: PD-L1-PD1 interactions in human FFPE tonsil and bladder cancer tissue were identified using the NaveniFlex Tissue Atto647N kit, following the guidelines provided by the manufacturer. This method is capable of detecting proteins within a proximity of less than 40 nm, utilizing oligonucleotide-antibody conjugates that generate an enhanced fluorescent signal. After completing the Naveni® detection process, we performed multiplexed immunofluorescence (IF) using the Phenocycler platform and a panel of 14 barcoded antibodies, to generate isPLA and multiplexed IF data on the same tissue section. Results &amp; Discussion: We have successfully established an automated workflow for the isPLA protocol. In this work, we aim to continue this effort and combine the isPLA, with downstream highly multiplexed immunofluorescence using the Phenocycler platform. We have generated proof of concept data for the successful integration of the two methods, using tonsil and bladder cancer tissue to detect protein interactions between PD1 and PD-L1, as well as phenotypic profiling of the tumor microenvironment with a 14 plex panel. This panel allows us to phenotype the relevant cell types (B cells, dendritic cells, T cells, macrophages, tumor cells and their proliferation status) and subsets of T-cells like cytotoxic CD8+ cells. The integration of the isPLA and multiplexed IF is poised to significantly advance our understanding of the TME and hopefully aid in patient stratification for immune checkpoint inhibition therapy. The clinical significance of this method integration will later be explored in a retrospective cohort of muscle invasive bladder cancer, receiving immune checkpoint inhibition therapy with pembrolizumab as a second line treatment. Citation Format: Tony Ullman, David Krantz, Hampus Elofsson, Carolina Oses Sepulveda, Agata Zieba-Wicher, Päivi Östling, Anders Ullén, Subham Basu, Charlotte Stadler. Integrating in situ proximity ligation assay for PD1-PDL1 interaction with multiplexed immunofluorescence imaging [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 7517.

Abstract 4991: Radiotherapy-induced immunological and therapeutic response depends on stem-like TCF-1+PD-1+CD8+ T-cells

Abstract Radiotherapy is a frequently used treatment for cancer. Recent data, including ours, showed that radiotherapy promotes an inflammatory response in the tumor that supports tumor-specific immunity, and in fact, the efficacy of radiotherapy in pre-clinical models depends on CD8+ T-cells. According to our preliminary data, the response to radiotherapy is independent of de novo recruited CD8+ T-cells, suggesting that radiation drives differentiation and proliferation of preexisting intratumoral CD8+ T-cells. Intratumoral CD8+ T-cells are heterogeneous concerning phenotype and function. Under conditions of chronic stimulation by antigen, a subset of CD8+ T-cells expressing PD-1 and the transcription factor TCF-1 was described. These so-called stem-like CD8+ T-cells, which give rise to effector cells, were shown to be essential for the clinical response to PD-1 blockade. How radiotherapy influences the different CD8+ T-cell subsets in the tumor microenvironment has not been comprehensively investigated. We propose that the efficacy of radiotherapy depends on the presence of stem-like CD8+ T-cells, presumably by giving rise to effector cells. To address this, we selectively depleted TCF-1+ cells from tumor-bearing mice immediately before radiotherapy. Subsequently, we correlated tumor regression with the immunological response using single-cell analyses of intratumoral CD8+ T-cells. In the absence of TCF-1+ cells, we found a reduced efficacy and reduced number of intratumoral effector cells after radiotherapy. We currently analyze our single-cell RNA-sequencing data and expect to discover novel radiotherapy-induced pathways in CD8+ T-cells that contribute to therapeutic efficacy. Citation Format: Hakan Köksal, Michael Herbst, Nicola Marti, Maries van den Broek. Radiotherapy-induced immunological and therapeutic response depends on stem-like TCF-1+PD-1+CD8+ T-cells [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 4991.

