bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of TIGIT inhibitors by phage display
Authors: Huang Xueting , Hsiao Chia-Hung Christine , Wiemer Andrew J 
Published: August 2023

Abstract
TIGIT is an emerging immune checkpoint receptor expressed higher than PD-1 in some tumors especially anti-PD1 resistant tumors. By competing with the co-stimulatory receptor CD226/DNAM-1 for binding to CD155/PVR, TIGIT transduces inhibitory signals and suppresses the immune response. Therefore, we sought to discover TIGIT inhibitors for improving tumor immunotherapy. Through directional cloning, bacterial transformation and phage amplification techniques, we generated a novel genetically encoded, phage-displayed bicyclic peptide library comprised of more than a million peptide sequences. Depending on the two combinations of different disulfide bonds, each peptide backbone is predicted to be folded into either endo-bicyclic or exo-bicyclic structure. We conducted three rounds of phage display panning against recombinant TIGIT IgV domain that enriched high-affinity peptides and identified promising TIGIT binding peptides. Phage ELISA showed binding of phage-presented peptides to recombinant TIGIT IgV and competitive ELISA evaluated the ability of the peptides to disrupt interactions between TIGIT and PVR. This work validated the efficiency of the phage-displayed bicyclic peptide library for discovery of ligands targeting protein receptors and led to identification of novel TIGIT inhibitors.
AAI Careers in Immunology Fellowship
Systems approaches to characterize the local heterogeneities in NK cell antitumor immunity in MHC I-disparate human non-small cell lung cancer
Authors: Dolatshahi Sepideh , Erdogan Remziye , Ageeb Nardin , Obeid Youssef , Mauldin Ileana S , Goundry Kate , Hossain Mahdin , Slingluff Craig , Bullock Timothy N , Brown Michael G 
Published: August 2023

Abstract
Checkpoint immunotherapy has shown encouraging yet limited success in non-small cell lung cancer (NSCLC) patients. We combined multiplexed fluorescence imaging with quantitative spatial analysis to investigate antitumoral immunity in NSCLC. As seen before, we observed frequent MHC class I (MHC I) loss and development of CD8 T cell refractory tumors. MHC I-deficiency suggested NK cells may confer protection in NSCLC. Indeed, we found higher CD3−CD56+ NK cell numbers were associated with both disease-free and overall survival. Using partial least squares regression, we found that both T cells and NK cells were significantly enriched in MHC I-bearing tumors. Quantitative spatial characterization of tumor cell MHC I expression revealed vast intra- and inter-tumoral heterogeneity, which was highly associated with the local lymphocyte landscape. To infer functional differences in local cell-cell communication, we built computational models based on spatial single cell neighborhood profiles to discriminate between IFNg-disparate lymphocytes. We found IFNg+ NK cells more frequently associated with other IFNg+ NK cells or T cells in comparison to IFNg− NK cells, or IFNg+ T cells which more frequently had IFNg− lymphocyte neighbors. Moreover, IFNg+ NK cells were unique in their capacity to also associate with MHC I− tumor cells. Together these data implicate a key role for NK cells in recruiting and activating other lymphocytes in MHC I-bearing tumors, and further suggest NK cells may be key to developing effective therapies even in CD8 T cell refractory tumors.
Supported by UVA Carter Immunology Center Collaborative Research Award
Single cell RNA sequencing reveals heterogenous immune landscape of tumor infiltrated immune cell population against glioblastoma
Authors: Kang ByeongHoon 
Published: August 2023

Abstract
Glioblastoma (GBM) is the most aggressive glioma. Recently, immunotherapy using immune-checkpoint blockage (ICB) has provided therapeutic efficacy to various tumors. Despite an attractive ICB therapy, there have not been beneficial outcomes about GBM patients due to the characteristic of immunosuppressive environment. Thus, it is essential to understand the features of GBM immune microenvironment. Here, we profile immune cells of GBM microenvironment via single cell RNA sequencing (scRNAseq) according to GBM progression in orthotopic glioma model. We identify that kinetics of immune cell population throughout the GBM : macrophages are recruited first and T cells are recruited later. In addition, we analyze early and late stage of microglia and macrophages. Especially, GBM progression down-regulates pro-inflammatory genes and interferon responsive genes in microglia and induces M2 phenotype of recruited macrophages. We further identify that at later stage, overall T cells are increased, but regulatory T cells (Tregs) are significantly increased. In particular, CD8T cells express Nur77 but they also increase multiple inhibitory molecules and show reduction of effector molecules. These findings reveal overall profiling and features of immune cells in GBM microenvironment and provide comprehensive landscape of immune cells throughout GBM progression.
IL-17A-mediated JMJD3 regulation of integrin alpha 3 gene expression alters migration of diabetic keratinocytes and impairs wound repair
Authors: Moon Jadie Yoonjoo , Wolf Sonya , Audu Christopher , Melvin William , Joshi Amrita , Mangum Kevin , Barrett Emily , Davis Frank , Mazumder Purba , Rocco Sabrina , Erturk Ilkim , Gallagher Katherine 
Published: August 2023

