Immune Checkpoint Blockade Treatment Research Articles

Exosome secretion related gene signature predicts chemoresistance in patients with colorectal cancer

BackgroundColorectal cancer (CRC) is a highly heterogeneous malignancy, and patients often have different responses to treatment. In this study, the genetic characteristics related to exosome formation and secretion procedure were used to predict chemoresistance and guide the individualized treatment of patients. MethodsFirstly, seven microarray datasets in Gene Expression Omnibus (GEO) and RNA-Seq dataset from the Cancer Genome Atlas (TCGA) were used to analysis the transcriptome profiles and associated characteristics of CRC patients. Then, a predictive model based on gene features linked to exosome formation and secretion was created and validated using Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) machine learning. Finally, we evaluated the model using chemoresistant/chemosensitive cells and tissues by immunofluorescence (IF), western blot (WB), quantitative real-time PCR (qRT-PCR) and immunocytochemistry (IHC) experiments, and the predictive value of integrated model in the clinical validation cohort were performed by Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) curves analyses. ResultsWe established a risk score signature based on three genes related to exosome secretion in CRC. Better Overall Survival (OS) and greater chemosensitivity were seen in the low-risk group, whereas the high-risk group exhibited chemoresistance and a subpar response to immune checkpoint blockade (ICB) therapy. Higher expression of the model genes EXOC2, EXOC3 and STX4 were observed in chemoresistant cells and specimens. The AUC of 5-year disease-free survival (DFS) was 0.804. Compared with that in the low-risk group, patients' DFS was found to be significantly worse in the high-risk group. ConclusionsIn summary, the gene signature related to exosome formation and secretion could reliably predict patients' chemosensitivity and ICB treatment response, which providing new independent biomarkers for the treatment of CRC.

ImmunoChemoradiation for Non-Small Cell Lung Cancer: A Meta-Analysis of Factors Influencing Survival Benefit in Combination Trials

PurposeAdding immune checkpoint blockade (ICB) to concurrent chemoradiotherapy (cCRT) has improved overall survival (OS) for inoperable locally advanced non-small cell lung cancer (LA-NSCLC). Trials of cCRT-ICB are heterogeneous for factors such as tumor stage and histology, PDL1 status and cCRT-ICB schedules. We therefore aimed to determine the ICB contribution to survival across studies and identify factors associated with survival gain. Methods and materialsData were collated from cCRT-ICB clinical studies published 2018-2022 which treated 2196 NSCLC patients (99% stage III). Associations between 2-year OS and ICB, CRT, patient and tumor factors were investigated using meta-regression. A published model of survival following RT or CRT was extended to include ICB effects. The model was fitted simultaneously to the cCRT-ICB data and data previously compiled for RT/CRT treatments alone. The net ICB contribution (‘OS gain’) and its associations with factors were described by fitted values of ICB terms added to the model. Statistical significance was determined by likelihood-ratio testing. ResultsThe gain in 2-year OS from ICB was 9.9% overall (95% CI: 7.6%, 12.2%; p=0.018). Both OS gain and 2-year OS itself rose with increasing planned ICB duration (p=0.008, 0.002 respectively) and with tumor PDL1 ≥1% (p=0.034, 0.023). Fitted OS gains were also greater for patients with stage IIIB/C disease (p=0.021). OS gain was not associated with tumor histology, patient performance status, RT dose, ICB drug type (anti-PDL1 vs anti-PD1) or whether ICB began concurrently with or after cCRT. ConclusionFitted gains in 2-year OS due to ICB were higher in cohorts with greater fractions of stage IIIB/C patients and patients with tumor PDL1 ≥1%. OS gain was also significantly higher in a single cohort with a planned ICB duration of two years rather than one, but was not associated with whether ICB treatment began during vs after CRT.

Immunological Mechanisms behind Anti-PD-1/PD-L1 Immune Checkpoint Blockade: Intratumoral Reinvigoration or Systemic Induction?

Anti-PD-1/PD-L1 immune checkpoint blockade (ICB) has been widely used to treat many types of cancer. It is well established that PD-L1 expressing cancer cells could directly inhibit the cytotoxicity of PD-1+ T cells via PD-L1-PD-1 interaction. However, histological quantification of intratumoral PD-L1 expression provides limited predictive value and PD-L1 negative patients could still benefit from ICB treatment. Therefore, the current major clinical challenges are low objective response rate and unclear immunological mechanisms behind responding vs. non-responding patients. Here, we review recent studies highlighting the importance of longitudinal pre- and post-ICB treatment on patients with various types of solid tumor to elucidate the mechanisms behind ICB treatment. On one hand, ICB induces changes in the tumor microenvironment by reinvigorating intratumoral PD-1+ exhausted T cells ("releasing the brakes"). On the other hand, ICB can also affect systemic antitumor immunity in the tumor-draining lymph node to induce priming/activation of cancer specific T cells, which is evident by T cell clonal expansion/replacement in peripheral blood. These studies reveal that ICB treatment not only acts on the tumor microenvironment ("battlefield") but also acts on immune organs ("training camp") of patients with solid tumors. A deeper understanding of the immunological mechanisms behind ICB treatment will pave the way for further improvements in clinical response.

