There is an urgent need for strategies that can improve vaccine immunogenicity, especially for vulnerable populations such as newborns and young infants. Growing evidence supports Toll-Like Receptor agonists (TLRa) as potent stimulatory molecules to increase vaccine efficacy. We have previously demonstrated that the inclusion of either flagellin (TLR5a) or R848 (TLR7/8a) in an inactivated influenza virus vaccine can improve responses in newborn NHP, with R848 being superior at providing protection upon challenge. This study aimed to identify early immune events triggered by either inactivated virus alone or in combination with R848 or flagellin using scRNA-seq analysis of draining lymph nodes (dLN) collected 24 h after vaccination. Our study reveals that globally, R848 enhanced gene expression associated with B cell activation, while flagellin was a stronger modulator of T cells. Analysis of distinct lymph node populations showed that surprisingly, while APCs had a potent transcriptional response to inactivated virus, we observed minimal additional changes in transcriptional activity with addition of a TLRa. In contrast, R848 had a potent effect on cellular translation, while flagellin resulted in increased expression of type I interferon genes in B cells. All vaccines resulted in a population of T cells bearing an interferon response signature that was further modified by TLRa inclusion. R848 uniquely increased the expression of genes involved with cellular migration and inflammation in this population, while flagellin increased genes involved in vesicular trafficking, cAMP responsiveness, and calcium signaling. Together, these results suggest R848 promotes newborn B cell activation and enhanced migration/retention in the dLN. In contrast, flagellin amplifies the type I interferon signature of B cells and had broad impacts on the responding T cell population. Our findings provide new insights into the modulation of early vaccine responses in newborns following administration of inactivated influenza virus, R848 and flagellin.

Abstract In newly diagnosed multiple myeloma (NDMM), measurable residual disease (MRD) status is prognostically important, but its role in treatment decisions remains unclear. In a phase 2 trial, we assessed daratumumab, carfilzomib, lenalidomide, and dexamethasone (Dara-KRd) induction followed by a next-generation sequencing–based MRD-adapted strategy. The primary outcome was complete response (CR) and stringent CR (≥CR) after induction. Flow cytometry was used to profile T cells. Among 39 patients, 21 (54%) achieved ≥CR after induction (P = .375), with MRD-negative rates of 59% (10−5) and 41% (10−6). Patients who were MRD-negative (n = 24, group A) received lenalidomide maintenance, showing sustained MRD negativity in 14 of 18 (77.8%) for ≥12 cycles. MRD-positive transplant-eligible patients (n = 8, group B) underwent autologous stem cell transplantation, with 62.5% converting to MRD-negative at 10−5 (37.5% at 10−6) posttransplant. MRD-positive, transplant-ineligible patients (n = 4, group C) received KRd consolidation. Best MRD-negative rates improved to 77% (10−5) and 72% (10−6). No new safety concerns were identified for Dara-KRd. With a median follow-up of 30.1 months, 3, 2, and 1 patient(s) in groups A, B, and C, respectively, have progressed or died. We observed that Dara-KRd strongly activated memory T cells, which was associated with an MRD-negative state post induction. Although the primary outcome was not met, Dara-KRd induction in NDMM achieved high ≥CR and MRD-negative rates without new safety concerns. The post induction MRD-adapted strategy deepened responses in MRD-positive patients and maintained durable MRD control in MRD-negative patients. This trial was registered at www.clinicaltrials.gov as #NCT04113018.

High grade immune-related adverse events (irAEs) in vital organs are likely to cause permanent discontinuation of ICI therapy, greatly affecting the efficacy of ICI as well as patients' health conditions. This study analyzed the correlation between high-grade irAEs and tumor sequencing data from 430 nonsmall cell lung cancer (NSCLC) patients from 2015 to 2022. Our data suggest that specific gene mutations are associated with the occurrence of high-grade irAEs which offers novel insights of post-ICI monitoring. Objectives: Compared to low-grade irAEs, high-grade irAEs are more often dose-limiting and can alter the long-term treatment options for a patient. Predicting the incidence of high-grade irAEs would help with treatment selection and therapeutic drug monitoring. Materials and methods: We performed a retrospective study of 430 stage III and IV patients with non-small cell lung cancer (NSCLC) who received an immune checkpoint inhibitor (ICI), either with or without chemotherapy, at a single comprehensive cancer center from 2015 to 2022. The study team retrieved sequencing data and complete clinical information, including detailed irAEs medical records. Fisher's exact test was used to determine the association between mutations and the presence or absence of high-grade irAEs. Patients were analyzed separately based on tumor subtypes and sequencing platforms. Results: High-grade and low-grade irAEs occurred in 15.2% and 46.2% of patients, respectively. Respiratory and gastrointestinal irAEs were the 2 most common irAEs. The distribution of patients with or without irAEs was similar between ICI and ICI+chemotherapy-treated patients. By analyzing the mutation data, we identified 5 genes (MYC, TEK, FANCA, FAM123B, and MET) with mutations that were correlated with an increased risk of high-grade irAEs. For the adenocarcinoma subtype, mutations in TEK, MYC, FGF19, RET, and MET were associated with high-grade irAEs; while for the squamous subtype, ERBB2 mutations were associated with high-grade irAEs. Conclusion: This study is the first to demonstrate that specific tumor mutations correlate with the incidence of high-grade irAEs in patients with NSCLC treated with an ICI, providing molecular guidance for treatment selection and drug monitoring.

