bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of the Pentose Phosphate Pathway in Cytotoxic T Lymphocytes Preserves Neuronal Function and Ameliorates Neuroinflammatory Disease
Authors: Grund Ethan , Clarkson Ben D S , Howe Charles L 
Published: January 2023

Abstract
In diseases such as multiple sclerosis and autoimmune encephalitides, activated CD8+ cytotoxic T cells infiltrate the brain and are found in clonally expanded clusters that outnumber CD4+ cells in progressive stages of disease. At present, the pathophysiological role of these cells is poorly understood and therapeutic strategies for preventing or ameliorating autoinflammatory disease progression are limited. T cells exhibit profound metabolic reprogramming that facilitates the energetic and proliferative demands of effector T cells. Key metabolic pathways in this reprogramming include upregulation of glycolysis and the pentose phosphate pathway (PPP). Here we show that 1) pharmacologic inhibition of the PPP suppresses effector phenotype acquisition and proinflammatory cytokine secretion by CD8+ T cells; 2) engagement of the PPP is enhanced by pharmacologic Nrf2 activation, implicating reactive oxygen species-induced activation as a transcriptional regulator of PPP-dependent immune activation; 3) Nrf2-driven PPP flux promotes the acquisition of specific CD8+ effector phenotypes; 4) limiting the metabolic flux of glucose-derived metabolites through the PPP prevents CD8+ T cell-mediated injury of neurons expressing cognate antigen and preserves their electrophysiological function; and 5) pharmacologic inhibition of the PPP in B6 mice at symptom onset is sufficient to delay and ameliorate motor disability in the MOG EAE preclinical model of MS. Overall, these results underscore the potential of immunometabolic therapies to limit T cell mediated injury in autoinflammatory and autoimmune diseases across organ systems including the prevention of neurologic deficits in patients with T cell driven neurologic disease.
This work was supported by the NIH (R01NS115126 to CLH; T32GM065841 to EMG), the Mayo Clinic Graduate School of Biomedical Sciences, the Mayo Clinic Center for MS and Autoimmune Neurology, and generous donations from Eugene and Marcia Applebaum, Donald J. and Frances I. Herdrich, Bob and Loralee Marvin, and Rob and Debbie Mudge.
Characterization of thymic epithelial cell and thymocyte function and development in patients with thymic defects using scRNAseq profiling
Authors: Bosticardo Marita , Pala Francesca , Oguz Cihan , Branco Mackenzie , Zhao Chen , Carr Shamus R , Rajan Arun , D’Udekem Yves , Delaney Meghan , Notarangelo Luigi D 
Published: January 2023

Abstract
The interaction between thymocytes and thymic epithelial cells (TEC) in the thymus is critical for the correct function and maturation of both cell populations and for the development of a diverse repertoire of non-self-reactive T-cell lymphocytes. Limited information is available on lympho-stromal crosstalk in the thymus of patients carrying thymic defects. We have previously shown that thymic tissues from DiGeorge syndrome (DGS) and Down syndrome (DS) patients have alterations in architecture and TEC composition, leading to altered T-cell development. Based on these results, we are performing single cell RNAseq (scRNAseq) to explore the transcriptional landscape of both stromal and hematopoietic components in the human thymus. Thanks to a collaboration with the pediatric cardiothoracic surgery center at the Children’s National Medical Center in Washington D.C., we have access to discarded thymic samples obtained from pediatric patients with partial DGS and DS, and from patients without immune defects. Preliminary results of scRNAseq analysis comparing tissues from normal donors and DS patients revealed a different distribution of cell subsets in both hematopoietic and stromal compartments, with several pathways differentially regulated, such as stress and metabolic processes. Additionally, we established a collaboration with the Thoracic and Gastrointestinal Malignancies Branch at the National Cancer Institute and are evaluating samples obtained from resected thymic epithelial tumors. Integration of data obtained from normal and diseased thymic tissue will provide novel insights into the function and development of the human thymus that could be helpful in the clinical management of patients with thymic defects.
This research was supported by the Intramural Research Programs of the NIAID and the NCI (Center for Cancer Research), NIH
Immune and hematological disorders in Primary Immunodeficiency in children
Authors: Fazal Nadeem , Nasrullayeva Gulnara M , Mammadova Vafa R , Aliyeva G Z , Babayeva B A 
Published: January 2023