Abstract
Keratinocytes are key structural cells in cell migration during wound repair. Keratinocyte migration is dysfunctional in diabetes and results in non-healing, however, the reason for this is unclear. Using bulk and single cell sequencing, we identified that Th17 CD4+ T-cells predominate as does an IL-17A signature in human diabetic wound tissue compared to non-diabetic controls. The effects of increased IL-17A in diabetic skin on keratinocyte function is unknown. To examine this, we subjected isolated keratinocytes to scratch injury and a 24hr rIL-17A (20ng) stimulation. We observed a significant decrease in migration rate in IL-17A stimulated keratinocytes compared to their controls. Next, we examined migration related genes in keratinocytes from mice fed with a normal (ND) or a high fat (HFD) diet. Integrin alpha 3 subunit, Itga3, (a protein known to delay keratinocyte migration during wound re-epithelialization) was higher in diabetic (HFD) keratinocytes compared to ND controls at baseline and with rIL-17A. We analyzed epigenetic enzymes known to increase gene expression and identified that JMJD3, a histone demethylase that relaxes chromatin, was increased both in diabetic keratinocytes from our human scRNA-seq and in murine diabetic keratinocytes with rIL17A. Further, treatment with a JMJD3-specific inhibitor (GSK-J4) decreased Itga3 in diabetic keratinocytes, suggesting that JMJD3 may be relevant to IL-17A-mediated regulation of integrin alpha 3 and other keratinocyte migration genes. Continued investigation into upstream IL-17A signaling in normal and diabetic keratinocytes that alters downstream migration is crucial for our understanding of impaired keratinocyte functions associated with diabetic wound repair.
NIH T32 AI 007413, Research Training in Experimental Immunology Rackham Pre-Candidate Graduate Student Research Grant, University of Michigan
High-dimensional analysis of the T cell response in multiple myeloma and the potential efficacy of harnessing tumor-reactive CD8 T cells
Authors: Prazich Jack , Jiang Jenny , Dhodapkar Madhav 
Published: August 2023

Abstract
Multiple myeloma is an incurable malignancy of plasma cells in the bone marrow increasingly being treated by immunotherapies with improved response and survival over traditional chemotherapy, however an unexplored potential immunotherapy is the adoptive transfer of tumor-specific CD8+ T cells. Here, we investigated the tumor-specific CD8+ T cell response in highly progressed multiple myeloma patients. We predicted neoantigens and tumor-associated antigens for each patient and grew out tumor-specific CD8 T cells from patient TIL’s using autologous B cells loaded with the predicted epitopes. We then utilized TetTCR-SeqHD, a high-throughput tetramer-based workflow, to isolate paired tumor-specific T cell receptor (TCR) sequence and antigen specificities. We subsequently transduced and functionally validated these TCR specificities and their cytotoxicity in vitro. In addition, we performed single-cell transcriptomic and proteomic analyses on TIL’s and peripheral blood T cells before and after immunomodulatory treatment to capture high-dimensional data on the cellular states of the T cell response and their response to stimulation. We observed T cells within the tumor were largely exhausted, but that patients had neoantigen-specific CD8+ T cell populations present responding to a broad array of antigens suggesting adoptive transfer of tumor-specific CD8 T cells is potentially efficacious. Last, we measured TCR repertoire changes and identified T cell clones that had expanded. We also found a number of peripheral blood T cells markers that correlated with treatment response in our patients. Next, we aim to transfer transduced tumor-specific T cells into PDX mouse models to measure preclinical therapeutic potential.
Supported by grants from CRI-STAR and NIH R01
Impaired pathogen-specific CD4+ T cell functionality in patients with CLL
Authors: Wu Jinghua , Ribeiro Oriana Jesus , Österborg Anders , Gao Yu , Buggert Marcus 
Published: August 2023