Abstract 6861: PIK3CA activating mutation promotes an immune suppressive microenvironment in squamous cell carcinoma

Abstract Head and neck squamous cell carcinoma (HNSCC) is a leader in cancer incidence worldwide. Recently, immunotherapies such as immune checkpoint blockade (ICB) have offered great promise in treating many solid tumors, including HNSCCs, that are refractory to chemotherapy and radiation. Challengingly, HNSCC patients often relapse following ICB treatment due to the lack of a thorough understanding of the mechanisms underlying cancer immune evasion. These disparities in patient outcomes strongly suggest the existence of genetic variations that underlie their distinct responses to ICB. Although the specific oncogenic mutations responsible for driving relapse in SCC patients remain unclear, it is imperative to grasp the mechanisms of cancer immune evasion in individuals with specific genetic profiles to enhance the precision of immunotherapy. Cancer immune evasion has emerged as a hallmark of cancer and is facilitated by a highly complex tumor microenvironment (TME). We aim to understand the genetic basis shaping the immune suppressive TME and hypothesize that oncogenic driver mutations play a dominant role in preventing the immune clearance of transformed cells by reprogramming the immune landscape in the tumors. To determine the critical genetic signatures enriched in SCC patients that can impact anti-tumor immunity, we analyzed TCGA data which revealed a strong negative correlation between PIK3CA level and CD8 T cell signatures. We have identified that activating mutations in the PIK3CA gene, found in 20% of HNSCCs, promote rapid tumor relapse after initial response to anti-PD-L1 and anti-CTLA-4 ICB treatments. Utilizing single-cell analysis, quantitative immune profiling, and multiplexed imaging, our lab showed that tumor-initiating cells (TICs) in SCCs can have an intricate dialogue with myeloid-derived suppressor cells (MDSCs) where TICs secrete factors to enhance MDSC recruitment and suppressive function on cytotoxic T cells. Additionally, our data supports that the tumor interstitial fluid (TIF) of PIK3CA mutant SCC tumors can enhance the suppressive activity of MDSCs on cytotoxic T cells. These results suggest that the acquisition of PIK3CA mutation may trigger TICs to release additional factors to further modify MDSC activities. A critical method by which MDSCs suppress T cells is through the production and respiratory burst of reactive oxygen species (ROS). RNA sequencing revealed that PIK3CA mutant SCCs have multiple mechanisms of increasing ROS in the TME and specifically in MDSCs, while simultaneously upregulating lipid metabolism genes, such as SCD1, to protect itself from MDSC-derived ROS. This study reveals a potential strategy for targeting PIK3CA mutant SCCs as a promising precision immunotherapy to enhance the efficacy of ICB treatments. Citation Format: Benjamin T. Nicholson, Weijie Guo, Yuxuan Miao. PIK3CA activating mutation promotes an immune suppressive microenvironment in squamous cell carcinoma [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 6861.

Abstract 1854: Plasma proteomic biomarkers identify non-responders and reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade

Abstract Most patients treated with immune checkpoint blockade (ICB) do not have durable treatment responses, stressing a critical need to identify early non-invasive biomarkers of response. Circulating biomarkers provide easy access for serial monitoring and can provide insight on the mechanisms of response to ICB. We performed plasma proteomics (~3000 proteins) on 250 metastatic melanoma patients before and on ICB treatment and performed analysis to identify response- and time point-associated peripheral protein biomarkers. We next generated patient-matched peripheral blood lymphocyte (PBL) surface proteomic data and tumor sample bulk transcriptomic data to build a multimodal dataset. We leveraged these data to train machine learning models for unsupervised analysis and to classify treatment responses and learned features predictive of survival and patient endotypes. Using univariate linear models to predict protein abundance based on time point, response and the interaction term for time point and response, we identified 343 time point-associated proteins, 141 response-associated proteins, and one interaction-associated protein. We further investigated response-related proteins by fitting multivariate logistic regression and cox proportional hazards regression models to further investigate the ability of these proteins to predict response, progression-free survival (PFS), and overall survival (OS) and identify those proteins that are most important in predicting response. We calculated covarying modules of proteins that were found to be either response-associated or time point-associated to discover underlying biological networks at different treatment time points and disease response states. Additionally, we leveraged these modules to endotype patients and identified trends in protein modules across patient subsets, including modules related to biological processes such as immune infiltration, apoptosis, metaplasia and cell adhesion. To understand the contribution of different compartments on plasma proteomic abundance, we studied correlations of plasma protein abundance with PBL surface protein abundance and tumor bulk mRNA-sequencing expression. Finally, we integrated our data modalities and fit various statistical models to evaluate the relative importance of plasma protein biomarkers in predicting response compared to PBL surface proteins and tumor bulk mRNA-sequencing expression. Together, these data represent one of the deepest peripheral biomarker studies using paired samples in melanoma patients treated with anti-PD1 therapy. Citation Format: Samuel J. Wright, Deepika Yeramosu, Milan Parikh, Marijana Rucevic, Ngan Nguyen, Russell W. Jenkins, Keith T. Flaherty, Nir Hacohen, Genevieve M. Boland, Arnav Mehta. Plasma proteomic biomarkers identify non-responders and reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1854.

Abstract 3972: Personalized immune-organoid co-culture system for modeling the anti-tumor immune response in breast cancer patients