Abstract
Primary immunodeficiency (PID) was previously considered an extremely rare pathology in childhood, now it has been established that congenital deficit of quantity and functional activity of the lymphocytes, platelets and neutrophils occurs in 1:500–1:4000 newborns. Severe chronic neutropenia in PID is characterized by a stable decrease or absence of circulating neutrophils (&lt;500/cm) and accompanied with recurrent bacterial skin and lung infections. We identified 135 patients with PID. Patient’s examination included clinical observation, general blood test, immunological tests, X-ray of chest and ultrasound examination. We report that six children with PID had significant hematological disorders. The age of these patients was from 1 month to 13 years. Four of them were born from consanguineous marriages, 3 patients died before the age of 5 years. 2 patients with PID had congenital neutropenia, repeated skin infections, pneumonia, diarrhea, stomatitis. Two brothers with WAS syndrome had repeated bleeding, skin hemorrhages, anemia, lymphadenitis, hepatosplenomegaly. The platelet count was about 30–70/ml. Genetic analysis in these patients revealed a hemizygous c.12_13insGG mutation in exon 1 of the WAS gene. 2 children with SCID were found to be carriers of thalassemia B. All our patients showed a significant decrease in Ig classes, CD3+, CD4+, CD8+ and NBT test. We conclude that patients with suspected PID should be continuously monitored by Immunologists and Hematologists. Timely detection of hematological disorders in patients with PID allows for correct diagnosis and prevents fatal complications. Genetic testing can help in making a definitive diagnosis.
Supported by Azerbaijan Medical University
Analysing the cellular mechanisms underlying activated PI3K δ Syndrome (APDS) reveals differences between APDS1 and APDS2
Authors: Deenick Elissa , Lau Anthony , Nguyen Tina , Bier Julia , Brink Robert , Tangye Stuart 
Published: January 2023

Abstract
APDS is a primary immunodeficiency condition caused by heterozygous gain-of-function mutations in PIK3CD (APDS1), which encodes the leukocyte-restricted p110-δ catalytic subunit of phosphoinositide 3-kinase (PI3K) or heterozygous loss-of-function mutations in PIK3R1 (APDS2), which encodes the regulatory subunit of PI3K. PI3K is activated downstream of many receptors expressed by lymphocytes and plays important roles in their activation and differentiation. The increased PI3K activity in cells from APDS patients leads to multiple immune manifestations including lymphoproliferation, respiratory tract infections, Th2-related pathologies, impaired Ab responses and autoimmunity.
We previously dissected the cellular defects that lead to disease in APDS1 by studying patient cells and our novel mouse model. This revealed changes in lymphocytes including increased memory T cells, defective Tfh function, decreased isotype switching and a break in B cell tolerance and production of autoantibodies. We have now generated a mouse model of APDS2 (Pik3r1E11SpD) and use this together with studies of patients’ cells to determine whether increased PI3K signalling due to loss of regulatory function causes the same cellular dysregulation. While we observed many of the same changes previously observed in APDS1, including altered cytokine production and decreased isotype switching, we also identified multiple differences in the cellular phenotype in APDS2 compared to APDS1.
Together, these studies reveal that although APDS1 and 2 both cause increased PI3K signalling and result in similar clinical phenotypes, there are distinctions between how these two types of mutations affect cellular function.
Supported by grants from the NHMRC and an AAI Careers in Immunology Fellowship
Dysfunction in B cell tolerance and activation in obesity.
Authors: Vanz Carlo , Hägglöf Thomas , Dudley Elizabeth A , Leadbetter Elizabeth 
Published: January 2023

Abstract
Obesity is a complex condition that affects a large part of the global population, making it a major risk factor for premature mortality and medical complications. Obesity profoundly engages the immune system, impacting cancer immunity, infections, and autoimmunity. Additionally, obesity is associated with a low-grade chronic inflammation which exacerbates metabolic dysfunction. B cells play a significant role in obesity-associated inflammation and metabolic dysfunction, but their effect is subset-dependent and can be either protective or pathogenic. Therefore, understanding how different B cell populations contribute to these phenotypes represent a crucial goal.
Our lab has identified a subset of B lymphocytes which is expanded in the adipose tissue of humans and mice during obesity. These B cells co-express the transcription factor T-bet and the integrin CD11c, and they produce IgG2c antibodies. In vivo studies with mice fed a high fat diet revealed that these Tbet+ B cells promote inflammation through the production of proinflammatory antibodies. Additionally, these B cells express high levels of the scavenger receptor CD36, a lipid-transport molecule associated with inflammation and atherosclerosis. As a potential consequence of the CD36 expression, the Tbet+ B cells maintain a higher intracellular lipid content and are capable of increased uptake of oxidized LDL compared to conventional B cells, suggesting a unique lipid metabolism.
Because of their unique nature, T-bet+ B cells represent a potential link between obesity, inflammation, and autoimmunity. Identifying the mechanisms regulating their function will provide new potential targets to reduce inflammation and immunological dysfunction in obese patients.
Supported by R01 AI132798
Diet-induced obesity promotes CD11c+ T-bet+ B cell expansion in liver and adipose tissue
Authors: Enslow Benjamin , Vanz Carlo , Dudley Elizabeth A , Hägglöf Thomas , Leadbetter Elizabeth A 
Published: January 2023

