bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing the immunological variability in T cell/tumor interactions to identify a subpopulation of CD8+ T cells (Spark T cells) that drives succesful cancer immunotherapy
Authors: Cavazos Emanuel Salazar , Yeh Michael , Krishnan Anagha Yogam , Achar Sooraj , Jia Dongya , DeVoe Don , Altan-Bonnet Grégoire 
Published: August 2023

Abstract
Thousands of patients have benefited from the growing use of cancer immunotherapies. However, the success of these therapies can be highly variable. Strikingly, some murine tumor models show large variability in the outcome of cancer immunotherapies, even when the mice, tumor cells and anti-tumor immune cells injected into mice are all genetically identical. Here, we sought to analyze this variability in adoptive cell therapies, in order to identify the immune population driving this variability.
To search for the occurrence of large variability ex vivo, we extracted mouse TCR-transgenic CD8+ T cells, and co-cultured them with antigen-expressing tumor cells. By using multiplexed in vitro assays and single-cell analysis of thousands of samples, we identified conditions (e.g. cell numbers, antigen quality, tumor cell types) where large variations in the immune activation against cancer cells is observed even between technical replicates. We then developed a quantitative framework that uses statistical modeling and machine learning to extract useful information from this immunotherapeutic variability. Our framework allowed the prediction and identification of a rare population of naïve CD8+ T cells (“Spark T cells”) that is necessary and sufficient to spark massive anti-tumor immune reactions.
We are currently performing experiments to test the efficacy and functional significance of the identified immune population in vivo. We are also applying this framework in human TCR-engineered T cell blasts to identify the equivalent of the Spark T cells in humans. We envision this framework being applied to identify other relevant immune cell types that act as catalysts for successful cancer immunotherapies.
Supported by the Intramural Research Program of the National Institutes of Health, the National Cancer Institute
Salt-induced maladaptive innate immune memory impedes stroke recovery
Authors: Lin Tze-Yen , Chen Wan-Ru , Lin Jhih Syuan , Chen Chih-Hung , Chang Che-Feng 
Published: August 2023

Abstract
A high salt diet (HSD) is a top risk factor for human mortality. Beyond its heavily implicated role in hypertension, it is now linked to the development of inflammatory diseases before the onset of cardiovascular events. Even after salt reduction, HSD can induce prolonged tissue damage, yet the mechanisms by which HSD induces persistent negative effects on immune system are largely unexplored. While HSD is an established risk factor for stroke, its impact on long-term stroke recovery is unknown. Here, we model two major stroke types, intracerebral hemorrhage, and cerebral ischemia, to investigate how HSD induces unfavorable immune responses and subsequently impacts long-term tissue repair. We found HSD exclusively hampers alternative activation in monocytes-derived macrophages (MDMs) while sparing the major parenchymal macrophage—microglia—in the stroke brain. HSD induces innate immune memory in the hematopoietic stem and progenitor cells through downregulating mitochondrial oxidative phosphorylation and NR4a orphan nuclear receptors expression. This immunological memory was retained in the brain-infiltrating MDMs and restrained their reparative functions. Consequently lead to impaired tissue repair and neurobehavioral recovery during stroke recovery phase. Pharmacological treatment with NR4a1 activator and genetic overexpression of NR4a1 restored MDMs reparative phenotype suppressed by HSD and enabled stroke recovery. These findings establish a new mechanism linking HSD-induced maladaptive innate immune memory to a hindered macrophage alternative activation and delayed tissue recovery. Our data unveil innate immune memory and NR4a1 as potential therapeutic targets for treating HSD-associated diseases.
Dysregulation of circulating MAIT cell subsets in patients with hidradenitis suppurativa
Authors: Toor Jugmohit , Dimitrion Peter Michael , Hans Aakash , Hamzavi Iltefat , Zhou Li , Mi Qing-Sheng 
Published: August 2023

Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory condition characterized by painful and debilitating skin lesions. Recent reports purport HS as an autoinflammatory keratinization disease with numerous pathways and features of systemic inflammation however few studies have been conducting to characterize peripheral immune dysregulation. Mucosal associated invariant T (MAIT) cells are an invariant T cell subset responding directly to bacterial threats and their dysregulation contributes to the pathogenesis of autoimmune disorders, cancers and inflammatory skin conditions. Here, we analyzed MAIT cells in the blood of 16 HS patients and 12 healthy controls (HC) by flow cytometry. We found that the frequency of MAIT cells did not change in HS patients, but their function changed drastically. We observed a significant reduction in the frequency of IFNy+ and TNFα+ MAIT cells in the periphery of HS patients. Furthermore, we analyzed MAIT cell subsets by their CD4 surface expression. Here, we found that the frequency of CD4+MAIT cells in the periphery of HS patients is significantly increased, while the frequency of CD4-MAIT cells is significantly decreased. Furthermore, HS patients have a reduction in CD4− IFNg+ and TNFa+ MAIT cells. Overall, these findings suggest that peripheral MAIT cells are dysregulated in HS patients which may contribute to the pathogenesis of the disease.
NIH/NIAMS (1R21AR079089 and 1R01AR078688) for Dr. Mi and Henry Ford Immunology Program grant (T71017 for Dr. Mi and T71016 for Di Zhou).
Peripheral T helper CD4+ cells mediate autoimmunity in Aire-deficient model of chronic inflammatory demyelinating polyneuropathy
Authors: Seyedsadr Maryamsadat , Su Maureen 
Published: August 2023

Abstract

Background
Chronic inflammatory demyelinating polyneuropathy (CIDP) occurs spontaneously in NOD mice with Aire deficiency (NOD.AireGW/+). The disease is mainly driven by CD4+ cells. However, the contribution of different CD4+ T cell subsets to the pathogenicity of neuropathy is not well studied.

Results
scRNA-seq of the immune cells infiltrating the sciatic nerves show that the majority of the CD4+ cells express genes associated with T follicular helper (Tfh) and T peripheral helper (Tph) cells, a newly described T helper type. Tph cells are similar to Tfh cells as they have prominent expression of ICOS, PD1, and IL-21. These IL-21+ Tph cells are also IFN-γ, IL-10 and CXCR6 positive, suggesting an effector phenotype. We verified high levels of IL-21 expression in Tfh and Tph cells in spleen and nerves by flow cytometry using IL-21 reporter mice. Transfer of CD4+ IL-21+ cells from NOD.AireGW/+ donor mice to immunodeficient mice resulted in higher neuropathy incidence than transfer of CD4+ IL21− cells. In adoptive transfer model, inhibition of Tfh specific transcription factor BCL6 decreased the frequency of Tfh and Tph cells in the peripheral nerves and protected against neuropathy development.

Conclusion
IL-21 producing Tfh and Tph cells may play a major pathogenic role in neuropathy development and suggests new therapeutic targets for CIDP.

Supported by grants from NIH
Triplication of HSA21-encoded genes modulates Alzheimer’s Disease-related phenotypes in vivo
Authors: Araya Paula , Schade Kyndal A , Waugh Katherine A , Busquet Nicolas , Brindley Connie , Winkler Caitlin , Dunn Lauren N , Siegenthaler Julie , Lyford Hannah R , Britton Eleanor C , Brown Chrisstopher , Ludwig Michael , Kinning Kohl , Galbraith Matthew D , Espinosa Joaquin M , Sullivan Kelly D 
Published: August 2023

Abstract
People with Down syndrome (DS), the genetic condition caused by Trisomy 21 (T21), exhibit early appearance of Alzheimer’s disease (AD), likely due to the triplication of the Amyloid Precursor Protein (APP) gene. However, the impact of many chromosome 21 (HSA21) genes on AD phenotypes in the context of DS remains unknown. To test this, we conducted a detailed phenotypic characterization of how AD-related neuropathology is modulated by an extra copy of genes orthologous to HSA21 by creating a novel DS-AD mouse strain, by crossing Dp16 with 5xFAD mice (models for DS and AD, respectively), generating: WT, Dp16, 5xFAD, and 5xFAD-Dp16 mice. Here, we performed a battery of behavioral assessments longitudinally and paired these analyses with endpoint transcriptional profiling and high-content imaging. We identified that DS-AD mice exacerbate cognitive deficits and show increased neuronal cell loss in multiple brain regions compared to DS and AD mice. Although, DS-AD mice do not present altered amyloid-β (Aβ) pathology compared to AD mice at 9-months of age, an increased number of activated microglia associated to Aβ plaques are present with a distinct transcriptional signature indicative of disease associated and interferon-activated microglia cells in these animals. These results indicate that DS contributes to the neuroinflammation network of AD, causing changes in cellular states consistent with alterations in memory and cognitive decline. However, deeper characterization is needed to understand the mechanisms by which T21 contributes to AD-pathogenesis to determine potential therapeutic intervention to significantly improve neurological health in people with DS. Supported by grants from NIH (R01AI145988 and R01AI150305).
Supported by grants from NIH (R01AI145988 and R01AI150305)
Characterization of the transcriptome and TCR of brain and cerebrospinal fluid infiltrated CD8+ T cells in an Alzheimer’s disease mouse model
Authors: Chen Joseph Ruixin 
Published: August 2023