Abstract Recent studies have reported the effectiveness of immune checkpoint blockade (ICB) therapy in breast cancer patients. However, only a subset of patients benefits from ICB therapy due to various immunosuppressive mechanisms. The development of personalized predictive models for the anti-tumor immune response is essential to broaden the indication of ICB therapy. Here, we suggest a novel model platform using a co-culture system with patient tumor-derived organoids and matched immune cells to predict the immune response of individual patients. We successfully established fifty-nine cases of patient-derived breast cancer organoids with matched peripheral blood mononuclear cells (PBMCs) (subtype: Luminal A, 18.6%; Luminal B, 28.8%; Triple-negative breast cancer, 35.6%; HER2-positive, 17.0%). Three rapidly proliferating organoids (one Luminal B and two TNBC organoids) were selected to develop an immune-organoid co-culture (IOC) system. To mimic the anti-tumor immune response, cytotoxic immune cells were expanded from PBMCs by modified cytokine-induced killer (CIK) cell expansion protocol utilizing IL-2/IL-15. The CIK cells were co-cultured with patient-derived tumor organoids for killing assay to enable the prediction of ICB responsiveness in vitro. The CIK cells were expanded in the IOC system by stimulation of PBMC with IL-2/IL-15 in the presence of matched tumor organoids for 11 to 14 days. The CIK cells exhibited tumor organoid-specific killing (measured by Caspase-3, 15.22% ± 8.58, mean ± SEM) on organoid co-culture and showed induction of CD107a and CD137 expression in CD8+ T cells and NK cells with the PD-1 blocking antibody. The CIK-mediated tumor organoid deaths and immune cell activation were reduced by HLA class I blocking antibody (W6/32) treatment, confirming HLA-TCR mediated immune response and killing of tumor organoids in the IOC system (-14.85% in organoid-specific lysis and -7.46% in CD107a expression). In the live cell imaging of the IOC system, the interaction between T cells and tumor organoid cells and subsequent induction of Caspase 3 was noted. Our IOC system could directly measure the immunogenic tumor organoid killing by immune cells on ICB treatment in individual breast cancer patients. Moreover, the analysis of immune receptor profiles may reveal immune modulating mechanisms in each patient. We expect the IOC system to serve as a useful platform for personalized immunotherapy and exploration of combinatory therapy to enhance the anti-tumor efficacy of ICB in breast cancer patients. Citation Format: Cheol-Hwa Hong, Won-Ji Ryu, Shinyoung Park, Tae Yeong Kim, Yumi Hwang, Hyunju Han, Seongyeon Jo, Taeyong Kweon, Gun Min Kim, Min Hwan Kim, Hyung Seok Park, Joo Hyuk Sohn. Personalized immune-organoid co-culture system for modeling the anti-tumor immune response in breast cancer patients [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 3972.

Abstract 3861: Associations of intragenic rearrangement burden with immune cell infiltration and response to immune checkpoint blockade in cancer

Abstract While immune checkpoint blockade (ICB) induces durable cancer remission, only a small subset of patients can receive benefits, whereas a substantial portion of patients encounter severe immune-related adverse events. Further, about 4-29% of patients experience dramatic acceleration of disease progression after ICB treatment. Predictive biomarkers of ICB responses are in high demand to ensure patient benefits and avoid tragic clinical outcomes. In addition to PD-L1 tests, several genetic biomarkers are associated with ICB effectiveness, such as tumor mutation burden (TMB), somatic copy number aberrations, indels, and microsatellite instability. However, none of these neoantigen markers are sufficient to discriminate ICB responders in diverse cancer entities of distinct genetic profiles. In particular, TMB fails to predict in the cancer types with low simple mutation rates, such as triple-negative breast cancer (TNBC), ovarian cancer, and esophageal cancers. In TNBC, high TMB only accounts for 5-10% of patients, whereas a much larger proportion of tumors are inflamed (26-50%), which suggests a possible uncharacterized major source of neoantigens. Similarly, TMB is not predictive of ICB response in ovarian cancers according to the IMagyn050 trial. In esophageal cancer, TMB is not associated with T cell infiltration and does not predict ICB response. Our analyses of Pan-cancer whole genomes revealed that intragenic rearrangement (IGR) burden is a pivotal contributor to immune infiltration in breast, ovarian, esophageal, and endometrial cancers, which correlates with increased Macrophage M1 and CD8+ T cell signatures. IGRs result in exon duplications or deletions through rearrangements of a genomic distance of tens of kilobases. Multivariate regression against spatially counted tumor infiltrated lymphocytes in breast, endometrial, and ovarian cancers suggest that IGR burden is a more influential covariate than other genetic aberrations in these cancers. In the MEDI4736 trial evaluating durvalumab in esophageal adenocarcinoma, IGR burden correlates with patient benefits. In the IMVigor210 trial evaluating atezolizumab in urothelial carcinoma, IGR burden increases with platinum exposure and predicts patient benefits for TMB-low, platinum-exposed tumors. Altogether, we demonstrate that IGR burden contributes to T-cell inflammation and predicts ICB benefits in TMB-low, IGR-dominant tumors, or in platinum-exposed tumors. IGRs as a cryptic class of structural variants have been heretofore overlooked in cancer genomics studies. The association of IGRs with ICB response has not been previously reported in cancer in general. The development of IGR burden-based predictive marker could increase effectiveness of ICB therapy, reduce severe side-effects and unnecessary costs. Citation Format: Han Zhang, Sanghoon Lee, Renee R. Muthakana, Binfeng Lu, David N Boone, Daniel Lee, Xiaosong Wang. Associations of intragenic rearrangement burden with immune cell infiltration and response to immune checkpoint blockade in 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 3861.

Anti-PD-L1 nanobody guided in situ self-assembly and release of IOX1 and FDU for enhanced cancer chemo-immunotherapy

The clinical outcomes of immunotherapy are limited by the immunosuppressive tumor microenvironment (TME) and immune-related adverse effects. To address these issues, here we develop a tumor-specific chemo-immunotherapy prodrug FDU-IOX1-FF-Nb for highly-effective and low-toxic cancer therapy. This prodrug incorporates fluorouracil (FDU) to induce immunogenic cell death and reshape the TME, while the checkpoint inhibitor 5-carboxy-8-hydroxyquinoline (IOX1) provides immune checkpoint blockade (ICB) treatment and inhibits the expression of P-glycoproteins to overcome drug resistance. Furthermore, a small-sized anti-PD-L1 nanobody selectively delivers the prodrug to PD-L1 overexpressing tumor cells and blocks the PD-1/PD-L1 pathway for improved ICB treatment effect. The prodrug self-assembles into large nanoparticles within tumor cells via the π-π stacking interaction between FF after the reduction of glutathione, accumulating and preserving the drugs in the tumor sites. Finally, the esterase that are highly expressed in tumor cells cleave the ester bonds on nanoparticles, releasing free IOX1 and FDU for the chemotherapy and immunotherapy. Through the process of PD-L1 targeting, glutathione-triggered self-assembly, and esterase-mediated release of IOX1 and FDU, efficient cancer chemo-immunotherapy and precise tumor suppression with minimal non-target toxicity are achieved.