Abstract
Immune cells are increasingly appreciated to play a role in inflammation in adipose and hepatic tissue during obesity and may contribute to the development of non-alcoholic fatty liver disease (NAFLD). Both invariant Natural Killer T (iNKT) cells and B cells are enriched in the liver and adipose tissues of humans and mice, but the degree and nature of their influence in the development of NAFLD remains unclear. iNKT cells interact with B cells in many contexts, including during the chronic inflammation associated with autoimmune disease and infection, so it is likely they interact during obesity. Emerging evidence implicates intrahepatic B cells in the progression of human NAFLD, and proinflammatory B cells increase in the steatotic livers of HFD-fed mice. Our preliminary studies demonstrate an iNKT cell-dependent expansion of inflammatory CD11c+ T-bet+ B cells in the subcutaneous adipose tissue of obese humans and perigonadal adipose tissue of obese mice. We now extend those findings to other iNKT cell-rich fatty depots. Flow cytometry identified increased frequencies of T-bet+ B cells in the livers, but not the omenta or mesenteric adipose tissue, of obese mice. In parallel to the in vivo studies, in vitro co-cultures revealed that iNKT cells are sufficient to mediate expansion of T-bet+ B cells. Ongoing experiments will examine the potential role and mechanism of iNKT cells in mediating hepatic Tbet+ B cell expansion. Characterization of the specific contribution of immune inflammation in the progression NAFLD to NASH will allow for the design of successful therapeutic interventions for this increasingly frequent public health problem.
Funding support from NIH K12GM111726 (BTE), NIH TL1 TR002647 (TS), Swedish Research Council (TH), and NIH R01 AI32798-01A1 (EAL).
A gut feeling about Complement in Early Onset Colorectal Cancer
Authors: Anand Sudarshan , Affleck Arthur , Gardner Ivy , Watson Katherine , Ruhl Rebecca , Tsikitis Liana V 
Published: January 2023

Abstract
Colorectal cancer (CRC) remains the second leading cause of cancer-related death in the United States, with a significant increase in incidence observed in young adults below the screening age. We hypothesized that differences in the immune tumor microenvironment (TME) between early-onset (≤50 years) and late-onset (≥65 years) CRC drives tumor progression and responses to treatment. Our studies in a cohort of 121 patients indicate that complement pathway genes including C7 and Complement Factor D (CFD) and the anti-apoptotic gene Bcl2 are significantly increased in early onset CRC vs late onset disease. Moreover, the immune genes in this signature also correlate with progression free survival in our cohort. Analyses of this signature in an independent TCGA cohort also shows association of these genes with progression free survival. Surprisingly, tumor intrinsic CFD gain of function experiments in preclinical mouse tumor models increased tumor burden and recapitulated a subset of the early onset human immune gene signature. Inhibition of CFD, in combination with a Bcl2 inhibitor, significantly decreased clonogenic survival in human CRC lines in vitro. Our data associates a distinct complement enhanced immune microenvironment and hints at a putative role for the microbiome in shaping this immune microenvironment in younger patients with more aggressive disease. Taken together, our work highlights complement and the innate immune response as a potential contributor to early onset CRC.
Supported by grants from NIH to SA (R01 HL137779 and R01 HL143803)
Circulating extracellular vesicles from patients with severe COVID-19 upregulate Cathepsin B and activate STAT3 in normal human mesangial cells
Authors: Glover Sarah C , Scindia Yogesh , Liu Lauren P , Dhaliwal Neha , Williams Haley , Pride Yilianys , Owings Anna H , Robinson Tanya , Alli Abdel A 
Published: January 2023