Abstract 2627: PanCancer epigenetic regulators of lymphocyte activation states

Abstract Several immune cell types have been successfully targeted for immunomodulatory therapy; however, the efficacies of such therapies are hindered by incompatible immune cell activation states. CD8+ T-cell exhaustion is one of the most studied T-cell states in the context of cancer and was shown to limit checkpoint blockade efficacy. Although CD8+ T-cell exhaustion studies in mice showed this state is tightly regulated by chromatin accessibility of cis-regulatory elements (CREs) and transcription factor activation, the exploration of these mechanisms, their prevalence, and their specificity in human cancers remains limited. In addition, chromatin accessibility signatures of other lymphocyte (CD4+ and NK) states frequently found in solid tumors have not been carefully characterized in a pan-cancer setting. Here we introduce the first single-nuclei atlas of pan-cancer and disease-specific cis- and trans-regulatory elements in tumor infiltrating lymphocytes. We profiled ~140K T-cell and NK cell nuclei with snATAC-seq and snRNA-seq from 227 tumor and normal samples from eleven cancer types. We distinguished two major subpopulations among exhausted CD8+ T-cells: GZMK expressing (CD8+ GZMK+ Tex) and ITGAE+ tissue-resident (CD8+ Trm ex). CD8+ GZMK+ Tex was enriched in clear cell renal cell carcinoma, while CD8+ Trm ex was found in all other cancers. Both exhausted groups featured high motif accessibility and expression of NR4A1, NFATC2, and NFKB2 transcription factors (previously reported to regulate exhaustion), but differed in EOMES motif accessibility and gene expression. We have identified other lymphocyte subpopulations showing exhaustion signatures, including CD4+ follicular helpers (CD4+ Tfh), CD4+ regulatory cells (CD4+ Tregs), and weakly cytotoxic tissue-resident NK cells (trNK weak). All these subpopulations showed increased expression and motif accessibility of the NR4A1 transcription factor, highlighting its role in regulating dysfunctional states not only in CD8+ T-cells, but also in CD4+ and NK cells. Additionally, CD4+ Tfh and Tregs showed enhanced activity of NFKB1, NFKB2, and POU2F2, and trNK weak cells had increased activity of NR4A2 and NR2F2. To put our results into clinical perspective, we have collected cohorts of renal cancer, melanoma and triple-negative breast tumors treated with immunotherapy in clinical trial settings, and showed elevated GZMK expression in exhausted T-cells in responders compared to non-responders. Citation Format: Alla Karpova, Nadezhda V. Terekhanova, Siqi Chen, Reyka G. Jayasinghe, Andrew Houston, Wagma Caravan, Ryan C. Fields, Li Ding. PanCancer epigenetic regulators of lymphocyte activation states [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 2627.