Abstract 6200: Single-cell analyses unravel novel immune and tumor cell characteristics linked to the response to neoadjuvant immune checkpoint blockade in patients with gastric cancer

Abstract Background: Gastric cancer remains the leading cause of cancer-related deaths worldwide, ranking fifth for incidence and fourth for mortality. Combining neoadjuvant therapy with immune checkpoint inhibitors has demonstrated improved outcomes for patients with gastric cancer. However, responses exhibit heterogeneity, and the understanding of the mediators influencing therapy response is limited. Methods: In this study, we collected 80 blood and tumor samples from 22 gastric cancer patients treated with XELOX/SOX alone or its combination with Nivolumab (anti-PD-1). Paired single-cell RNA-, TCR-, and BCR-sequencing were performed on pre- and post-treatment samples to investigate the dynamics of immune and tumor cells during the development of response/resistance to therapy. Results: Our findings revealed that elevated levels of baseline CD4 and CD8+ tissue-resident memory T (TRM) cells, in activated and stressed states, are associated with a superior response to combined therapy, and treatment further amplifies this cell population in responsive patients. Tracking T cell receptor clones across pre-/post-treated blood and tumor samples disclosed that the expanded clonotypes of TRM cells are exclusively detected in tumors, and considerable preexisting clones contribute to the expansion of these T cell populations following treatment. The simultaneous presence of TRM, B, and dendritic cells in pre-treated tumors predicted a favorable response, and they concertedly expanded in tumors responsive to anti-PD-1 therapy. Conclusions: Our findings highlight the significance of TRM cells in effective responses to anti-PD-1 therapies and indicate that their cellular communication with B and dendritic cells play a pivotal role in shaping the antitumor immunity elicited by combination therapy. Together, this study illuminates vital immune cell subsets during immune checkpoint blockade treatment, provides biological insights into the mechanism of successful combination therapy, and unravels potential targets for improving treatment efficacy in gastric cancer. Citation Format: Enyu Dai, Jiang-Jiang Qin, Can Hu, Zhiyuan Xu, Guangchun Han, Yanshuo Chu, Ruiping Wang, Minghao Dang, Yunhe Liu, Guangsheng Pei, Jiahui Jiang, Fuduan Peng, Yuanyuan Zhang, Andre Luis Faustino, Jaffer A. Ajani, Linghua Wang, Xiangdong Cheng. Single-cell analyses unravel novel immune and tumor cell characteristics linked to the response to neoadjuvant immune checkpoint blockade in patients with gastric 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 6200.

Abstract 3914: IGSF8 is a novel innate immune checkpoint and cancer immunotherapy target

Abstract Background: Loss of MHC-I antigen presentation is often associated with T-cell excluded tumors, and represents a common mechanism of both primary and acquired resistance to immune checkpoint blockade (ICB) treatment. MHC-I normally acts as a marker of “self” and cells that lack MHC-I are recognized and killed by innate immunity. In this study, we investigated the mechanism of innate immune evasion in tumors with MHC-I antigen presentation defects. Methods: Integrating functional genomics, big data, and artificial intelligence, we discovered that IGSF8 expressed on cancer cells is an evolutionarily conserved innate immune checkpoint. IGSF8 is normally expressed in neuronal tissues and is not essential in vitro or in vivo. However, knockout of IGSF8 in B16-F10 melanoma cell line decreased tumor growth in vivo. For clinical relevance of IGSF8 in tumor immunity, we analyzed genomics, transcriptomics, and clinical data from The Cancer Genome Atlas (TCGA). We developed an antibody (GV20-0251) against IGSF8 and tested its function to induce immune cell killing of cancer cells in vitro and inhibit tumor growth in vivo. Results: IGSF8 has receptors on both natural killer (NK) cells and dendritic cells (DC) to strongly suppress NK cytotoxicity and antigen presentation. In the TCGA tumor profiles, IGSF8 has highest mRNA expression in melanoma and is significantly overexpressed in many cancer types. IGSF8 also shows frequent copy number amplifications. In addition, IGSF8 expression is associated with low antigen presentation, low immune infiltration, and worse overall survival in patients with low MHC class I expression. Immunohistochemistry staining of various cancers showed that IGSF8 expression was primarily observed in malignant cells with low MHC-I. We developed a cross-species reactive antibody against IGSF8 (GV20-0251) which blocks IGSF8 interaction with NK and DC. Flow cytometry of the tumor infiltrating CD45+ cells revealed that IGSF8 inhibition significantly increased NK and dendritic cell infiltration. GV20-0251 enhances NK killing of cancer cells in vitro and increases antigen presentation, NK-mediated cytotoxicity, and T cell signaling in vivo. In multiple syngeneic tumor models (B16-F10, CT26, LLC, 4T1 and EMT6), anti-IGSF8 shows single-agent efficacy and is synergistic with anti-PD1 in controlling tumor growth. Conclusions: IGSF8 is a novel innate immune checkpoint and cancer immunotherapy target. A phase 1 study is ongoing to explore the IGSF8 inhibitor GV20-0251 in patients with advanced or metastatic solid tumors (NCT05669430). Citation Format: X. Shirley Liu, Yulong Li, Xiangyang Wu, Hailing Liu, Huizhu Liu, Caibin Sheng, Qingyang Ding, Yixuan Tang, Chao Liu, Bin Xie, Xi Xiao, Quan Yu, Rongbin Zheng, Xihao Hu, Tengfei Xiao. IGSF8 is a novel innate immune checkpoint and cancer immunotherapy target [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 3914.