Abstract
Severe COVID-19 disease is associated with acute kidney injury in up to 57% of infected patients. The etiology of this is likely multifactorial. Extracellular vesicles (EVs) contain unique molecular cargo that contributes to health and disease in many different organ systems and can contain useful surrogate biomarkers. To gain insight into SARS-CoV2’s impact on the human kidney, we prospectively collected blood and urine from individuals hospitalized with severe COVID-19 infection and isolated EVs. Using these EVs, we investigated the impact of circulating EVs released during COVID-19 infection on healthy human glomerular mesangial cells. Nanoparticle tracking analysis and electron microscopy showed that EVs isolated from the plasma of COVID-19 patients were larger in size compared to those isolated from the plasma of non-COVID-19 patients, suggesting the presence of unique cargo within circulating EVs in the setting of COVID-19. The plasma derived EV’s from COVID-19 patients also increased glomerular cell proliferation, STAT3 activation, and cathepsin B protein expression in normal human glomerular cells when compared to EVs isolated from the plasma of non-COVID-19 patients. These data suggest systemic EVs during COVID-19 infection alter normal human mesangial cell function. and provide insight into the effects of SARS-CoV2 on the kidney.
This work was supported by the University of Florida College of Medicine and the University of Mississippi Medical Center.
Single-Cell Transcriptomics Of CD8 T Cells During CMV Viremia In Kidney Transplant Recipients Identify Transcriptional States Of Advanced Differentiation
Authors: Sen Subha , Pickering Harry C , Sun Yumeng , Parmar Rajesh , Reed Elaine F 
Published: January 2023

Abstract
Acute versus chronic viral infections define the dogma of strictly segregated pathways of generating memory or exhausted T cells. Paradoxically, chronic human cytomegalovirus (HCMV) infection elicits an inflationary T cell response with accumulation of progressively differentiated T cells occupying up to 30% of total CD8 T cells. The mechanisms of HCMV-driven memory T cell inflation remains poorly understood.
HCMV infection is asymptomatic but immunocompromised transplant recipients often experience clinical episodes of CMV viremia correlating with graft injury and mortality. We leveraged a defined clinical cohort of renal transplant recipients and profiled the T cells from 31 CMV PCR+ patients with/without prior CMV exposure and 31 matched PCR− controls at baseline, longterm post-transplantation and at 1wk and 1month post-viremia for PCR+ patients.
We observed contraction of naïve and central memory T cells and reciprocal expansion of terminal effector memory CD8 T cells post-viremia. ScRNASeq of CD8 T cells further defined early (CD28+CCR7+), transitional (CD28+GZMK+) and advanced (CD28-KLRG1+) stages of differentiation. Pseudotime analyses revealed specific transcriptomic modules and transcription factors associated with distinct CD8 T cell differentiation states. We report that HCMV induced progressively differentiated T cells with memory-progenitor features lacking inhibitory receptors but with stemness (kat6a, rnf138) and anti-apoptotic markers (bcl2, braf). Thus HCMV skewed the balance of CD8 T memory cells from pro-exhaustion to a prolonged non-classical memory phenotype. This study revealed important mechanisms underlying memory inflation over exhaustion in the setting of chronic antigen exposure.
This work was funded by NIH grant U19AI128913 to EFR.
Differential CD4+ and CD8+ T cell recognition of mycobacteria antigens in pediatric versus adult TB
Authors: Lancioni Christina , Morrow Erin , Liu Qijia , Swarbrick Gwendolyn , Kiguli Sarah , Nsereko Mary , Toerien Megan , Cansler Meghan , Lewinsohn David Michael , Lewinsohn Deborah 
Published: January 2023