Treatment of non-small cell lung cancer (NSCLC) has drastically changed in recent years owing to the robust anticancer effects of immune checkpoint inhibitors (ICI). However, only 20% of the patients with NSCLC benefit from ICIs, highlighting the need to uncover the mechanisms mediating resistance. By analyzing the overall survival (OS) and mutational profiles of 424 patients with NSCLC who received ICI treatments between 2015 and 2021, we determined that patients carrying a loss-of-function mutation in neurotrophic tyrosine kinase receptor 1 (NTRK1) had a prolonged OS when compared with patients with wild-type NTRK1. Notably, suppression of the NTRK1 pathway by knockdown or entrectinib treatment significantly enhanced ICI efficacy in mouse NSCLC models. Comprehensive T-cell population analyses demonstrated that stem-like CD4+ T cells and effector CD4+ and CD8+ T cells were highly enriched in anti-PD-1-treated mice bearing tumors with decreased NTRK1 signaling. RNA sequencing revealed that suppression of NTRK1 signaling in tumor cells increased complement C3 expression, which enhanced the recruitment of T cells and myeloid cells and stimulated M1-like macrophage polarization in the tumor. Together, this study demonstrates a role for NTRK1 signaling in regulating cross-talk between tumor cells and immune cells in the tumor microenvironment and provides a potential therapeutic approach to overcome immunotherapy resistance in patients with NSCLC with NTRK1 wild-type. Significance: Inhibition of NTRK1 signaling confers sensitivity to immunotherapy by enhancing complement C3-mediated T-cell and macrophage functions, leading to improved responses to immune checkpoint inhibitors in patients with lung cancer with NTRK1 mutations.

Identification of early immune signatures associated with acute myeloid leukemia (AML) relapse following hematopoietic stem cell transplant (HSCT) is critical for patient outcomes. We analyzed PBMCs from 58 patients with AML undergoing HSCT, focusing on T cell subsets and functional profiles. High-dimensional flow cytometry coupled with Uniform Manifold Approximation and Projection dimensionality reduction and PhenoGraph clustering revealed distinct changes in CD4+ and CD8+ T cell populations in 16 patients who relapsed within 1 y of HSCT. We observed increased IL-2, IL-10, and IL-17-producing CD4+ T cells, alongside decreased CD8+ T cell function early in relapsing patients. Notably, relapsing patients exhibited increased TCF-1intermediate cells, which lacked granzyme B or IFN-γ production in the CD4+ T cell compartment. We then developed a supervised machine learning algorithm that predicted AML relapse with 90% accuracy within 30 d after HSCT using high-throughput assays. The algorithm leverages condensed immune phenotypic data, alongside the ADASYN algorithm, for data balancing and 100 rounds of XGBoost supervised learning. This approach holds potential for detecting relapse-associated immune signatures months before clinical manifestation. Our findings demonstrate a distinct immunological signature potentially capable of predicting AML relapse as early as 30 d after HSCT.

Accurate integration of high-dimensional single-cell sequencing datasets is important for the construction of cell atlases and for the discovery of biomarkers. Because the performance of integration methods varies in different scenarios and on different datasets, it is important to provide end users with an automated system for the benchmarking and selection of the best integration among several alternatives. Here, we present a system that uses an ensemble of auditors, trained by supervised machine learning, which quantifies residual variability of integrated data and automatically selects the integration with the smallest difference between observed and expected batch effects. A rigorous and systematic validation was performed using 6 popular integration methods and 52 benchmark datasets. Algorithmic and data biases were uncovered and shortcomings of existing validation metrics were examined. Our results demonstrate the utility, validity, flexibility and consistency of the proposed approach.

