bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropilin-1, an immune checkpoint for controlling tumor-specific CD8 T-cell functions whose blockade improves anti-PD-1 immunotherapy
Authors: Mami-Chouaib Fathia 
Published: January 2023

Abstract
Neuropilin-1 (Nrp-1) has been defined as a marker of murine CD4+Foxp3+ regulatory T (Treg) cells and a subset of human CD4+ Treg cells. It is also expressed by a subpopulation of CD8+ T cells infiltrating some human solid tumors. However, little is known about its contribution to regulation of tumor-specific CD8 T-cell functions. We show that Nrp-1 defines a subset of CD8+ T cells displaying PD-1high (PD-1hi) status and infiltrating human non-small cell lung cancer (NSCLC). Using a human cytotoxic T lymphocyte (CTL) clone model, we show that the interaction of Nrp-1 with its ligand semaphorin-3A (Sema-3A), secreted by autologous NSCLC cells, inhibits both CTL migration and tumor-specific lytic function. In vivo experiments revealed that this Nrp-1+PD-1hi CD8+ tumor-infiltrating T lymphocyte (TIL) subset is also found in engrafted B16F10 mouse melanoma, and is enriched with tumor-specific T cells exhibiting an exhausted state, with co-expression of Tim-3, LAG-3 and CTLA-4 inhibitory receptors. Functionally, anti-Nrp-1 neutralizing antibodies increase the migratory capacity of Nrp+PD-1hi CD8+ TIL toward autologous cancer cells and enhance their specific cytotoxic activity ex vivo. Remarkably, in vivo immunotherapeutic blockade of Nrp-1 results in control of tumor growth, with a parallel increase in tumor infiltration by CD8+ TIL and enhanced proliferative and cytotoxic potential. This blockade is cumulative with anti-PD-1 treatment in improving tumor regression. Thus, Nrp-1 appears to be a novel immune checkpoint target on CD8+ tumor-specific T cells for combined antibody-based cancer immunotherapies. More recent advances on Nrp-1 expression regulation and functions in CD4+ and CD8+ T cells will be presented.
Thrombin contributes to cancer immune evasion via proteolysis of platelet-bound GARP for LTGF-β activation
Authors: Metelli Alessandra , Li Zihai 
Published: January 2023

Abstract
Cancer-associated thrombocytosis and high concentration of circulating TGFβ1 are hallmarks of progressive tumor disease in cancer patients. Using genetic and pharmacological approaches, we show a direct link between thrombin catalytic activity and maturation of LTGFβ bound to platelet GARP. We found that GARP protein has two conserved thrombin binding sites through which thrombin cleaves platelet-bound GARP to release active TGFβ from GARP/LTGFβ complex. Crystal structure models docked thrombin onto the concave surface of GARP supporting the notion that thrombin is able to bind and cleave GARP/LTGFβ complex. We observed that inhibition of thrombin obliterates TGFβ maturation in platelet releasate and in serum of WT mice, which translates in better tumor control alone and in combination with checkpoint blockade therapy, in two tumor preclinical models. Of note, the reduction of serum active TGFβ and the anti-tumor properties of thrombin were not observed in absence of platelet GARP. In the tumor microenvironment we found that blocking thrombin reduced active TGFβ signaling and increased the infiltrating CD8+ T cells as well as the innate NK cells and neutrophils. Also, we demonstrated that thrombin cleavage releases soluble GARP/LTGFβ complex and that high concentration of GARP in plasma, alone or in complex with LTGFβ, is a biomarker of poor clinical outcome in prostate cancer patients. We conclude that thrombin-GARP interaction and consequent GARP cleavage induce the activation of TGFβ derived from platelets. Considering that platelets are the major TGFβ reservoir, these observations demonstrated that blocking GARP cleavage opens a new therapeutic window to overcome TGFβ-mediated resistance to immune check point inhibitors.
Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers with low mutational burden
Authors: Saini Sunil Kumar , Ørskov Andreas , Bjerregaard Anne-Mette , Unnikrishnan Ashwin , Holmberg-Thydén Staffan , Borch Annie , Anande Govardhan , Bentzen Amalie , Marquard Andrea , Tamhane Tripti , Gang Anne , Defva Inge , Szallasi Zoltan , Eklund Aron , Pimanda John , Grønbæk Kirsten , Hadrup Sine 
Published: January 2023