Abstract 6691: Engraftment as a determinant of response in fecal microbiome transplantation interventions for immunotherapy in melanoma

Abstract Background: Distinct gut microbiome signatures are associated with response, resistance, and toxicity to immune checkpoint blockade (ICB). Fecal microbiome transplants (FMT) have validated the importance of the gut microbiome in enhancing response and overcoming resistance to immunotherapy. However, donor selection remains a key challenge for FMT. Heterogenous responses using Healthy Donors (HD) and ICB Complete Responders (CR) as FMT donors suggest donor characteristics alone do not determine response. Here, we posit that donor-recipient relationships are critical in determining clinical responses to FMT. Methods: We studied a cohort of ICB-refractory, metastatic melanoma patients treated with combined FMT and ICB (10 recipients, 2 donors). Patient gut microbiomes were profiled using whole metagenomic sequencing (WMS) of longitudinal stool collections (baseline, day 7, day 31, and day 65 post-FMT). Immune infiltration of on-treatment tumor and colon biopsies was quantified with immunohistochemistry. mTraCX, an Earth Mover’s Distance-based algorithm, was used to evaluate taxonomic engraftment between donors and recipients. Bray-Curtis distance was used to measure functional similarities between donor and recipient gut microbiome. Clinical findings were validated in pre-clinical FMT experiments performed on BrafV600EPten−/− melanoma-bearing mice. Results: One-third of recipients (3/10) developed an objective response (R) to ICB following FMT. mTraCX demonstrated an association between clinical response to FMT and durable engraftment of donor microbiota at day 65 post-FMT (p=0.025). Taxonomic engraftment (mTraCX) correlated positively with functional engraftment (Bray-Curtis distance) (r=0.89, p<0.0001). Enhanced engraftment was associated with increased CD4 (r = -0.87, p=0.0045) and CD8 (r = -0.6, p=0.09) T-cell infiltration in the colon, and a trend towards increased CD8 T-cell infiltration (r = -0.5, p=0.2) in the tumor following treatment with FMT+ICB. Pre-clinical models paralleled our clinical findings as responding mice showed better donor engraftment than non-responding mice (p<0.0001 on day 4 and day 24 following FMT). Conclusions: Our data shows that donor engraftment is a favorable prognostic factor for ICB treatments combined with FMT. Future investigations will aim to develop donor-recipient matching criteria to enhance the feasibility and integration of FMTs into clinical practice. Citation Format: Manoj Chelvanambi, Ashish V. Damania, Sarah B. Johnson, Golnaz Morad, Rossana N. Lazcano, Beth A. Helmink, Lon W. Fong, Khalida Wani, Y David Seo, Elizabeth M. Park, Reed I. Ayabe, Bhavana Singh, Matthew C. Wong, Davis R. Ingram, Michael G. White, Alexander J. Lazar, Aditya K. Mishra, Nadim J. Ajami, Erez N. Baruch, Jennifer A. Wargo. Engraftment as a determinant of response in fecal microbiome transplantation interventions for immunotherapy in melanoma [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 6691.

Abstract 873: Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA profiles

Abstract Background: Despite the recent success in Immune checkpoint blockade (ICB) therapy, limited patients benefit due to immune-related adverse events or treatment resistance, especially in solid tumors. To overcome these hurdles, understanding the molecular mechanisms behind treatment response is essential. However, the current lack of immune gene transcriptional programs (GTPs) hampers data-driven immunological discovery. Constructing immunity-specific knowledgebases with rigorously curated gene sets (irGSs) and rich immunological language can unlock new insights, enabling interpretation of high-throughput immune microenvironment profiling studies and fostering personalized, effective cancer treatments. Methods: We collected 83 BulkRNAseq datasets from the ImmuneSigDB. These datasets contain 1826 samples challenged with infections, cytokines or immunological perturbations of different kinds and magnitude, possessing yet-to-be discovered immune functions that lie beneath the transcriptomic profiles. Using non-negative matrix factorization (NMF), we identified gene sets with coordinated expression. We used CITE-seq and selected scRNAseq to annotate the immunological functions of each gene set and validated the clinical utilities of these gene sets from different aspects using data from Cancer Genome Atlas Program (TCGA) pan-cancer, ICB cohorts and a 10X Genomics Visium FFPE Human Breast Cancer spatial slide. Results: We presented 19 lymphoid-data derived and 9 myeloid-data derived gene sets (irGSs), encompassing a diverse array of immune functions. Through extensive validation using BulkRNAseq, scRNAseq and spatial transcriptomics data, we revealed six irGSs-defined pan-cancer microenvironment subtypes in TCGA with significantly distinct survival patterns regardless of cancer types. Moreover, irGSs are associated with T cell exhaustion phenotypes, which in turn well predicted (classification accuracy of 72%) Nivolumab response using 104 treatment-naïve melanoma patients. Lastly, irGSs simultaneously isolated out tumor regions and highlighted immune infiltration with high specificity in breast cancer spatial transcriptomics H&E image. Conclusions: These pioneering gene sets, originally derived from non-cancerous experiments, hold tremendous promise for cancer research across diverse contexts. Similarities between cancerous and sepsis immune microenvironments underscore their wide applicability. By studying gene set activities, immunologists can gain profound insights into cancer survival drivers, unravel the intricacies of ICB treatment mechanisms, and potentially conquer therapeutic resistance. These translational utilities herald a transformative era in cancer immunotherapy and open new frontiers in the fight against cancer. Citation Format: Shan He, Vakul Mohanty, Matthew Gubin, Hind Rafei, Rafet Basar, Merve Dede, Xianli Jiang, Yukun Tan, Maura Gillison, Katayoun Rezvani, Weiyi Peng, Ken Chen. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA profiles [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 873.