Abstract
Chronic lymphocytic leukemia (CLL) is the most common type of leukemia in adults and remains an incurable disease. Many patients with CLL are affected by non-malignant complications, including infectious diseases, as witnessed during the past years, with very high COVID-19 mortality rates. Accumulating data indicate that T cells might become exhausted in patients with CLL, which might be a contributing factor to poor control of pathogenic infections. Here we developed flow cytometry protocols to combine activation-induced molecule (AIM) assessment and functional read-outs to understand if bacteria- and virus-specific CD4+ T cell responses are impaired in patients with CLL. PBMCs were collected from indolent CLL patients (n=23) and age and gender-matched blood donors (n=17) to assess CD4+ T cell dysfunction against pathogenic bacteria (S. Pneumonia, H. Influenzae, M. Catarrhalis, K. Pneumoniae) and viruses (CMV, EBV, IAV). We show that the frequency of CD4+ T cell responses against most assessed bacterial species was of lower frequencies in CLL patients compared to matched control groups. Both bacteria- and virus-specific CD4+ T cells experienced, in general, signs of functional exhaustion, including diminished capacity to produce IFN-γ, TNF, IL-2, IL-17, and/or IL-21, during indolent CLL. Functional exhaustion was not coupled to increased expression of inhibitory receptors but instead reduced stem-like phenotypes of CD4+ T cells. These data indicate that untreated CLL is coupled to impaired functional capacity of bacteria and virus-specific CD4+ T cells, which might lead to poor pathogen control.
Swedish Cancer Foundation(Cancerfonden)
UCP2 Deficiency Renders Th1/2 Pathogenic Phenotype to CD4+ T cells
Authors: Choi Seungho , Mehrotra Shikhar 
Published: August 2023

Abstract
Uncoupling protein 2 (UCP2) is an anion transporter in the mitochondrial matrix that controls ROS production, calcium influx, and C4 metabolites. It is regarded as a metabolic regulator. A lack of UCP2 has led to an extreme clinical score with higher oxidative stress and inflammation in autoimmune illness, even though elevated UCP2 has been found in many tumors and is known to be a potential target for tumor therapy. Uncertainty still exists regarding UCP2’s function in T cells. A significant rise in the Th2/Th1 ratio was seen in this work using CD4 cells from UCP2−/− mice. These cells exhibited an improved Th2 phenotype with decreased calcium influx, elevated iNOS expression, and elevated urea metabolism. CD4 cells were treated with NOC-18, a source of nitric oxide, or Genipin to demonstrate nitric oxide-mediated Th2 polarization (inhibitor for UCP2). There were more cytotoxic markers and Th2/Th1 double positive cells. The B16/F10 tumor cells were controlled in vitro in a tumor killing assay utilizing genipin-treated CD4 cells, according to the findings. However, in UCP2−/− mice, the severity of EAE worsened, and heterogenic Th2 cells were infiltrated into central nerves system. Our findings imply that the loss of UCP2 in CD4 increases Th2 polarization with a cytotoxic phenotype and may be relevant to various illnesses.
R01 CA250458, R01 CA236379
Tet2 deficient conventional dendritic cells contribute to clonal hematopoiesis inflammation and alter immune response
Authors: Franceski Alana Marie , Luca Francesca , Goel Paran , Crown Brittany , Kuznetsova Valeriya , Costa Amanda , Welner Robert 
Published: August 2023

Abstract
Clonal mutations accrue with age and 20% of the elderly have dominant clonal hematopoiesis. Mutations to demethylating enzymes (including Tet methylcytosine dioxygenase 2, TET2) are common in these patients and loss of functional TET2 in mature myeloid cells increases pro-inflammatory cytokine secretion (such as interleukin 6, IL-6) leading to immune cell dysfunction.
Our group investigated the impact of TET2 mutations in immune cells and effects of altered hematopoiesis on non-mutated cells in chimeric mouse models. We utilized an MxCre x Tet2fl/fl mouse model on a CD45.1 background. After polyinosinic:polycytidylic acid excision, bone marrow was collected and transplanted retro-orbitally into CD45.1/CD45.2 hosts. Peripheral blood was analyzed at 8-, 14-, 18-, and 24-weeks using flow cytometry to test for engraftment of Tet2−/− cells. Mice were taken down and marrow, spleen, and mediastinal lymph nodes (medLN) were analyzed at 18- and 24-weeks of age.
We saw increases by frequency and counts of TET2−/− cDCs in the spleen and medLNs along with reduced production of host cDCs. Specifically, there was a slight increase in TET2−/− cDC1s and frequency of mutant cDC2s was three times greater than host, indicating host cDCs are being outcompeted. Loss of Hdac2 acylation in TET2−/− cDCs causes sustained production of IL-6, influencing Th17 and Tfh cell production and inflammatory cytokine secretion. This suggests cDCs play a role in disease progression and altering immune response. Mutant and disease-exposed cDCs are being explored using scRNAseq and ATACseq in combination with functional assays to determine gene regulatory networks governing mutant pro-inflammatory mechanisms and consequences in the education of adaptive immunity.
Live bacterial ligands universally regulate mTOR activity but are not essential for homeostatic innate immunity
Authors: Song Baobao , Zhang Xuan , Steele Hope , Chou Chih-Hsing , Ferchen Kyle , Salomonis Nathan , Herro Rana , Grimes H Leighton 
Published: August 2023