Abstract
Human endogenous retroviruses (HERVs) form a substantial part of the human genome. However, most elements remain transcriptionally silent. Malignant transformation and epigenetic therapies may induce transcription of HERV elements. Such HERV elements could potentially trigger adaptive immune responses and provide targets for immunotherapy applications. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies. We studied 66 HERV genes reported to retain transcriptional activity and generated a library of 1,169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Through the use of DNA barcode-labeled MHC-I multimers, we identified CD8+ T cell populations recognizing 29 HERV-derived peptides, represented by 18 different HERVs. T cell recognition of HERVs was detected in half of the 34 patients analyzed and was significantly enhanced in patients compared to healthy donors. Patients with HERV-derived T cell reactivity demonstrated improved viral-antigen recognition following treatment, indicating that HERV-derived T cell recognition may contribute to the therapy-induced clinical improvement and immune reconstitution. In line with the T cell data, transcriptomic analyses revealed a significantly enhanced transcription of the HERVs in patients compared to healthy donors. DNA-demethylating therapy did not result in additional transcriptional enhancement of the HERVs evaluated for T cell recognition. Our study demonstrates substantial T cell recognition of HERVs in myeloid malignancies. These HERVs could serve as a reservoir of antigens potentially exploited as immunotherapeutic targets in malignancies with low mutational burden.
Identifying host-intrinsic resistance mechanisms to therapeutic anti-tumor antibody
Authors: Glassbrook James E , McCarthy Claire , Hackett Justin , Muñiz Maria , Dyson Greg , McCasland Jennifer , Gibson Heather 
Published: January 2023

Abstract
Monoclonal antibody (mAb) therapies have greatly improved outcomes for many cancer subtypes, many of which target tumor-associated antigens (TAA). Trastuzumab targets the TAA human epidermal growth factor 2 (HER2), inducing antibody dependent cellular cytotoxicity and phagocytosis (ADCC/ADCP) as well as interfering with receptor signaling. Despite its reputation as the gold standard treatment for HER2-overexpressing cancers, response rates remain low in metastatic breast cancer (≤30% as a monotherapy, ≤50% with chemotherapy). Multiple studies suggest induction of endogenous anti-tumor immunity is a determinant of therapeutic success. Utilizing the genetically heterogeneous Diversity Outbred (DO) mouse model, we seek to identify host-intrinsic mechanisms of resistance to TAA-mediated immunotherapy. We find a divergent response to αNeu (HER2 homolog) mAb clone 7.16.4 in (DOxBALB/c)F1 mice bearing established BALB/c-syngeneic TUBO mammary carcinoma. We find host genetic background regulates anti-tumor immune activity. ~25% showed complete response (CR) to therapy, ~60% a partial response (PR), and ~15% failed to respond (NR). CR mice were protected from a contralateral rechallenge, suggesting adaptive anti-tumor immunity was promoted by mAb therapy. Peripheral anti-tumor IgG, measured by flow cytometry, and IFNγ producing T cells, measured via ELISpot, also trend toward CR&gt;PR&gt;NR. Genetic linkage analysis using R/qtl2 identified loci associated with robust response to mAb therapy. Genes within these loci may represent potential routes of ingress toward addressing innate and acquired resistance during anti-TAA mAb therapy, particularly as regulators of immunogenicity of ADCC and ADCP. NIH R37 CA220482.
Irreversible electroporation can alter immune cell composition and enhance antigen presentation potential in pancreatic cancer
Authors: Brock Rebecca Michaela , Beitel-White Natalie , Hendricks Alissa Danielle , Zeher Allison , Manuchehrabadi Navid , Davalos Rafael V , Allen Irving C 
Published: January 2023