Abstract 2486: Dissecting tumor-immune interaction in response and resistance to immune checkpoint blockade in metastatic melanoma

Abstract Background: Immune checkpoint blockade (ICB) has revolutionized the treatment and prognosis of various cancers, including melanoma. Nevertheless, intrinsic or acquired resistance is common, and the interactions between tumor-intrinsic features and the microenvironment underlying these resistances remain unclear for most patients. Methods: In this study, we developed a framework to analyze response and resistance, both intrinsic and acquired, via tumor-intrinsic programs, immune features, and tumor-stromal-immune interactions in a standardized, uniformly processed, and deeply clinically annotated cohort of metastatic melanoma patients (n=61) treated with ICB as part of the NCI funded human tumor atlas network (HTAN) initiative. From the same tumor samples (pre-treatment (n=33) and post-progression (n=28)), we conducted bulk whole-exome sequencing (WES), single-nucleus RNA sequencing, and for a subset of the samples high-resolution spatial imaging (including protein mIHC, CODEX, and transcriptomics MERFISH). Standardized processing and data pipelines allowed for integration of genomic, transcriptomic, and spatial features to elucidate shared tumor and microenvironmental states and their relationships with resistance. Results: Our preliminary analysis on a subset of 28 samples identified an enrichment of B cells, plasma cells, and T follicular helper-like cells in the tumor microenvironment (TME) of patients sensitive to treatment. The TME of non-responders was predominantly characterized by macrophage/monocyte cell populations. Post-treatment responder samples showed an enrichment of CD4+ T cells. Genomic heterogeneity, assessed through WES, was confirmed as a feature of intrinsic resistance across different ICB treatment settings, while ploidy was associated with treatment response in pre-treatment, ipilimumab-naïve patients treated with PD-1 inhibitors. Comparing the immune compartments of samples with high and low heterogeneity revealed NK cell enrichment in samples with a high proportion of subclonal mutations. Conclusions and Future Directions: Overall, our work provides a high-resolution understanding of the tumor-stromal-immune interaction in metastatic melanoma, shedding light on the factors contributing to therapy response and resistance, and contributing a repository of data from deeply clinically annotated, multimodally characterized and uniformly processed patient samples. Ongoing spatial analysis will further enhance our understanding of these compartments at a spatial level. The results of our study have the potential to guide more personalized and effective treatment strategies for metastatic melanoma in the future. Citation Format: Giuseppe Tarantino, Yiwen He, Priyanka Solanky, Aaron Thorner, Tyler Aprati, Ryan Sullivan, Emily Robitschek, Timothy Blosser, Xiaowei Zhuang, Xiaowei Zhuang, Elliot Boblitt, Allison Frangieh, Marta Holovatska, Aleigha Lawless, Michael Manos, Kathleen Pfaff, Karla Helvie, Tatyana Sharova, Dennie Frederick, James Liam Fahey, Diego Villamarin, Sami Farhi, Scott Rodig, Bruce Johnson, Alex K. Shalek, Eliezer Van Allen, Stephen Hodi, Genevieve M. Boland, David Liu. Dissecting tumor-immune interaction in response and resistance to immune checkpoint blockade in metastatic melanoma [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 2486.

Abstract 2902: CA-4948 (emavusertib) improves treatment response of preclinical metastatic brain melanoma to anti-PD-1 immune checkpoint blockade

Abstract Background: Although recent advances in immunotherapy for metastatic melanoma have transformed the treatment paradigm for a disease that once carried a grim prognosis, nearly 50% of patients fail to reach a complete response to immune checkpoint blockade (ICB) due to multiple mechanisms of tumor-induced immune resistance. These challenges are amplified in the CNS tumor microenvironment (TME) where metastatic brain melanoma (MBM) demonstrates diminished clinical benefit to ICB treatment. A deeper understanding of these mechanisms are required to improve therapeutic response to ICB for these patients. Our group has previously identified that aberrant activation of the myddosomal cascade through downstream interleukin (IL)-1 receptor-associated kinase (IRAK-4) signaling results in chronic stimulation of MAPK and NF-κB in MBM. Further investigation reveals myddosome signaling emanates in large part from the TME, resulting in reflexive immune suppression. CA-4948 (emavusertib), a small molecule inhibitor of IRAK-4, is capable of reaching therapeutic dose levels in the brain where it demonstrates on-target inhibition of this pathway. These data highlight a unique therapeutic opportunity where selective inhibition of immune-suppressive signaling via targeted IRAK-4 blockade may sensitize MBM to anti-PD-1 ICB. Methods Multispectral imaging of patient MBM samples were analyzed for myddosome expression in the TME. Melanoma preclinical models, including both primary site (cutaneous) and metastatic brain disease, were evaluated for tumor burden and survival in response to CA-4948 treatment alone and in combination with anti-PD-1 ICB. Immunological responses of tumor to treatment were evaluated in two transgenic reporter models, CCR2RFPCX3CR1GFP and IFNγIRES-EYFP, to determine both the distribution and activation of infiltrating immune cells. Tumor-associated myeloid cells were assessed for phenotypic markers by multiparameter flow cytometry. Results Myddosome signaling was found to be elevated in tumor-associated immune cells in patient MBM specimens. Treatment of preclinical melanoma with CA-4948 combined with anti-PD-1 ICB resulted in significantly reduced tumor growth and improved survival in three independent models. CA-4948 treatment was associated with reduced tumor recruitment of peripherally derived tumor-associated macrophages, as well as increased lymphocyte infiltration and improved pro-inflammatory signaling measured by increased IFNγ expression in the combinatorial setting. Conclusion Targeted inhibition of IRAK-4 with CA-4948 improves immune surveillance and activation in preclinical models when combined with anti-PD-1 ICB, resulting in reduced tumor growth and increased survival. Thus, CA-4948 may be an effective adjuvant treatment strategy alongside anti-PD-1 ICB for the treatment of metastatic melanoma. Citation Format: Christina A. von Roemeling, Bently P. Doonan, Amanda M. Acevedo, Jeet A. Patel, Savannah L. Carpenter, Alisha Bhatia, Reinhard W. von Roemeling, Jamison Hoffman, Maureen Lane, Duane A. Mitchell. CA-4948 (emavusertib) improves treatment response of preclinical metastatic brain melanoma to anti-PD-1 immune checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2902.