Abstract
T cells from young children may be limited in capacity to mount pro-inflammatory responses to intracellular pathogens, thus contributing to vulnerability to TB disease. We compared CD4+ and CD8+ T cell cytokine production in response to mycobacterial antigens and mitogen SEB, between Ugandan children &lt;5 yr (PedTB) and adults (ATB) with culture-confirmed pulmonary TB. HIV-uninfected children (n=12) and adults (n=41) had blood drawn for PBMC isolation prior to TB treatment. CD4+ and CD8+ T cell production of IFNγ, IL2, and TNFα in response to ESAT6/CFP10 (EC), ESXJ, PE12/13, PE3, PPE15, and PPE51 peptide pools, and SEB, were assessed by intracellular flow cytometry. Proportions and frequencies of CD4+ and CD8+ T cells producing cytokines were compared using Fisher’s Exact and Kruskal-Wallis tests, respectively, with adjusted p-values &lt;0.05 significant. PedTB and ATB had equivalent CD4+ and CD8+ T cell production of IFNγ, IL2, and TNFα, including polyfunctional responses, to EC. T cell cytokine responses to ESXJ and PPE51 were equivalent; significant differences were noted in CD4+ T cell responses to PE3 and PPE15, and CD8+ T cell responses to PE12/13. Frequencies of CD4+ T cells producing IFNγ or IL2 in response to SEB were lower (p&lt;0.0001) in PedTB versus ATB. Young children with PedTB exhibited adult-like capacity to generate Th-1 cytokines in response to EC, ESXJ, and PPE 51. Pediatric responses to PE3, PPE15, and PE12/13 were impaired, suggesting that the breath of antigen recognition differs between infants and adults with TB. Differential T cell recognition of mycobacterial antigens between adults and children should be considered in development of novel T cell based diagnostics and vaccines targeting pediatric TB.
Supporting from grants by NIH: AI157807; HHSN272200900053C
Distinct Subpopulations of Mouse and Human Kidney Resident Macrophages in Acute Kidney Injury
Authors: Cheung Matthew David , Erman Elise , Lever Jeremie , Porrett Paige , Agarwal Anupam , George James 
Published: January 2023

Abstract

Introduction
Kidney resident macrophages (KRMs) are important in renal homeostasis and the response to acute kidney injury. Preliminary data suggests that the KRM population consists of several undescribed subpopulations. Here, we combined single-cell RNA sequencing (scRNAseq) and spatial transcriptomics to identify and localize KRM subpopulations during homeostasis and injury.

Methods
KRMs were isolated from C57BL/6J mice without treatment and after bilateral ischemia-reperfusion injury (BIRI) as well as from a human donor kidney. ScRNAseq was performed using the 10X Genomics Chromium platform and spatial transcriptomics using the 10X Visium platform. Gene expression data were integrated and analyzed using the R package, Seurat 4.0.

Results
UMAP plots of integrated data revealed seven major clusters of mouse KRMs with unique transcriptional profiles associated with distinct functions. Spatial transcriptomics revealed that these clusters reside in distinct cellular compartments within the kidney and appear to associate with specific renal structures. Following BIRI, these subpopulations appear in cellular compartments distinct from those occupied in the controls. Several human KRM clusters were correlated with those of the mouse and localized to specific regions of the kidney.

Conclusion
Transcriptionally distinct subpopulations of mouse KRMs reside within specific kidney microenvironments and change location as a function of injury. Similar subpopulations of KRMs were identified in the human kidney as well. Therefore, further study of the temporal and spatial characteristics and signaling pathways of these subpopulations in the context of homeostasis and injury is warranted.
Supported by grants from NIH (R01-DK-59600, T32-AI007051)
Role of CD73 on peritoneal macrophages in age-associated immune dysfunction and tumor immunity
Authors: Rivera-Escalera Fátima , McGinty Mitchell T , Rutkowski Melanie R , Murphy Patrick S , Elliott Michael R 
Published: January 2023

Abstract
Aging is a major risk factor for cancer and many other life-threatening diseases due in part to a wide range of age-associated immune dysfunctions. In the context of cancer, chronic, low-grade inflammation seen with aging is thought to contribute to cellular transformation and tumorigenesis. Tissue resident macrophages (TRM) are key innate immune regulators of the inflammatory milieu in all tissues, and studies from our laboratory have shown that expression of the 5’-ectonucleotidase CD73 on macrophages suppresses inflammatory responses and promotes the resolution of tissue inflammation in the lung and peritoneum. However, the role of CD73 on TRM in modulating inflammation during aging or how age-associated changes in CD73 on TRM contribute to cancer development are not known. We have found that large peritoneal macrophages from aged mice (18+ months) show significantly increased levels of surface CD73 compared to young mice (&lt;4 months). To test the role of CD73 in regulating inflammation in vivo, we utilized mouse models of ovarian cancer and peritonitis. Our preliminary studies suggest that blocking CD73 in aged mice reduces LPS-mediated production of TNF-a in vivo and ex vivo when compared to young mice. In addition, we found that treatment of ID8-Def29/Vegf-a tumor-bearing mice with anti-CD73 monoclonal antibody significantly prolongs the survival of aged mice compared to young mice. In ongoing experiments, we are utilizing conditional deletion approaches to address the role of CD73 specifically on macrophages in these models. Results from this study will provide insight into the immunoregulatory role of CD73 on TRM during aging and cancer, and will help refine therapeutic approaches targeting CD73 in cancer immunotherapy.
Supported by NIH grants T32 AI007496 and R01 AI114554.