Abstract
Alzheimer’s disease (AD) is a common form of dementia characterized by the accumulation of protein aggregates in the brain of older adults. It has been observed that CD8+ T cells, particularly CD8+ TEMRA cells, infiltrate the brain and cerebrospinal fluid (CSF) of AD patients. However, the precise role of these cells in the development and progression of AD is not well understood. In this study, we used single-cell RNA sequencing (scRNAseq) and single-cell T cell receptor sequencing (scTCRseq) to examine the CD8+ T cells in the brain and CSF of a mouse model of AD (5xFAD) and its wild-type (WT) littermate controls. The AD mice (age 40–70 weeks) used in our experiments have developed memory deficits. Our analysis revealed a significant increase in the number of CD8+ T cells in the brain and CSF of AD mice compared to WT controls (n=4, p&lt;0.05). Furthermore, these cells displayed a distinct transcriptome profile characterized by increased expression of inflammatory pathways, compared to WT mice. Through TCR sequence analysis, we also observed significant clonal expansion of CD8+ T cells in AD mice compared to WT mice. These findings provide a starting point for further investigation into the role of infiltrating CD8+ T cells in the pathogenesis of AD in this mouse model.
Aiolos restrains acquisition of a cytotoxic program by CD4+ T cells
Authors: Jones Devin M , Read Kaitlin A , Pokhrel Srijana , Tuazon Jasmine , Leonard Melissa R , Salem Miriam , Varkey Aditi , Warren Robert , Collins Patrick L , Oestreich Kenneth 
Published: August 2023

Abstract
CD4+ cytotoxic T lymphocytes, or CD4-CTLs, comprise a CD4+ subset capable of performing functions normally observed in CD8+ T and Natural Killer cells. CD4-CTLs play critical roles in many immune contexts, including protective anti-viral responses to viruses such as SARS-CoV-2 and influenza. Despite their well-documented importance, the complete mechanisms that underlie their formation remain unclear. Here, we define the transcription factor Aiolos as a novel repressor of CD4-CTL differentiation. We find that Aiolos deficiency results in increased CD4-CTL responses in lungs of influenza-infected mice, as assessed by elevated expression of Granzyme B and Perforin, as well as the CTL marker NKG2A/C/E. We further find that Aiolos-deficient CD4-CTLs exhibit increased expression of transcription factors associated with cytotoxic programming, including Eomes and Blimp-1. Mechanistically, we find that Aiolos-deficient cells have a heightened sensitivity to IL-2/STAT5 signaling due to enhanced expression of IL-2 receptor subunits. This translates into increased chromatin accessibility and STAT5 association at regulatory regions of hallmark CD4-CTL genes in the absence of Aiolos. Consistent with these data, in silico analyses demonstrate that STAT5 DNA-binding motifs are significantly enriched at these same regions. Intriguingly, the STAT5 motif partially overlaps with that of the core Aiolos DNA binding motif, suggesting that Aiolos may function to broadly antagonize STAT5 activity throughout the genome. Collectively, this work establishes Aiolos as a novel repressor of cytotoxic programming in CD4+ T cells and highlights its potential as a therapeutic target for enhancing anti-viral immunity.
This work was supported by grants from The National Institutes of Health AI134972 and AI127800 to K.J.O, AI156411 to P.L.C. K.A.R. is supported by funding through The Ohio State University College of Medicine Advancing Research in Infection and Immunity Fellowship Program. J.A.T. and S.P. are supported through funding from the Infectious Disease Institute T32 in Host-Microbe Interactions fellowship.
CD4 T cell intrinsic arginase 1 controls the kinetics of Th1 induction and contraction
Authors: West Erin E , Merle Nicolas S , Kamiński Marcin M , Palacios Gustavo , Kumar Dhaneshwar , Wang Luopin , Overdahl Kristen , Jarmusch Alan K , Freeley Simon , Taylor Naomi , Sitbon Marc , Green Douglas R , Bohrer Andrea , Mayer-Barber Katrin , Afzali Behdad , Kazemian Majid , Scholl-Buergi Sabine , Karall Daniela , Huemer Martina , Kemper Claudia 
Published: August 2023

