bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic mediated immune exhaustion persists after successful Tuberculosis therapy
Authors: DiNardo Andrew R , Rajapakshe Kimal , Nishiguchi Tomoki , Mtetwa Godwin , Maphalala Gugu , Makedonas George , Coarfa Cristian , Mandalakas Anna M 
Published: January 2023

Abstract

BACKGROUND
Chronic antigen stimulation from HIV, HPV, LCMV and schistosomiasis induce epigenetic-mediated immune exhaustion. Individuals with successful anti-TB therapy (ATT) have a thirteen-fold increased risk of developing recurrent TB.

METHODS
From a cohort of HIV infected and uninfected individuals with TB and their asymptomatic household contacts (n=32), genome-wide DNA methylation (DNA MethylEPIC) and epigenetic deconvolution (EDEC) identified cell-specific DNA methylation. Cell-specific results were validated with MSRE-PCR, gene expression and flow cytometry-based Mtb-specific multi-dimensional immune profiling.

RESULTS
Participants with TB had DNA hypermethylation in the IL-2, TCR and IFN-γ signalling pathways. The IFN-γ signalling pathway was affected in both innate (NK cells and monocytes) as well as adaptive (CD4 and CD8 T cells) lineages. Select DNA hyper-methylated differences were validated using MSRE-PCR. Pioneer and Transcription factors critical for cell-mediated immunity were also significantly differentially methylated with enrichment scores compatible with previous epigenetic-mediated immune exhaustion. After overnight stimulation with IFN-γ, TB patients have decreased IFN-γ-inducible gene expression. Six months after the completion of successful ATT, participants with TB have persistent DNA hypermethylation.

DISCUSSION
Persistent DNA hypermethylation may be a potential mechanism by which individuals with TB are at increased risk of recurrent disease. This may also assist in identifying potential new targets for host-directed therapy.
High-dimension flow cytometry reveals comprehensive deviations in immunophenotypes associated with non-response to melanoma immunotherapies
Authors: Woods David M , Laino Andressa , Winters Aidan , Alexandre Jason , Weber Jeffrey , Chattopadhyay Pratip 
Published: January 2023

Abstract
Immunotherapies have revolutionized the treatment of many cancers, but most patients fail to respond. To investigate immune phenotypes associated with patient response, we assessed 68 unique peripheral blood markers using high-dimension flow cytometry. Samples from 41 metastatic melanoma patients treated with αPD1 or αCTLA4 and 12 healthy donors (HD) were evaluated. To avoid a loss of higher order data, we used a novel computational approach, CytoBrute, to analyze the data through semi-comprehensive Boolean gating. Lineages (e.g. CD3+CD4+) were evaluated for all possible combinations for up to 15 markers. In αPD1 treated patients 1,051 immune signatures differentiated patient response at baseline with a p-value &lt;0.05, while 823 differentiated αCTLA4 treated patients. Only eight signatures overlapped between the two therapies. Signatures included both low (e.g. CD4+CD45RO+CD278−) and high-dimension immunophenotypes (e.g. CD14+CD33+CD11C+CD163+PDL2+41BBL+CD86+CD40+PDL1−CD66B−CD80−GAL9−CD15−CD19−OX40L−). A total of 2,895 signatures significantly differentiated HD versus patients, of which 270 significantly differed (p&lt;0.05) based on patient response. Samples from non-responding patients less closely resembled HD relative to responding patient in 205 of these 270 signatures (p&lt;1e-8). Comparisons of all 102,000 assessed phenotypes showed that non-responding patients had a lesser degree of similarity in immunophenotypes in comparison to responders. Our data demonstrate a novel and powerful approach to interrogating complex immunophenotypes and show that comprehensive immunophenotypic deviations are associated with non-response to melanoma immunotherapies.
The natural human IgG1 mAb Pritumumab targets cell surface expressed vimentin and inhibits tumor growth
Authors: Glassy Mark C , Babic Ivan , Mukthavaram Rajesh , Jiang Pengfei , Nomura Natsuko , Glassy Eric , Kesari Santosh 
Published: January 2023