Abstract
Pancreatic cancer has a devastating survival rate of only 9%. A major treatment limitation is the immunosuppressive nature of pancreatic tumors created by high amounts of tumor-associate stromal cells such as myeloid-derived suppressor cells (MDSCs) and regulatory T-cells (Tregs). These form a barrier that inhibits anti-tumor immunity and has yet to be overcome by current immunotherapy options. Irreversible electroporation (IRE), an ablative technology that utilizes short electrical pulses to disrupt tumor cell membranes, shows evidence of inducing proinflammatory cell death in pancreatic tumors, but its effect on innate and adaptive immune responses, vital for long-term survival, has not been investigated. We hypothesize that IRE treatment for pancreatic cancer can reduce pro-tumor immune cells, recruit anti-tumor immune cells such as cytotoxic T-cells, and increase tumor-specific antigen presentation potential. We utilized in vivo immunocompetent Pan02 murine pancreatic cancer models to assess progression-free survival and tumor immune cell populations via flow cytometry, as well as an ex vivo antigen presentation model with murine bone marrow-derived dendritic cells and splenic T-cells to determine the ability of IRE to generate viable antigens. Our findings show a temporal increase in anti-tumor immune cell populations, reduction in tumor-associated immune cell populations, and strong antigen presentation potential. However, we also observed an increase in Pdl-1, normally down-regulated in pancreatic cancer, in response to increased immune signaling. This may make IRE a candidate for cotherapy options such as anti-Pdl-1 antibodies or other immunotherapies that could increase patient survival.
IRF1 regulates apoptotic caspases to thwart the development of colorectal cancer
Authors: Karki Rajendra , Sharma Bhesh , Kanneganti Thirumala-Devi 
Published: January 2023

Abstract
Interferon regulatory factor 1 (IRF1) is a transcription factor that is induced in response to interferons and inflammatory cytokines. We have previously identified the role of IRF1 in mediating inflammasome activation. These inflammasomes are associated with providing protective responses against colorectal tumorigenesis. The relevance of IRF1 to the immunobiology of cancer is still emerging, and the crucial role of IRF1 in colorectal cancer (CRC) remains unknown. The multiple inflammatory mediators produced during colorectal tumorigenesis have the ability to mediate cellular death; this may represent alternative forms of apoptosis that cannot readily be recapitulated in vitro by using classical apoptosis inducers. The precise regulatory mechanisms by which IRF1 governs the activation of cell death in response to inflammatory milieu remains elusive. Given that IRF1 is a transcription factor, it may induce the expression of upstream cell death mediators that are dependent on cytokines and that subsequently activate the executioner caspases. Here, we found that Irf1−/− mice were hyper-susceptible to CRC. IRF1 played roles in both myeloid and epithelial compartments to confer protection against CRC. Interestingly, IRF1 did not regulate inflammatory cytokines production and inflammasome activation in colons. However, IRF1 promoted cell death mediated by the inflammatory cytokines. The decreased cell death in the colons of Irf1−/− mice was associated with impaired activation of apoptotic caspases. Mechanistically, we demonstrated that IRF1 deficiency attenuated the induction of Fas and activation of caspase-8 that lead to reduced effector caspase-3 and caspase-7 activation in the colons.
Elucidating the immune response in metastatic ovarian cancer using single cell transcriptomics
Authors: Olalekan Susan , Xie Bingqing , Back Rebecca , Eckart Heather , Basu Anindita 
Published: January 2023

Abstract
Ovarian cancer is a highly metastatic and the most lethal malignancy of the female reproductive tract. In high grade serous ovarian carcinoma, the presence of tumor infiltrating lymphocytes suggests that this disease can be treated using an immunotherapeutic approach. However, determining candidates who will benefit from immunotherapies such as immune checkpoint inhibitor remains a crucial hurdle. Since immune checkpoint inhibitors work by reactivating an already existing anti-tumor response, a knowledge of the immune cell types within the tumor is required to predict the efficacy of this therapy. The objective of this study was to determine the cellular composition of metastatic ovarian cancer samples using single cell RNA sequencing. Hierarchical clustering of 6 patient samples revealed 2 main groups: a high T cell (2 samples) and 2) a high monocyte signature group (4 samples) suggesting differences in immune response. To assess the immune response in these patient samples, we performed an unsupervised clustering of the T cell population in the two groups. The T cell population clustered into 4 and 3 subpopulations in the high T cell and high monocyte group respectively. A granulysin expressing population was unique to the High T cell group. Interestingly, although both groups had tissue-resident memory CD8+T (CD8+Trm) cells, only the CD8+Trm cells in the high T cell group expressed TOX, a recently described transcription factor. TOX is expressed by exhausted CD8+ T cells that are reactivated in response to PD-L1 immunotherapy. In conclusion, our data reveals a subset of patients that may benefit from novel therapy.
Leveraging the power of high parameter cell sorting and single-cell multi-omics to profile intratumoral immune cells in a model of B cell lymphoma
Authors: Shi Xiaoshan , Baracho Gisele Vanessa , Lin Wai , Sedy John , Lomas Chip , Widmann Stephanie , Tyznik Aaron J 
Published: January 2023