Abstract 3856: Nodal metastasis as an immune indicator in cancer (ca) therapy

Abstract Introduction: Nodal Metastasis as an Immune Indicator in Cancer (Ca) Therapy Staging (sg) is widely used to identify appropriate treatment options &amp; implement therapy. Tumor-Node-Metastasis (TNM) is the most utilized sg system. In it, nodal involvement is viewed simply as an adverse metric without biologic connotation, and gross metastasis (M1) eclipses other variables and denotes the least favorable sg. Ca’s ability to thrive within the lymph node itself was intriguing to us in the immune-oncology (IO) era. Failure to overcome an immunogenic ca (e.g., dysfunctional apoptosis) leads to T-cell exhaustion (TCE) typified by PD-1 expression. Immune Checkpoint Inhibitors (ICI) address TCE by intercepting the PD-1:PDL-1 synapse. We reasoned that immune actions are distinct in tumor beds vs nodes &amp; hypothesized that immunogenic N(+), implies ca’s ability to defend itself (e.g., PDL-1 expression); N(0), reflects immune susceptibility and effective clearance outside the tumor bed. In the latter scenario, TCE is nonexistent; ICIs are less beneficial. Tumor beds (T, M) are sanctuaries exempt from immune action due to factors such as hypoxia, acidity, and poor tumor vasculature which lead to poor T-cell trafficking, to name a few. M1 develop from circulating ca stem cells, an immune-exempt entity. Methods: We examined the interaction between ICIs &amp; nodal involvement dichotomizing surveillance, epidemiology and end results SEER cases into N(0) or N(+) within M1 melanoma &amp; lung cancer. 2005, 2015-17 denote pre-, and post ICI, respectively to provide mature survival data. Results: Table 1 depicts the 4- or 5-year overall survival in the specified subsets. Conclusions: ICI benefit is more prominent in N(+) ca, where TCE is likely. N(0) ca represents immune-prone ca with less TCE &amp; need to be viewed as a biologically distinct subset. Agents influencing T-cell access (angiogenic)/functionality should be considered in these cases. Finally, we suggest that PDL-1 testing should specify testing sites as nodal vs tumor bed expression. Expectations SEER results: % Overall Survival at 5-y (melanoma) or 4-y (Lung ca) Pre-ICI Post ICI Metric Melanoma Mechanism 2005 2015 Increment in 5yr OS N(0) favorable prognosis Immunogenic tumor N(0): 302 cases 20 29 8 (20 -12) N+ Predicts benefit to ICI T-cell exhaustion in N(+) only N(+): 210 cases 12 37 N(+): +25 &amp;gt; N(0): +9 2005 2017 Increment in 4yr OS Lung Cancer N(0) similar to N(+) Less immunogenic tumor N(0) 9,583 cases 18 18 4 (18 -14) N+ Predicts benefit to ICI T-cell exhaustion in N(+) only N(+): 17,887 cases 14 20 +6 Citation Format: Bradley Fugere, Jim Chen, Tyler C. Fugere, Farah Mazahreh, Nishanth Thalambadu, A Mazin Safar. Nodal metastasis as an immune indicator in cancer (ca) therapy [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 3856.

Abstract 4571: Combination of FOLFIRI (5-FU, Leucovorin, and Irinotecan) and ProAgio on colon cancer growth and metastasis

Abstract Background/Objective: One of the common mechanisms of resistance of solid tumors, including colon cancers, is activation of integrins on endothelial cells (ECs) and cancer-associated fibroblasts (CAFs). ProAgio is a small molecule developed to target integrin alpha V beta 3 (αvβ3), located on surface of abnormal ECs and CAFs. ProAgio enhances apoptosis and inhibits angiogenesis via targeting αvβ3. The aim of the current study is to evaluate the ProAgio combination with FOLFIRI on the immune profile and tumor growth of colon cancer. Material and Methods: Female BALB/CJ and male NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice were acquired from the Jackson Laboratory, and experiments were performed under the approval of The University of Alabama at Birmingham-Institutional Animal Care and Use Committee. For orthotropic tumor efficacy studies, BALB/CJ mice were injected with 2×105 CT-26 wild type and CT26.CL25 cells in 30ul 1:1 Matrigel Matrix and PBS into the Cecum. PDX (10mg) was orthotopically implanted into the NSG mice cecum. At Day five, mice were divided into four treatment groups: including 1) sterile water (vehicle), 2) ProAgio (15mg/kg; IP; once daily for nine days), 3) FOLFIRI (5-FU: 30mg/kg; Leucovorin 50mg/kg; Irinotecan; 20mg/kg - once every three days intraperitoneal) or 4) combination of ProAgio and FOLFIRI. The study completed on day 15, tumor weight was noted, and tumors were processed for histology and flow cytometry. Results: ProAgio plus FOLFIRI significantly (p&amp;lt;0.001) reduced tumor weight in both models compared to individual treatments and vehicles. Combination-treated mice showed a significant (p&amp;lt;0.001) reduction in T-cell exhaustion (CD8+ T cells that are positive for PD-1, TIM-3, and CTLA-4). Analysis of the myeloid compartment showed a significant (p&amp;lt;0.001) increase in the M1 macrophages that express F4/80 as well as CD86, MHC-II and a decrease in the M2 macrophage in the mice treated with ProAgio plus FOLFIRI. The combination therapy exhibited a significant (p&amp;lt;0.001) increase in the dendritic cell infiltration into the tumor microenvironment. Histology analysis showed that ProAgio treatment reduced the incidence of organ site metastasis (disseminated and locoregional spread) such as liver, pancreas, and diaphragm. Conclusion: Our study offers encouraging observations that ProAgio plus FOLFIRI can suppress colon cancer growth and metastasis by inhibiting αvβ3 preclinically and may provide a novel therapeutic combination for the management of colon cancers. Citation Format: Purnachandra Nagaraju Ganji, Jeremy B. Foote, Madhu Sudhana Saddala, Falguni Mishra, Sujith Sarvesh, Midhun Malla, Ashiq Masood, Zhi-Ren Liu, Bassel F. El-Rayes. Combination of FOLFIRI (5-FU, Leucovorin, and Irinotecan) and ProAgio on colon cancer growth and metastasis [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 4571.