Abstract
Cancer patients generate tumor-specific B lymphocytes which can be isolated to develop human mAbs against tumor-associated antigens. Pritumumab (also referred to as CLNH-11, CLN-IgG, or ACA-11) is a classic example of a natural human anti-cancer antibody. It is a natural human IgG1 kappa antibody developed by human hybridoma technology, using B lymphocytes isolated from a regional draining lymph node of a patient with cervical carcinoma. Phase II clinical trials with pritumumab have demonstrated an objective response as a therapeutic antibody for glioblastoma. Here we demonstrate pritumumab binds cell surface expressed vimentin, also referred to as ecto-domain vimentin (EDV). Vimentin is an intracellular cytoskeletal protein overexpressed during epithelial-to-mesenchymal transition (EMT), a process integral to cancer cell metastasis. The potential of pritumumab as a therapeutic antibody targeting glioblastoma was evaluated. We demonstrate pritumumab binding to patient glioblastoma cells and antibody binding to these cells induces antibody-dependent cell-mediated cytoxicity (ADCC). Furthermore, pritumumab effectively inhibited glioma tumor growth in a xenograft mouse model. Overall, these data provide pre-clinical validation of pritumumab mAb as a therapeutic for glioblastoma.
Intratumoral delivery of RIG-I agonist induces robust anti-tumor immune responses
Authors: Jiang Xiaodong , Fedorova Olga , Linehan Melissa , Dong Huiping , Pyle Anna Marie , Iwasaki Akiko 
Published: January 2023

Abstract
Recent studies have revealed that cytosolic nucleic acid-sensing pathways such as cGAS-STING and RIG-I-MAVS are involved in cancer biology. How to employ agents or agonists of these pathways to develop new approaches for cancer treatment is a promising direction. In this study, we synthesized a unique, binding-specific RIG-I agonist called Stem Loop RNA (SLR) 14 and evaluated its in vivo anti-tumor efficacy. When tumor volume reached 40–80 mm3, SLR14 was delivered intratumorally, every 2–3 days, for a total of 5–6 doses. Our results show that, after SLR14 treatment, B16 melanoma growth was dramatically blocked and the mice displayed long-term survival. We also observed a significant increase of tumor-infiltrating lymphocytes, and demonstrated that anti-tumor efficacy of SLR14 was T cell-dependent using RAG−/− mice and T cell depletion. Next, we tested anti-tumor efficacy of SLR14 in the mice with immunogenic tumor --YUMMER1.7 (melanoma) or MC38 (colon cancer). Similarly, we also observed a significant delay of tumor growth and extended mouse survival. Moreover, combination treatment with SLR14 and anti-PD1 in these mice led to more remarkable antitumor effects than single treatment. Lastly, we found that SLR14 was mainly taken up by CD45+CD11b+ leukocytes including neutrophils and myeloid cells, suggesting that anti-tumor efficacy of SLR14 is initiated through activation of the RIG-I pathway in innate cells within the tumor microenvironment. Taken together, our data demonstrate that synthetic RIG-I agonist SLR14 is a promising therapeutic agent for a broad spectrum of tumor subtypes. A better understanding of nucleic-acid sensing mechanisms within the tumor microenvironment may yield novel approaches for cancer immunotherapy.
Detection and Quantification of Circulating Tumor Cells in PBMCs or Blood Using Flow Cytometry
Authors: Lei Ming , Ye Peifang , Wang Andy , Li Nancy , Wang Xiaobo 
Published: January 2023