Cells are the basic building blocks of human organisms, and the identification of their types and states in transcriptomic data is an important and challenging task. Many of the existing approaches to cell-type prediction are based on clustering methods that optimize only one criterion. In this paper, a multi-objective Genetic Algorithm for cluster analysis is proposed, implemented, and systematically validated on 48 experimental and 60 synthetic datasets. The results demonstrate that the performance and the accuracy of the proposed algorithm are reproducible, stable, and better than those of single-objective clustering methods. Computational run times of multi-objective clustering of large datasets were studied and used in supervised machine learning to accurately predict the execution times of clustering of new single-cell transcriptomes.

Introduction: The FDA’s approval of immune checkpoint inhibitors (ICI) in 2015 drastically changed the survival of late-stage non-small cell lung cancer (NSCLC) patients. However, only about 30% of NSCLC patients respond to treatment, while the other 70% are immune resistant. Through an analysis of 424 NSCLC patients at Atrium Wake Forest, we have identified a loss-of-function mutation in Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1) as a biomarker for response to ICI. We hypothesize that by treating wild-type immune-resistant tumors with Entrectinib, we can mimic the effect of the mutation in NTRK1 and induce immune responses. Methods: To identify biomarkers, we collected genomic sequencing data and comprehensive clinical characteristics on 424 NSCLC patients who received ICI or chemo-ICI treatment at Atrium Health Wake Forest Baptist. To determine the role of NTRK1 in vivo, we implanted LL/2-scramble (wild-type NTRK1) or LL/2-shNTRK1, which diminished NTRK1, into C57/B6 mice. The animals were injected with either IgG or Anti-PD1. To determine if we could mimic the effect of a mutation in NTRK1, C57/B6 mice were inoculated with LL2-wildtype NTRK1 and treated with either a) IgG, b) Entrectinib, c) Anti-PD-1, or d) Anti-PD-1 + Entrectinib. All in vivo experiments had tumor growth monitored, and a flow cytometry panel was performed at the endpoint to understand the immune responses. Bulk RNA-Sequencing was performed on cell cultures and tumors. Results: Mice given the LL/2-shNTRK1 responded to Anti-PD-1 treatment and had a significant increase in CD4+ stem-like effector T cells in the spleen and tumor-draining lymph nodes. Animals that were inoculated with the LL/2 cell lines and treated with Anti-PD-1 + Entrectinib also responded. Mice treated with Anti-PD-1 + Entrectinib were found to have a significant increase in CD4+ stem-like effector T cells as well. RNA-Sequencing revealed that in the mutant cell line LL/2-shNTRK1 and LL/2 tumors treated with Anti-PD-1 + Entrectinib, there was a significant upregulation of C3 production. Conclusion: Our studies demonstrate that the loss of NTRK1 function, through either genetic ablation or enzymatic inhibition combined with Anti-PD-1, provides a potent treatment for immune-resistant NSCLC tumors. Citation Format: Margaret R Smith, Yuezhu Wang, Caroline B. Dixon, Ralph D'Agostino, Yin Liu, George C. Oliver, Lance D Miller, Umit Topaloglu, Michael D Chan, Micahel Farris, Jing Su, Kathryn F Mileham, Wencheng Li, Jason M. Grayson, Thomas Lycan, Fei Xing. Enhancing immune checkpoint inhibitor efficacy by targeting neurotrophic receptor tyrosine kinase 1 signaling in immune resistant non-small cell lung cancer patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A050.

Abstract Studies over the last 100 years have suggested a link between inflammation, infectious disease, and Alzheimer’s Disease (AD). Understanding how the immune system changes during the development of AD may facilitate new treatments. Here, we studied an aging cohort who had been assessed for AD pathology with amyloid positron emission tomography and cognitive testing, and conducted high dimensional flow cytometry on peripheral blood mononuclear and cerebrospinal fluid cells. Participants were assigned a classification of being amyloid negative cognitively normal, amyloid positive cognitively normal (APCN), or amyloid positive mild cognitive impairment (APMCI), an early stage of AD. We observed major alterations in the peripheral innate immune system including increased myeloid and plasmacytoid dendritic cells in the blood of APMCI participants. When the adaptive immune system was examined, amyloid positive participants, regardless of cognitive status, had increased CD3+ T cells. Further analyses of CD4+ and CD8+ T cells revealed that APMCI participants had an increase in more differentiated phenotype T cells, such as effector memory and effector memory CD45RA expressing (TEMRA), compared to those with normal cognition. When T cell function was measured, we observed that T cells from APCN participants had increased IFNγ+GzB- producing cells compared to the other participants. In contrast, we demonstrate that APMCI participants had a major increase in T cells that lacked cytokine production following restimulation and expressed increased levels of PD-1 and Tox, suggesting these are exhausted cells. Rejuvenation of these cells may provide a potential treatment for AD.