Abstract
The pathogenesis and progression of B-cell lymphomas is a dynamic process involving reciprocal interactions between malignant cells and surrounding components in the tumor microenvironment. Neoplastic B cells migrate to lymphoid sites and prompt the immune cell infiltration. The infiltrated cytotoxic lymphocytes potentially contribute to tumor cell killing and good prognosis. However, most immune cell types in the tumor niche often become unresponsive or end up promoting tumor growth. In this study we present a sorting strategy using the BD FACSymphony™ S6 Cell Sorter that enables concurrent isolation of six cell populations from a tumor niche in a murine B-cell lymphoma model. Single-cell sequencing was used downstream to unravel the respective roles of each cell subset for the tumor’s progression and/or evasion. The six cell subsets were isolated from mice that had been inoculated with an OVA-expressing B-cell lymphoma cell line and subsequently with either wild-type or BTLA-deficient OVA-specific CD8+ T cells. The cell sorting aided more robust single-cell profiling of rare cell subsets within the sorted populations. In summary, we demonstrated a high-throughput approach that enabled a comprehensive characterization of critical cell populations in tumor responses. Since these cell populations constitute potential targets for the treatment of B-cell lymphomas, this platform, notably through the analysis of protein expression, offers an opportunity for identification of new therapeutic targets.
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Identifying regulators of reversible MHC I loss in Merkel cell carcinoma through genome-scale screens
Authors: Lee Patrick C , Le Phuong , Korthauer Keegan , Cheng Jingwei , Doench John , DeCaprio James A. , Keskin Derin B. , Wu Catherine J. 
Published: January 2023

Abstract
Loss of surface MHC I is an important mechanism by which cancer cells evade immune surveillance, and it can correlate with worse prognosis and resistance to immunotherapy. MHC I surface expression can be affected by genomic or transcriptional alterations to HLA-A/B/C, β2M, or the class I antigen processing machinery. In the case of transcriptional loss, we hypothesized that certain cancers might employ specific epigenetic programs to enforce downregulation of the MHC I pathway. Thus, we sought to identify novel MHC I regulators in MHC I-low cancers. In particular, we focused on Merkel cell carcinoma (MCC), a rare but aggressive neuroendocrine skin cancer that is caused by the Merkel cell polyomavirus in 80% of cases. Notably, MHC I downregulation is prevalent in MCC. We first generated and characterized a series of patient-derived MCC cell lines, in which MHC I surface expression was low but inducible with IFN-γ. We then conducted genome-scale CRISPR-KO and open reading frame (ORF) gain-of-function screens in one of our virus-positive MCC lines, using FACS to select for perturbations that upregulated surface MHC I. One of the top hits from these screens was PRC1.1, a non-canonical Polycomb repressive complex. Polycomb complexes are known to mediate gene silencing through chromatin modification and play an important role in development and cancer. These studies suggest a possible role for PRC1.1 in suppressing MHC I in MCC.
Genome-wide CRISPR screen reveals cancer cell resistance to NK cells induced by NKderived IFN-γ
Authors: Zhuang Xiaoxuan , Long Eric O 
Published: January 2023