Abstract
Arginase 1 (ARG1), the enzyme catalyzing the conversion of arginine to ornithine and urea, is a hallmark of IL-10 producing immunosuppressive M2 macrophages, however ARG1 activity in T cells is disputed. Here we demonstrate that Arg1, but not Arg2, expression induction is a key feature of lung CD4 T cells during mouse in vivo influenza infection. Ablation of CD4 T cell-intrinsic Arg1 unexpectedly accelerated both the virus-specific Th1 effector response and its IL-10-associated contraction. Biologically, this led to efficient viral clearance, yet significantly reduced lung pathology. Surprisingly, loss of Arg1 in CD4 T cells did not result in disturbed intracellular ornithine or polyamine levels. Instead, by employing unbiased transcriptomic and metabolomic approaches, we found that Arg1 deficiency triggered altered glutamine metabolism, and rebalancing the glutamine flux normalized the Arg1 deficient T cell response. Further, the role of Arg1 in CD4 T cells was distinct from that of its’ isoenzyme Arg2, as ablation of CD4 T cell intrinsic Arg2 resulted in normal Th1 responses, and instead altered Th2 and Th17 responses. Finally, CD4 T cells from rare patients with a deficiency in ARG1, or from healthy donors with CRISPR-Cas9-mediated ARG1 deletion, recapitulated the mouse data, demonstrating that ARG1 also plays a CD4 T cell intrinsic role in human Th1 responses. Collectively, CD4 T cell-intrinsic ARG1, functions as an unexpected pace-keeper of human and mouse T helper 1 (Th1) responses with implications for Th1-associated tissue pathologies.
Supported by grants from NIH (5K22HL125593 to M.K.) the Intramural Research Program of the NIH (NIDDK ZIA/DK075149 to B.A. and NHLBI ZIA/HL006223 to C.K.)
Direct and Indirect type I Interferon signaling regulates Eomes-driven Th1-responses against Influenza Virus
Authors: Dhume Kunal , Finn Caroline M , Baffoe Eugene , McKinstry Kai 
Published: August 2023

Abstract
In the absence of Th1 master regulator, the T-box transcription factor, T-bet, CD4 T cells primed by Influenza A Virus (IAV) infection, gain Th17 attributes while still retaining robust Th1 functionality. We recently found the transcription factor Eomesodermin (Eomes), to regulate this residual Th1 identity of T-bet−/− CD4 T cells. However, it is unclear how Eomes is regulated in CD4 T cells, especially during antiviral responses. Here we find type I interferons to be potent inducers of Eomes but not of T-bet in naïve antigen specific CD4 T cells stimulated in vitro. Furthermore, blocking type I IFN signaling to T-bet−/− CD4 T cells in IAV infected WT host mice, reduces Eomes expression and drives functional shifts mirroring T-bet−/− Eomes−/− cells, including significantly reduced IFNγ production and stronger Th17 identity. To test the impact of direct type I IFN signals on Eomes-driven Th1 identity of T-bet−/− CD4 T cells, we compared the responses of T-bet−/− CD4 T cells versus T-bet−/− cells also deficient for type I IFN receptor. While the Th1 attributes of the double-deficient cells were compromised compared to T-bet−/− cells, T-bet−/− cells responding in hosts treated to block systemic type I IFN signaling were the most impacted. These results indicate a strong role for indirect type I IFN signals in regulating Eomes-dependent functions during antiviral CD4 T cells responses. Finally, we find depletion of plasmacytoid dendritic cells in IAV infected host mice, a major source of type I IFN, does not impact T-bet−/− CD4 T cell response. Together, these results identify an important axis controlling the expression of Eomes in antiviral CD4 T cells that may in the future be harnessed to fine-tune effector and memory attributes primed by vaccination
Supported by grants from NIH (R01 AI67994 and R21 AI146647)
Rare Factor VIII-reactive CD4 T cells in non-hemophilic blood characterized by ex vivo expansion and ELISPOTs with added costimulation
Authors: Vir Pooja , Pratt Kathleen P 
Published: August 2023

Abstract

Background
Autoimmune responses to self-FVIII can cause a rare but potentially life-threatening autoimmune bleeding disorder referred to as “acquired hemophilia A”.

Objectives
(1) To confirm the frequency and specificity of CD4 T cells recognizing factor (F)VIII in the periphery of non-hemophilic individuals; (2) to improve methodology for detecting rare self-reactive CD4 T cells that apparently escaped thymic editing.

Methods
CD4 T cells were isolated from healthy non-hemophilic blood donors, incubated with autologous irradiated PBMCs, and stimulated with FVIII 15-mer peptides, anti-CD28 and anti-CD49D. Positive interferon-gamma ELISPOT responses were detected, but they were poorly reproducible due to the low frequency of these autoreactive cells. Therefore, pre-expansion of FVIII-specific T-cell lines, followed by ELISPOT assays with added co-stimulation, was carried out to increase sensitivity and accuracy.