Abstract
Circulating Tumor Cells (CTCs) are cells that have detached from primary tumor tissues or metastases and entered into peripheral blood circulation, led to cancer recurrence and distal metastasis. Evaluation of CTCs conduces to tumor diagnosis, treatment, monitoring, and prognosis. Tumor cell spiking assay was frequently used to evaluate the sensitivity, specificity, accuracy, and repeatability of the methods or systems for enumeration of rare CTCs.
In this work, a novel flow cytometer NovoCyte® Quanteon™ was employed to measure and quantify spiked human tumor cells of colon carcinoma (SW620) in normal PBMCs or peripheral blood.
First, immunofluorescence labeled (EpCAM-APC antibody) SW620 cells (0–256 cells) were serially diluted in 1×106 PBMCs and tested directly on Quanteon. The data indicate that CTC detection using Quanteon has a sensitivity of 0.0001% (one CTC per million cells) and an excellent linear relationship between the number of cells detected and the predicted number added. Furthermore, SW620 cells (0–2000 cells) were serially diluted in 2mL normal whole blood, following the traditional isolation of PBMCs, magnetic EpCAM-positive selection, immunofluorescence labeling (CD45 FITC, EpCAM APC) and washing. The results show that the average recovery of CTCs is more than 75%.
Flow cytometry is a valuable tool for therapeutic monitoring and prognosis assessment. Detection of CTC is critical for a “liquid biopsy”. These experimental results demonstrate that the NovoCyte Quanteon flow cytometer can provide high specificity and accuracy of CTC detection through both direct identification and EpCAM affinity bead-based enrichment methods.
Inhibition of NK cell-MHCI interactions disrupts immune homeostasis by activation of the IFNγ/IL15 axis resulting in augmentation of anti-tumor immunity
Authors: Panda Abir Kumar , Shevach Ethan M 
Published: January 2023

Abstract
While TCR-MHC interactions are crucial for antigen recognition and induction of specific immune responses, all T cells have the potential to recognize “self” in the absence of foreign antigen. We have previously demonstrated that blockade of TCR-MHCII interactions in vivo resulted in a marked disturbance of immune homeostasis with an expansion of memory phenotype (MP) Treg, CD4+Foxp3−, and CD8+ T cells. To explore whether MHCI interactions also play a role in immune homeostasis, we treated unmanipulated mice with the pan-anti-H2 mAb, M1/42., for six days. Surprisingly, this treatment resulted in marked proliferation of NK cells, MP CD8+ T cells and to a lesser extent MP CD4+ T cells. All the effects of the anti-MHCI treatment were critically dependent on the presence of NK cells. Activated NK cells secreted high amounts of IFNγ which induced high levels of MHCI and MHCII expression on APC as well as IL-15 secretion by APC. IL-15 subsequently drove NK cell proliferation, and MP CD4+ and MP CD8+ T cell expansion. The global disruption of immune homeostasis induced by blockade of MHCI interactions created an environment that rendered the animals resistant to the growth of a transplanted tumor. Taken together, disruption of the interaction of specific lymphoid subpopulations with their MHCI targets in the steady state can paradoxically result in beneficial activation of immune responses against tumors. Blocking of MHCI interactions by anti-MHCI could also be useful to better understand immune responses against intracellular (viruses) and extracellular (bacteria) pathogens and the generation of long term memory responses.
TNF superfamily cytokines overcome immune evasion in medulloblastoma
Authors: Wechsler-Reya Robert , Garancher Alexandra , Suzuki Hiromichi , Haricharan Svasti , Masihi Meher Beigi , Rusert Jessica M. , Norris Paula S. , Carrette Florent , Romero Megan M. , Morrissy Sorana A. , Skowron Patryk , Cavalli Florence M.G. , Farooq Hamza , Ramaswamy Vijay , Jones Steven J.M. , Moore Richard A. , Mungall Andrew J. , Ma Yussanne , Thiessen Nina , Li Yisu , Morcavallo Alaide , Qi Lin , Henderson Jacob J. , Crawford John R. , Levy Michael L. , Olson James M. , Cho Yoon-Jae , Deshpande Ani , Li Xiao-Nan , Chesler Louis , Marra Marco A. , Becher Oren J. , Bradley Linda M. , Ware Carl F. , Taylor Michael D. 
Published: January 2023