Abstract 4282: Crosstalk between the immune system and the extracellular matrix in the context of melanoma and aging

Abstract Aging is an independent prognostic factor for the diagnosis of melanoma. The extracellular matrix of the skin has well-documented changes with age, such as the loss of HAPLN1, which can lead to differential metastasis in aged individuals. The aged microenvironment can contribute to the phenotype switch, where aged individuals have smaller primary tumors but more metastases, i.e., going instead of growing. The extracellular matrix (ECM) has been shown to modulate the immune response either through direct binding of ECM proteins or through mechanotransduction, but it is unclear how aging affects this crosstalk. Our hypothesis is that the ECM can modulate immune response to melanoma and affect response to immune checkpoint blockade (ICB) therapy. Melanoma cells cultured on cell derived matrices (CDMs) from young and aged human fibroblasts show differential levels of expression of PD-L1, a ligand that binds to PD-1 on T cells to induce T cell exhaustion. Antibodies targeting PD-1/PD-L1 are one of the main ICB treatments available to melanoma. We are also investigating T cell motility on young and aged CDMs, as well as correlating T cell infiltration in murine tumors with ECM signatures as identified by second harmonic generation microscopy. Therefore, we have compiled evidence that aging affects the crosstalk between the extracellular matrix and the immune system, providing a new horizon for therapeutic improvement of response in older patients. Citation Format: Elizabeth I. Harper, Yash Chhabra, Alexis Carey, Murilo Ramos Rocha, Laura Hüser, Vania Wang, Agrani Dixit, Ashani Weeraratna. Crosstalk between the immune system and the extracellular matrix in the context of melanoma and aging [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 4282.

Abstract 6411: The gut microbiome is associated with recurrence free survival in patients with resected Stage III or Stage IV melanoma treated with immune checkpoint inhibitors

Abstract The gut microbiome (GMB) plays a crucial role in immune checkpoint blockade (ICB) therapy outcomes for metastatic melanoma patients, yet there remains a lack of consensus regarding the specific microbiota associated with clinical outcomes, particularly across different geographic regions. Furthermore, investigations into the relationship between GMB and melanoma outcomes in the adjuvant setting are notably absent. This highlights the pressing need for a comprehensive, large-scale study spanning diverse geographic locations within a well-controlled clinical trial environment. In this study, we conducted shotgun sequencing on pre-treatment stool samples collected from 674 melanoma patients participating in an international, randomized, double-blind, phase III adjuvant trial evaluating clinical outcomes following adjuvant nivolumab plus ipilimumab versus nivolumab. Our recruitment encompassed three continents and five geographically distinct regions. Given the significant influence of geographic region on GMB composition, we employed three analytical approaches: (a) region-specific analyses, (b) combined meta-analyses across regions, and (c) sub-set paired analyses involving subjects closely matched for overall GMB. Additionally, we assessed GMB stability by examining samples collected serially prior to therapy and at weeks 7 and 29 of ICB treatment. Through region-specific and meta-analyses, we identified ten pre-treatment gut bacterial markers, including Eubacterium, Ruminococcus, Clostridium, and Firmicutes, which exhibited associations with melanoma recurrence in the adjuvant setting. The predictive capacity of these microbial markers was directly proportion to GMB similarity (Spearman correlation = 0.86, p<0.001 for AUC vs. beta-diversity). Notably, for closely matched patients in terms of their GMB composition, the prediction of recurrence using the recurrence-associated markers, in conjunction with clinical characteristics, yielded an AUC of 0.917 (95% CI: 0.825-1.00). Furthermore, GMB remained largely stable across serial samples collected before and after treatment (PERMANOVA R2 = 0.867, p-val<0.001, at baseline, week 7, and week 29). This study underscores the remarkable stability of GMB during adjuvant ICB therapy for melanoma and identifies specific bacterial biomarkers that hold promise for predicting melanoma recurrence within the adjuvant treatment setting. The gut microbiome emerges as a potential source of microbial biomarkers for individualized prediction of melanoma recurrence in clinical practice. Citation Format: Mykhaylo Usyk, Richard B. Hayes, Rob Knight, Antonio Gonzalez, Huilin Li, Iman Osman, Jeffrey S. Weber, Jiyoung Ahn. The gut microbiome is associated with recurrence free survival in patients with resected Stage III or Stage IV melanoma treated with immune checkpoint inhibitors [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 6411.

Abstract 2422: Liquid biopsy approaches for monitoring metastatic pancreatic cancer in immunotherapy treated patients