Results
Several immunodominant epitopes in FVIII restricted to H LA-DRB1* 01:01, 07:01 and 15:01 were identified. FVIII-specific T-cell lines generated from individual blood donors showed robust interferon-gamma secretion in response to FVIII, compared to ELISPOT assays with co-stimulation but no FVIII pre-expansion.

Conclusions
Our optimized protocol, involving generation of antigen-specific T-cell lines followed by ELISPOTs with added co-stimulation, shows promise for detecting, quantifying and characterizing rare autoreactive T cells in the periphery.

Intramural funds, Uniformed Services University
TIGIT limits anti-bacterial immunity and is a potential target for immunotherapy
Authors: Souza-Fonseca-Guimaraes Fernando , Rossi Gustavo Rodrigues , Wells Timothy , McCulloch Timothy Ryan 
Published: August 2023

Abstract
Inhibitory receptors called “immune checkpoints” restrict overzealous immune responses during inflammatory events such as infection or cancer. Blocking the function of these immune checkpoints using monoclonal antibodies can tip the balance towards immune activation and disease clearance, which has been a revelation in the treatment of various cancers. Considering recent advances have shown that immune dysregulation and evasion are shared hallmarks of cancer and persistent bacterial infection, a better understanding of immune checkpoints during bacterial infection may uncover novel therapeutic targets to help direct host immune responses towards clearing pathogens.
In this study, we use a murine model of Salmonella Typhimurium infection to investigate how immune checkpoints regulate immunity to bacterial infection. We found lymphocytes from infected mice exhibit a phenotype suggestive of dysfunction, characterised by upregulation of multiple co-inhibitory checkpoints. Most strikingly, T cell immunoglobulin and ITIM domain (TIGIT) was upregulated on the majority of CD4+ T cells. We used RNA-sequencing and ex vivo stimulation of CD4+ T cells to show that ligation of TIGIT leads to significant functional deficiencies, including reductions in proliferation and pro-inflammatory cytokine production. Importantly, blockade of this immune checkpoint in vivo using anti-TIGIT antibodies was able to enhance functional immunity leading to improved bacterial clearance. Taken together, this research suggests targeting immune checkpoints such as TIGIT has potential to restore host immune responses towards clearing bacteria and managing serious infection.
F.S.F.G is funded by a UQ Frazer Institute Laboratory Start-Up Package, and T.R.M. is supported by a UQ HDR PhD Scholarship.
T cell-intrinsic C5L2 activation protects against uncontrolled inflammatory Th responses and autoimmunity
Authors: Merle Nicolas S , Freeley Simon , Bibby Jack , Singh Parul , Rahman Jubayer , Kolev Martin , Niyonzima Nathalie , Morgensen Trine Hyrup , Woodruff Trent M , Monk Peter , Lappegard Knut , Espevik Terje , Mollness Tom Eirik , Christiansen Mette , West Erin E , Kemper Claudia 
Published: August 2023

Abstract
Intracellular/autocrine complement proteins have emerged as critical regulators of human Th1 induction and contraction. T cells contain both intracellular C3 and C5 activation systems, with intracellular C3aR1 and C5aR1 stimulation driving T cell homeostatic survival and normal Th1 IFNg production, respectively. Here we demonstrate how the intracellular/autocrine C5 system is regulated by using T cells from the first described patient with C5aR2 deficiency. This patient suffers from an autoinflammatory syndrome, with enhanced inflammatory Th responses and a profound loss of naïve CD4 T cells in the blood (95% have a memory phenotype). Thus, in contrast to intracellular C5aR1 stimulation, cell surface expressed C5aR2 is an important negative regulator of inflammatory Th induction. While both C5aR1 and C5aR2 can bind C5a, we found that the carboxypeptidase-processed form of C5a, C5a-desArg, was twice as potent as C5a in reducing Th1 induction. In addition, carboxypeptidase M (CPM) expression was highly induced upon T cell activation indicating that CPM may be mediating T cell-derived C5a-desArg generation and C5aR2 stimulation. In this vein, activation of CRISPR/Cas9 generated CPMKO T cells, or of T cells in the presence of a CPM inhibitor, induced Th1 hyper-induction, which was rescued by addition of a C5aR2 agonist and reduced by adding C5a-desArg, but not C5a. The in vivo importance of T cell-expressed CPM and autocrine C5aR2 activation is demonstrated by the enhanced inflammatory Th responses in Cpm−/− mice and increased pathology caused by Cpm−/− T cells in a T cell transfer colitis model. These data highlight the importance of intracellular/autocrine C5 system regulation by CPM through C5aR2 signaling in T cell responses.