Abstract 6593: Rejuvenation of tumor-infiltrating lymphocytes (TIL): A novel strategy to revitalize TIL antitumor function for cell therapy

Abstract TIL therapy is a promising approach for the treatment of metastatic solid tumors, but its efficacy is limited by T-cell exhaustion and terminal differentiation. In addition, recent studies have underscored the adverse effects of aging on T cells. Reprogramming T cells into induced pluripotent stem cells (iPSC) and differentiating them back to the T-cell lineage has proven to be complex and time-consuming. In particular for TIL applications, de novo T cell production via iPSCs requires each TCR in the final product to be derived from an independently established iPSC clone. To overcome these barriers, we developed a novel technology called Rejuvenation, which bypasses the need for reprogramming of T cells into iPSCs. Rejuvenated TIL products retain their TCR diversity while offering several significant advantages, including reduced T-cell epigenetic age, improved expansion capacity, stem cell-like phenotype, and enhanced secretion of cytokines upon activation by target antigens. In this study, we used TIL derived from patients with melanoma and NSCLC. Rejuvenated TIL were generated by the transient expression of transcription factors in a process called ‘Partial Reprogramming’ and returned back to a T-cell lineage phenotype by a process called ‘Redirection’. Partially reprogrammed TIL showed an altered morphology resembling adherent stromal cells and down-regulated conventional T-cell markers including CD3, CD4, and CD8. Redirected T cells reacquired a conventional CD4/CD8 phenotype including morphology, surface markers and function, and demonstrated decreased epigenetic age (&amp;gt;7 years younger, N=3). We also observed a higher proliferative capacity, improved metabolic state, and increased expression of biomarkers associated with T-cell stemness, including CCR7 and CD62L, when compared with untreated TIL. Rejuvenated TIL demonstrated improved cytokine secretion, including IFNγ, TNFα and IL-2 in functional assays. Immune repertoire analysis revealed a significant polyclonal population of putative tumor-reactive TCRs. In vivo functionality was also evaluated using a xenograft model of engineered A375 melanoma cell line that agonizes T-cells in hIL2-NOG mice. Adoptive transfer of rejuvenated TIL resulted in significantly improved suppression of tumor growth and prolonged survival compared with TIL expanded by conventional methods. These results were also confirmed in other surrogate models, including rejuvenated PBMC, TCR and CAR T cells, demonstrating the broad applicability of Rejuvenation technology. Our results indicate TIL Rejuvenation enhances the functionality and antitumor characteristics of T cells, while preserving a broad TCR repertoire. This technology holds substantial promise and may pave the way for the development of the first rejuvenated autologous polyclonal TIL therapy for treatment of advanced solid tumors. Citation Format: Raul Vizcardo, Yin Huang, Jessica Fioravanti, Takuya Maeda, Naritaka Tamaoki, Yasuhiro Yamazaki, Burak Kutlu, Kriti Bahl, Biao Wang, Zheng Zhong, Shobha Potluri, Nicholas P. Restifo, Gary Lee. Rejuvenation of tumor-infiltrating lymphocytes (TIL): A novel strategy to revitalize TIL antitumor function for cell therapy [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 6593.