Abstract
Many immunotherapies act by enhancing T cell killing of tumor cells. CD8+ cytotoxic T cells recognize antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. Here we show that medulloblastomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. Treatment with tumor necrosis factor (TNF) or lymphotoxin beta receptor agonist (LTβRag) rescues expression of Erap1, Tap1 and MHC-I on p53-mutant tumor cells. In vivo, TNF treatment prolongs survival and markedly augments the efficacy of the immune checkpoint inhibitor anti-PD-1. These studies identify p53 as a key regulator of immune evasion in vivo, and suggest that TNF could be used to enhance sensitivity of p53-mutant tumors to immunotherapy.
Identification and characterization of a unique KLRG1-expressing subset of CD4+FOXP3+ Tregs in Non-small cell lung cancer
Authors: Adeegbe Dennis O , Noyes David , Semidey-Hurtado Jon , Gamal Wael 
Published: January 2023

Abstract
It is well established that CD4+FOXP3+ T regulatory cells (Tregs) contribute to dampening anti-tumor responses. Despite our improved understanding of their role in cancer, there remains a knowledge gap with respect to the clonal composition and heterogeneity of tumor-infiltrating Tregs in solid cancers. We addressed this outstanding issue by conducting comprehensive phenotypic profiling of Tregs present in lung adenocarcinomas of a genetically engineered mouse model of non-small cell lung cancer (NSCLC) as well as those in resected tumors of NSCLC patients. Multi-parameter flow cytometric analysis revealed that unlike the peripheral tissues, the tumor harbors a distinct sub-population of Tregs that express the co-inhibitory receptor, KLRG1. Compared to their negative counterparts, the KLRG1+ Treg subset exhibited heightened expression of a number of Treg signature proteins as well as higher levels of activation and memory molecular markers suggesting that they are a highly activated and differentiated Treg pool that is recruited to, or induced in the tumor microenvironment. Consistent with this phenotype, these KLRG1+ Tregs were superior in their capacity to suppress T cell proliferation relative to the KLRG1-cells. Collectively, these findings demonstrate that the tumor microenvironment in non-small cell lung cancer harbors a unique Treg sub-population that is characterized by dominant expression of KLRG1, and which represents a clonal pool with the most potent inhibition of T cell responses. These studies highlight the installment of distinct Treg subsets in NSCLC that have implications for regulation of anti-tumor responses.
T-Cell Intrinsic Mechanisms of Resistance to PD-1 Checkpoint Blockade
Authors: Krogsgaard Michelle , Moogk Duane , Wang Lin , Li Kaito , Yuan Zhou , Weber Jeffrey , Osman Iman , Zhu Cheng 
Published: January 2023

Abstract
Although much clinical progress has been made in harnessing the immune system to recognize and target cancer, there is still a significant lack of an understanding of how tumors evade immune recognition and the mechanisms that drive tumor resistance to both T cell and checkpoint blockade immunotherapy. Our objective is to understand how tumor-mediated signaling through inhibitory receptors, including PD-1, combine to affect the process of T cell recognition of tumor antigen and activation signaling. Our goal is to understand the basis of resistance to PD-1 blockade and potentially identify new molecular targets to enable T cells to overcome dysfunction mediated by multiple inhibitory receptors. Biomembrane Force Probe(BFP) measurements show that that the activities of TCR-proximal signaling components affect T cell mechanosensing and sensitivity at the earliest stages of antigen recognition and are influenced by PD-1 and other inhibitory receptors via Shp-1/2 by targeting CD28 and Lckto directly suppress TCR-pMHC-CD8 binding. Phospho-proteomics and flow cytometry-based analysis of patient-derived T cells from PD-1 responders and non-responders identified additional mediators, signaling components and pathways associated with PD-1 checkpoint blockade resistance. CRISPR/Cas9 mediated genome editing was utilized to determine if resistance is mediated by the continued signaling of multiple IRs by perturbing IR signaling in mouse models of PD-1 blockade. Targeting these interactions and understanding the basis of resistance to PD-1 blockade would potentially allow identification of novel biomarkers of resistance or new molecular targets to enable T cells to overcome dysfunction during PD-1 checkpoint blockade.
The dark side of IL-1: role in prostate cancer progression
Authors: Udartseva Olga O , Gollnick Sandra O 
Published: January 2023