Abstract
The anti-leukemia activity of NK cells is important for preventing relapse during HSCT in leukemia patients. However, the factors that determine susceptibility of leukemia cells in the context of NK-mediated killing are not well established. Here we performed a genome wide CRIPSR screen in the human CML cell line K562 to identify genes that regulate vulnerability of leukemia cells to killing by primary human NK cells. Distribution of gRNAs in K562 cells that survived co-incubation with NK cells showed that loss of NCR3LG1 (encodes B7H6), the ligand of the activating receptor NKp30, predominantly protected K562 cells from killing. It indicates that B7H6 is a major ligand on K562 cells. In contrast, loss of genes that regulate pathways for antigen-presentation (B2M, HLA-I, PSMB5, TAP1, TAPBP) and IFN-γ signaling (IFNGRs, JAKs, STATs) increased the vulnerability of K562 cells. MHC-I on K562 cells was upregulated after co-culture with NK. Addition of IFN-γ neutralizing antibody during the co-culture increased the susceptibility of K562 cells to NK-mediated lysis. The results suggest that cancer cells respond to NK-derived IFN-γ and lead to NK-resistance and immune evasion. Moreover, Analysis of RNA-seq data from The Cancer Genome Atlas (TCGA) showed that low IFNGR2 expression in cancer tissues associated with improved overall survival in AML patients, indicating that the IFNGR-JAK-STAT pathway can be a contributor to worse prognosis of cancer patients, potentially related to IFN-γ–induced NK-resistance, despite the fact that IFN-γ signaling promotes T cell mediated immune surveillance. Our results suggest that targeting IFN-γ responses might be a promising approach to enhance NK cell anti-cancer efficacy.
Profiling the immune infiltrate in tumor samples at single cell resolution
Authors: Cheung Denise , Adams Bruce A. , McDonnell Wyatt J. , Jaffe David B. , Puleo Alaina R. , Sukovich David J , Reyes Daniel J , Royall Ariel J , Chi Javelin C. , Srinavas Niranjan J , Krishnan Sreenath J , Carli Natasha J , Montesclaros Luz J , Lau Julia J , Stubbington Michael J.T. , Taylor Sarah E.B. 
Published: January 2023

Abstract
Profiling the complex interactions of immune infiltrate with tumor cells in a tumor microenvironment is critical for advancing our understanding of tumor biology for developing personalized cancer therapies. Using a droplet-based single cell RNA sequencing (scRNA-seq) platform, we profiled the transcriptome and immune repertoire of gastric, kidney, and lung cancer cells that are primarily immune cells from three different donors. scRNA-seq analysis also identified similar fractions of CD45+ immune cells, CD4+ and CD8+ T cells, CD19+ B cells, and myeloid cells compared to flow. Targeted scRNA-seq was also used to identify paired, full length B-cell (BCR) and T-cell (TCR) receptors. In the gastric adenocarcinoma tumor cells, gene expression analysis identified a large population of B cells, but with no clonal expansion. T cells expressing CD8A constituted about 10% of cells with the top clonotype being 1% of all clones. The clear cell RCC sample had a modest fraction of infiltrating T cells with the top clonotype representing 7.4% of all clones, and no B cell infiltrate. The NSCLC cells were mainly T and B cells but limited clonal expansion was observed; the top TCR clonotype was present on 2.2% of all T cells, no expansion was seen in any of the B cell clonotypes. These findings highlight the value of profiling of tumor immune cells holistically and not relying on the presence of B or T cells alone to understand the immune dynamics of the tumor microenvironment. The presence of tumor-infiltrating lymphocytes is associated with favorable clinical outcomes in some cancers, but understanding their cellular subtype and clonality by high resolution profiling is key in the development of immune-based cancer treatments
Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their distinct responses to different treatment modalities
Authors: Haldar Malay , Dang Mai T 
Published: January 2023

Abstract
Tumor-associated macrophages (TAMs) are an important component of the tumor microenvironment (TME). Pro-inflammatory macrophages can suppress while anti-inflammatory macrophages can promote tumor growth. Despite their abundance in many tumors, the origins and diversity of TAMs are not well understood, especially in brain tumors. Our long-term goal is to uncover ways to modulate TAMs for the treatment of pediatric brain tumors.
Medulloblastoma (MB) is one of the most common pediatric brain malignancy. MB is heterogeneous with four molecular subgroups: WNT, sonic hedgehog (SHH), group 3, and group 4. Treatment includes surgical resection, cytotoxic chemotherapy, and radiation. Radiation is effective, but severe neurological side-effects limit its use to non-infants (&gt; 3 years). Therefore, treatment choices are even more limited in infants. SHH-MB dominates this age group and is characterized by constitutive activation of the SHH signaling pathway. Ptch1 is a negative regulator of SHH signaling that is often mutated in SHH-MB. In mice, germline deletion of Ptch1 and loss of Tp53 leads generates MB with 100% penetrance.
Using single-cell RNA sequencing (ScRNA-Seq) in the genetically engineered mouse model (Ptch+/−:p53−/−) of SHH-MB, we describe macrophage heterogeneity in medulloblastoma, demonstrate differential recruitment and function of macrophages under distinct modalities of tumor therapy (molecular-targeted vs. radiation), and use these insights to uncover potential strategies for immunomodulation as adjunctive therapy.