Abstract Introduction: Pancreatic cancer has a poor prognosis especially when identified at advanced stages. Globally in 2020, >450,000 people died from the disease. For those with locally advanced or metastatic cancer, the standard of care treatment is chemotherapy. Preliminary studies show that some patients with advanced-stage disease respond to immune checkpoint blockade treatment. Determining response to therapy using imaging techniques can be challenging. There is a clinical unmet need for noninvasive approaches that can provide a real-time assessment of response to therapy in these patients. We evaluated two methods for assessing response to therapy using circulating cell-free DNA (cfDNA) in patients with metastatic pancreatic cancer treated with immune checkpoint inhibition and radiation as part of the CheckPAC study (NCT02866383). Methods: For all patients with available samples (n=40), we evaluated one pre-treatment blood draw and one on-treatment blood draw (26-65 days after treatment start). We extracted cfDNA from each sample and performed low-coverage 1-2x whole genome sequencing (WGS). We evaluated tumor and matched buffy coat for the 34 patients who had > 10% tumor purity using WGS with at least 60x and 30x coverage, respectively. We compiled the mutated bases in the tumor genome and examined these positions in the cfDNA. We counted the number of mutant observations from cfDNA WGS and divided them by the total number of observations at these bases to calculate whole-genome mutant allele frequency (MAF). We categorized responders based on >30% drop in MAF from baseline. In a tissue independent approach, we detected changes in genome-wide cfDNA fragmentation patterns using the DNA evaluation of fragments for early interception (DELFI) approach. We evaluated survival using DELFI scores of on-treatment samples. Samples were designated DELFI high (above median) or DELFI low (below median.) Log-Rank tests were used to compare survival curves. Results: For the mutation based approach, molecular responders (n=7) had a median progression free survival (PFS) of 485 days compared to 57 days for non-responders (n=9) (p=0.02). Molecular responders had a median overall survival (OS) of 694 days compared to 200 days for non-responders (p=0.062). Patients with DELFI low scores after therapy (n=14) had a longer median PFS than those with DELFI high scores (n=14) (307 days versus 70 days, respectively) (p=0.013). DELFI low patients also had a longer median OS than DELFI high patients (627 vs 158 days, respectively) (p<0.0001). Conclusions: These analyses suggest that WGS mutation-based and fragmentation cfDNA approaches can identify individuals with metastatic pancreatic cancer who respond to immune checkpoint inhibition. Incorporation of these molecular methods for evaluation of tumor burden may provide information for patient-physician decision making to improve patient quality of life. Citation Format: Carolyn Anna Hruban, Inna Chen, Daniel C. Bruhm, Shashikant Koul, Jennie Yao, Susann Theile, Kavya Boyapati, Nicholas A. Vulpescu, Akshaya Annapragada, Leonardo Ferreira, Stephen Cristiano, Zachariah H. Foda, Vilmos Adleff, Julia Johansen, Jillian Phallen, Robert B. Scharpf, Victor E. Velculescu. Liquid biopsy approaches for monitoring metastatic pancreatic cancer in immunotherapy treated patients [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 2422.

Predicting the prognosis of glioma patients with TERT promoter mutations and guiding the specific immune profile of immune checkpoint blockade therapy.

The telomerase reverse transcriptase promoter (TERTp) is frequently mutated in gliomas. This study sought to identify immune biomarkers of gliomas with TERTp mutations. Data from TCGA were used to identify and validate survival-associated gene signatures, and immune and stromal scores were calculated using the ESTIMATE algorithm. High stromal or immune scores in patients with TERTp-mutant gliomas correlated with shorter overall survival compared to cases with low stromal or immune scores. Among TERTp-mutant gliomas with both high immune and high stromal scores, 213 commonly shared DEGs were identified. Among 71 interacting DEGs representing candidate hub genes in a PPI network, HOXC6, WT1, CD70, and OTP showed significant ability in establishing subgroups of high- and low-risk patients. A risk model based on these 4 genes showed strong prognostic potential for gliomas with mutated TERTp, but was inapplicable for TERTp-wild-type gliomas. TERTp-mutant gliomas with high-risk scores displayed a greater percentage of naïve B cells, plasma cells, naïve CD4 T cells, and activated mast cells than low-risk score gliomas. TIDE analysis indicated that immune checkpoint blockade (ICB) therapy may benefit glioma patients with TERTp mutations. The present risk model can help predict prognosis of glioma patients with TERTp mutations and aid ICB treatment options.

A method for predicting drugs that can boost the efficacy of immune checkpoint blockade.

Combination therapy is a promising therapeutic strategy to enhance the efficacy of immune checkpoint blockade (ICB); however, predicting drugs for effective combination is challenging. Here we developed a general data-driven method called CM-Drug for screening compounds that can boost ICB treatment efficacy based on core and minor gene sets identified between responsive and nonresponsive samples in ICB therapy. The CM-Drug method was validated using melanoma and lung cancer mouse models, with combined therapeutic efficacy demonstrated in eight of nine predicted compounds. Among these compounds, taltirelin had the strongest synergistic effect. Mechanistic analysis and experimental verification demonstrated that taltirelin can stimulate CD8+ T cells and is mediated by the induction of thyroid-stimulating hormone. This study provides an effective and general method for predicting and evaluating drugs for combination therapy and identifies candidate compounds for future ICB combination therapy.

Role of CD38 in anti-tumor immunity of small cell lung cancer.

Immune checkpoint blockade (ICB) with or without chemotherapy has a very modest benefit in patients with small cell lung cancer (SCLC). SCLC tumors are characterized by high tumor mutation burden (TMB) and low PD-L1 expression. Therefore, TMB and PD-L1 do not serve as biomarkers of ICB response in SCLC. CD38, a transmembrane glycoprotein, mediates immunosuppression in non-small cell lung cancer (NSCLC). In this brief report, we highlight the potential role of CD38 as a probable biomarker of immunotherapy response in SCLC. We evaluated the role of CD38 as a determinant of tumor immune microenvironment in SCLC with bulk and single-cell transcriptomic analyses and protein assessments of clinical samples and preclinical models, including CD38 in vivo blockade. In SCLC clinical samples, CD38 levels were significantly correlated with the gene expression of the immunosuppressive markers FOXP3, PD-1 and CTLA-4. CD38 expression was significantly enhanced after chemotherapy and ICB treatment in SCLC preclinical models and clinical samples. A combination of cisplatin/etoposide, ICB, and CD38 blockade delayed tumor growth compared to cisplatin/etoposide. Our study provides a preliminary but important direction toward exploring CD38 as a potential biomarker of ICB response and CD38 blockade as a combination strategy for chemo-immunotherapy in SCLC.