Abstract
Multiple studies have reported significant impact of gut microbiota on hematopoiesis, including granulocyte development and functional defects. Germ-Free (GF) mice show developmental defects due to lack of live bacteria; underscored by the development of Altered Schaedler Flora (ASF), a community of 8 bacterial species sufficient to rescue developmental immune and gastrointestinal defects. Mimicking gnotobiosis by using antibiotics perturbs the microbiome systemically. Therefore, results from such studies may represent sequelae of the drug perturbation rather than simply modifying microbiota. We studied the impact of gut microbiota signals on murine hematopoiesis without antibiotics or fecal transfer. Namely, by using mice (from Taconic) generated by embryonic transfer of C57/Bl6 fertilized eggs into females with controlled microbiota, totaling 4 groups of mice: 1. GF; 2. ASF (no Gammaproteobacteria); 3. Excluded Flora (EF, includes Gammaproteobacteria); 4. WildR7 (wild mouse microbiome). We found no significant differences in either number or effector function of bone-marrow neutrophil granulocytes, myeloid progenitors, or stem cells. The single-cell genomic landscape of CD117+ bone-marrow progenitors confirmed flow analyses but revealed a profound defect in gnotobiotic hematopoietic signatures. Importantly, standard pathogen free C57/BL6 mice were inappropriate controls. While gnotobiotic mice likely receive inert TLR stimulation via bedding and food, the addition of any group of live bacteria was sufficient to rescue gene expression downstream of mTOR signaling. Such robust signatures could be considered so essential to life that they do not depend on any single bacterial clade.
This project is supported by NIH R01HL122661.
The DEAD box RNA helicase DDX3X is required in natural killer cells
Authors: Mukhopadhyay Eshana , Krishnamurthy Durga , Ohayon David , Tuazon Jasmine , Ali Ayad , Waggoner Stephen N 
Published: August 2023

Abstract
The X-chromosome linked RNA helicase DDX3X plays multiple roles in RNA metabolism and antiviral interferon responses. Some viruses, including SARS-CoV-2, usurp the function of DDX3X to support viral genome replication and evasion of antiviral interferon. These findings have led to development of DDX3X inhibitors as potential antiviral agents. However, somatic loss of function mutations in this helicase are linked to neurological disease and malignancies, including a form of non-Hodgkin’s lymphoma initiated in the natural killer (NK) cell lineage. Given the critical role of NK cells in antiviral and antitumor immunity, we sought to determine how inhibition of DDX3X could affect NK-cell biology. Constitutive (Ncr1-iCre) or inducible (Ncr1-iCreERT2) deletion of Ddx3x in Ncr1-expressing cells (i.e. NK cells) in mice resulted in a complete loss of peripheral NK cells. Addition of the DDX3X inhibitor RK-33 to in vitro cultures of NK cells resulted in a similar loss of cellularity, while deletion of Ddx3x blocked development of NK cells from progenitor cells in an in vitro culture on stromal cells. Preliminary analyses suggest that loss of DDX3X results in rapid cell death of committed NK cells. Partial preservation of early stages of NK-cell development in the bone marrow of male but not female Ncr1DDdx3x suggests that the Y-chromosome DDX3Y may compensate for loss of DDX3X in supporting NK-cell survival at the earliest stages of differentiation. We identify a crucial role for DDX3 helicases in the development and survival of NK cells that may have implications for the clinical use of DDX3 inhibitors as antiviral agents.
R01 AI148080
R01 AR073228
Single-cell transcriptome reveals the developmental progression of human ILCs from the bone marrow to lymph nodes
Authors: Hashemi Elaheh , McCarthy Colleen , Malarkannan Surammaniam 
Published: August 2023