The Three Prime Repair EXonuclease I (TREX1) is critical for degrading post-apoptosis DNA. Mice expressing catalytically inactive TREX1 (TREX1 D18N) develop lupus-like autoimmunity due to chronic sensing of undegraded TREX1 DNA substrates, production of the inflammatory cytokines, and the inappropriate activation of innate and adaptive immunity. This study aimed to investigate Thelper (Th) dysregulation in the TREX1 D18N model system as a potential mechanism for lupus-like autoimmunity. Comparison of immune cells in secondary lymphoid organs, spleen and peripheral lymph nodes (LNs) between TREX1 D18N mice and the TREX1 null mice revealed that the TREX1 D18N mice exhibit a Th1 bias. Additionally, the T-follicular helper cells (Tfh) and the germinal celter (GC) B cells were also elevated in the TREX1 D18N mice. Targeting Bcl6, a lineage-defining transcription factor for Tfh and GC B cells, with a commercially available Bcl6 inhibitor, FX1, attenuated Tfh, GC, and Th1 responses, and rescued TREX1 D18N mice from autoimmunity. The study presents Tfh and GC B-cell responses as potential targets in autoimmunity and that Bcl6 inhibitors may offer therapeutic approach in TREX1-associated or other lupus-like diseases.

Background: In 2021, 235,760 new cases of lung cancer will be diagnosed in the United States. The treatment regimen of non-small cell lung cancer (NSCLC) has drastically changed owing to the superior anti-cancer effects generated by the immune-checkpoint inhibitor (ICI). However, only a subset of patients experience benefit after receiving ICI. Tumor Mutation Burden (TMB) and PD-L1 expression in tumor cells are known to be potential biomarkers in predicting a patient’s survival and response to ICI. Several studies showed that NSCLC patients with smoking history had a better response than never smokers due to increased TMB caused by carcinogens in cigarette smoke. However, the roles of tumor microenvironment especially immune microenvironment between smokers and never smokers in response to ICI are poorly understood. We hypothesize that the functions of T cells are influenced by the exposure of cigarette smoke prior to the ICI treatment which affect patients’ response to ICI. Method: A cohort of 216 patients diagnosed with NSCLC who had received at least one dosage of Immune Checkpoint Inhibitor (ICI) at Atrium Wake Forest Baptist Hospital were split into three groups: current smokers, former smokers, and never-smokers. Both PFS and OS analyses were performed to examine whether smoking history is correlated with the ICI response. To establish an in vivo model that recapitulates the patients with different smoking history, we treated mice with cigarette extract (CSE) followed by accessing the peripheral T cell functions by FACS analyses using antibodies targeting GZMB, TNF and IFNG. LL/2 and CMT167 cells will be inoculated to those CSE treated mice by flank injection once we observe a stable activation of T cells compared to control group. Tumor growth will be measured and the amount of tumor infiltrated CD4 and CD8 T cells will be examined by immunocytochemistry at the end point. Results: We found it took around 9 weeks of CSE treatment to observe a significant increase of CD8 and CD4 populations in CSE treated mice. We also treated mouse CD8 T cells isolated from the spleen with CSE and observed a strong activation of GZMB, TNF and IFNG by FACS analyses. Future directions: We will test the efficacy of anti-tumor effect of anti-PD-1 ab in tumor bearing mice exposed with or without CSE prior to the immune therapy. We will also establish a mice model that mimics the former smokers by halting the CSE treatment after 9 weeks of CSE exposure followed by examine the amount of memory T cells. We believe our study will provide additional mechanisms of how cigarette smoke affects the response of ICI by affecting the properties of immune cells. Citation Format: Margaret Rose Smith, Yuezhu Wang, Jimmy Ruiz, Jason Grayson, Yin Liu, Fei Xing. Novel lung cancer mouse model to study the effects of cigarette smoke on immune therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1347.