Abstract
IL-1 is a pro-inflammatory cytokine essential for host defense against pathogens, but its role in cancer progression remains understudied. Recently our lab identified the IL-1 pathway as a molecular mechanism responsible for myeloid-driven prostate cancer development. Here, we report that IL-1 signaling in tumor cells drives prostate cancer progression. To identify the contribution of IL-1 signaling in prostate cancer progression, we downregulated expression of IL1R1 (the only known functional receptor for IL-1α/β) using shRNA or Crisr/Cas9 in androgen-sensitive (LNCaP) and androgen-independent (PC-3M) prostate cancer cell lines. We found that IL-1α inhibited expression of androgen receptor in LNCaP while suppression of IL-1 signaling abrogated this effect. The expression of neuron-specific enolase which was shown to be a prognostic marker associated with poor survival outcome was significantly reduced in PC-3M cells lacking IL1R1. Downregulation of IL-1 signaling in cancer cells resulted in significant inhibition of prostate tumor growth while no effect on cell proliferation was detected. We established this phenomenon and found several possible mechanisms underlying it. We found that knocking down of IL1R1 in cancer cells resulted in suppression of mTOR and ACC signaling in tumors. TUNEL staining revealed increased number of apoptotic cells in shIL1R1-PC-3M tumors. Tumors lacking IL1R1 were characterized by impaired vascularization which was accompanied by reduced COX-2, VEGF-A and IL-8 expression. Taken together, our findings indicate that downregulation of IL-1 signaling modifies prostate cancer cell phenotype and suppresses tumor growth.
Immune checkpoint inhibitors reverse T-cell functional suppression in the bone marrow of a subset of AML patients
Authors: Lind Evan F , Lamble Adam J , Kosaka Yoko , Laderas Ted , Brady Lauren , Huang Fei , Druker Brian J , Tyner Jeffrey W , McWeeney Shannon 
Published: January 2023

Abstract
Acute Myeloid Leukemia is a blood cancer with poor prognosis despite decades of therapeutic development. Immune checkpoint inhibitors (ICIs) have been shown to be effective in many cancers, but their utility in AML has not been clearly established. To better understand the immune landscape of the AML microenvironment, we performed immunophenotyping on fresh bone marrow cells from AML patients using mass-spec based flow cytometry. In addition, we performed functional assays to evaluate T-cell proliferative capacity and determine whether AML bone marrow T cells can be modified by ICI treatment. Sixty two bone marrow samples from patients with AML were analyzed. We performed T-cell stimulation assays to measure proliferation and cytokine production in the presence and absence of ICIs. Samples were sub-categorized as being proliferators or non-proliferators based on the percent of T-cell division in response to TCR stimulation. Phenotypic analysis showed proliferation status correlated with a specific T-cell profile. Additionally, within the non-proliferator group, 70% overcame immune suppression and responded to at least one of the ICIs tested. In conclusion, we show that T-cell dysfunction is present in a subset of patients with AML. Nonetheless, this suppression can be reversed by ICIs in many cases, supporting the use of ICIs in AML therapy.
PD-1 checkpoint therapy promotes pro-survival phenotype in regulatory T cells in a model of claudin-low breast cancer
Authors: Vick Sarah C , Perou Charles M , Serody Jonathan S. 
Published: January 2023