Abstract
Innate lymphoid cells (ILCs) are largely tissue-resident and do not express clonotypic receptors. In humans, ILCs are primarily described within the mucosal tissues. However, their development and functions in the human draining lymph nodes (LN) and bone marrow (BM) are unknown. Here, we performed single-cell RNA sequencing to unravel the tissue-specific transcriptional profiles of 47,287 ILCs within the human abdominal and thoracic LNs and compared them with that of BM and spleen. We found a higher frequency of CD127+ ILCs in LNs than in BM or spleen. We identify different stages of early progenitors in BM including CD34+HSCs and NFIL3+ITGA4+TCF7+ EILP. Our data indicated BM ILC progenitor cells differentiate into a unique subset of IL7R+KIT+PLZF+ progenitor ILCs (pILCs) that are predominantly present in LNs. Transcriptomically, ILC3 are closer to pILCs compared to ILC1 and ILC2. Using unsupervised clustering, we defined three clusters of ILC1, six clusters of ILC3, and only a minimal presence of ILC2 in the LNs. ILC1 and ILC3 have clusters with a high level of heat shock protein genes including, HSPA1A, HSPA1B, and DNAJB and clusters possibly trafficking from BM with high level of chemokine receptor, CXCR4. ILCs from draining LNs are polyfunctional and can produce cytokines in response to cytokines in vitro. Our study is the first characterization of human ILCs in LNs that provides an in-depth understanding of ILC-mediated immunity in humans.
Primary immunodeficiency disorders (PID) or inborn errors of immunity : preliminary work West Africa Côte d’Ivoire
Authors: Siransy Liliane K , Adou A Honore , Kira Jokebed , Moussa N Salimata , Sery Jocelyne , Oura Doris 
Published: August 2023

Abstract
The immune system is a particularly sophisticated protection system. As a true guardian of our health, the immune system defends our body against external or internal aggressions. Sometimes, the immune system is not able to fight because it lacks or does not function properly causing an ineffective or absent immune response. Although more than 400 diseases exist, there is no data available in our country.
We analyze through a retrospective study carried out in the pediatric department at Hospital University Center, in Abidjan, between February and April 2022, involving 93 PID suspect children, the epidemiological, clinical, paraclinical and therapeutic aspects.
The average age of our patients was 2 years with extremes of 22 days to 15 years, with a male predominance: sex ratio of 1.45. The predominant geographical origin was Abidjan (85.32%). Consanguinity was found in 12.9%, death in siblings was found in 3.49% of patients. The most common clinical manifestations were repeated respiratory infections (60.71%), fever (16%), severe infections at least twice a year (13.04%), persistent fungal infections (12.90), thrive retardation in 48.7%. Abnormalities such as hyperleukocytosis (42.4%), neutropenia (29.23%), lymphopenia (16.44%), thrombocytopenia (38.36%) and mostly anemia (62.36%) were noted. Phagocytosis deficiency combined immune deficiencies and humoral deficiencies were respectively found at 95.16%, 89.78%.79.03%.
This work draws attention to the importance of PID which are often underdiagnosed, with absent or delayed treatment and poor prognosis. It is important to build a cohort with confirmed data to better support children with PID in our country.
no support
Proliferation, Plasticity, and Migration: Exploring the synergistic relationship between eosinophils and TH2 cells in development of HES-like syndrome
Authors: Trusiano Brie L , Allen Irving C 
Published: August 2023

Abstract
Aberrancies in eosinophil proliferation, activation and chemotaxis can lead to acute eosinophilic leukemia, paraneoplastic eosinophilia associated with T cell lymphoma and carcinomas, and Hypereosinophilic Syndrome (HES), respectively. HES is an idiopathic disease affecting humans and veterinary patients characterized by persistent eosinophilia (&gt;1,500 cells/uL) and eosinophilic infiltration of solid organs leading to increased morbidity and mortality. Previous studies have demonstrated the role of NF-κB inducing kinase, NIK, an upstream regulator of the noncanonical NF-κB signaling pathway, in development of a HES-like syndrome due to aberrant TH2 polarization in the Nik−/−murine model. However, the intricacies of eosinophilic granulopoiesis, eosinophil/neutrophil plasticity, and chemotactic ability has not been assessed during development of HES-like syndrome in Nik−/− mice. Here we show that loss of NIK potentially enhances eosinophilic chemotaxis to CCL11, enhances eosinophilic/neutrophilic plasticity, and affects granulopoiesis in the bone marrow and spleen beginning at the level of eosinophilic metamyelocytes, despite potentially decreasing the proliferative potential of these cells. Taken together, these results suggest that NIK and the noncanonical NF-κB signaling pathway plays a role in dictating the hematopoietic and chemotactic potential of eosinophils and highlights a synergistic relationship with TH2 cells and their respective cytokines during development of HES-like syndrome in Nik−/− mice. Overall, these findings warrant further study to better characterize the synergistic relationship described above to better understand development of HES and HES-like diseases.
Virginia-Maryland College of Veterinary Medicine and the Institute for Critical Technology and Applied Science