Abstract

Results
We have previously shown in our claudin-low genetically engeneired mouse model (GEMM) that Tregs are increased in the tumor microenvironment (TME), and express high levels of PD-1. We hypothesized that one cause for the lack of activity of α-PD-1 therapy in GEMMs and patients with claudin-low tumors was the activation of PD-1 expressing Tregs in the TME. To evaluate this hypothesis, Tregs were isolated from claudin-low tumors and functionally evaluated ex vivo. In vitro, PD-1 blockade decreased the suppressive activity of Tregs at high Treg:Tnaive cell ratios, but no difference was found in suppression at physiologically relevant ratios. We compared the transcriptional profiles of Tregs isolated from tumor bearing mice with or without α-PD-1 therapy using RNA-Seq. There were 27 signifcantly differentially regulated genes in Tregs from mice treated with α-PD-1 compared to untreated. These genes were associated with survival pathways using IPA with JUN, FOS (P &lt; 0.001) and BCL2 (P = 0.02) upregulated in Tregs exposed to α-PD-1 treatment. Based on these data, we hypothesized that α-PD-1 treatment on Tregs results in a pro-survival phenotype. We found in vitro that Tregs in the presence of α-PD-1 proliferated significantly more than untreated Tregs (P &lt; 0.0001). Importantly, PD-1 blockade did not significantly alter the expression of immunosuppressive proteins such as CTLA-4, CD25, TGFβ, or Il-10 as measured by flow cytometry.

Conclusions
We found that PD-1 blockade increases proliferation of Tregs in the T11 model, while not significantly altering suppressive capabilities thus leading to enhanced immunosuppression in the TME. Activation of Tregs by α-PD-1 therapy may be responsible for hyperacute tumor flares post therapy.
CD39+CD8+ T cells exhibit a distinct phenotype among tumor-infiltrating tumor-antigenspecific CD8+ T cells
Authors: Lee Yongjoon , Park Junsik , Park Su-Hyung , Shin Eui-Cheol 
Published: January 2023

Abstract
Recent studies have spotlighted CD39 expression on tumor-infiltrating CD8+ T cells as an exhaustion marker (Cancer Research 2018, 1:78) and tumor antigen reactivity (Nature Communications 2018, 9:1). In the present study, we examined characteristics of CD39+CD8+ T cells among tumor-infiltrating lymphocytes (TILs) obtained from various types of tumors, including ovarian cancer, stomach cancer and hepatocellular carcinoma, to gain better understanding of CD39 expression on CD8+ T cells. To identify tumor antigen-specific CD8+ T cells, we used 11 HLA-A*A201 multimers specific for tumor associated antigens, including MAGE A1, NY-ESO-1, and AFP. CD39 expression of tumor antigen-specific CD8+ T cells was significantly higher in TILs than in peripheral blood lymphocytes. However, all of tumor-infiltrating tumor antigen-specific CD8+ T cells did not express CD39. As known previously (Nature 2018, 557:7706), tumor-infiltrating bystander CD8+ T cells, specific to viral epitopes, lack CD39 expression. Among tumor-infiltrating tumor antigen-specific CD8+ T cells, CD39+CD8+ T cells exhibited more severely exhausted features than CD39−CD8+ T cells. For example, the percentage of multiple immune checkpoint receptors-expressing cells was significantly higher in CD39+CD8+ T cells compared to CD39−CD8+ T cells. Moreover, higher proportion of T-betlow/Eomeshighcells and and lower expression of CD127 were observed in CD39+CD8+ T cells. In addition, CD39+CD8+ T cells expressed higher levels of tissue residency markers, such as CD103 and CD69. In conclusion, CD39+CD8+ T cells exhibit distinct phenotypes that represent severe exhaustion and terminal differentiation among tumor-infiltrating tumor-antigen-specific CD8+ T cells.