bluuebunny/crossref_metadata_2025_split huggingface dataset:
CAR+ and CAR− T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion
Authors: Luciani Fabio , Louie Raymond Y , Cai Curtis , Singh Mandeep , Deveson Ira , Ferguson James , Amos Timothy , McGuire Helen , Samir Jerome , Gowrishankar Kavitha , Adikari Thiruni , Balderas Robert , Bishop David , Gottileb David , Blyth Emily , Micklethwaite Kenneth 
Published: August 2023

Abstract
Chimeric antigen receptor (CAR) T cells have demonstrable efficacy in treating B-cell malignancies. Factors such as product composition, lymphodepletion and immune reconstitution are known to influence CAR+ T cell survival and persistence, however the determinants of CAR+ T cells’ fate and differentiation and how the patients’ reconstituting immune system influence therapy outcomes remain poorly understood.
We applied single cell multi-omics analysis of RNA, protein and clonal profiles of CAR+ T and PBMC in patients receiving donor-derived products from a piggybac CAR19 clinical trial (N=8 patients). We used these data to reconstruct a differentiation trajectory, which explained the observed phenotype and fate of CAR+ and CAR− T cells within the first 30 days of post-infusion. Following initial lympho-depletion, endogenous CAR− CD8+, γδ T cells and CAR+ T cells clonally expanded, and differentiated across heterogenous phenotypes. They transitioned from a dominant resting or proliferating state into precursor of exhausted T cells, and finally into a terminal NK-like phenotype. The subset of terminal NK-like CAR+ T cells was associated with increased serum concentrations of proinflammatory cytokines including IL-12 and IL-18. Validation on a published cohort (61 patients) showed that this subset was associated with clinical outcome at 6 months. Finally, we analysed in detail one patient that developed CAR T cell induced lymphoma and discussed the impact of early phase therapy in determining this unexpected outcome.
These results demonstrate that CAR- and CAR+ T cells share a differentiation profile which may be determined by non-CAR derived signals and which may influence patients’ immune-recovery and outcome.
National Health And Medical Research Funding (Australia) (APP1121643, APP1128416) BD Bioscience
Combinatory analysis of immune cell subsets and tumor-specific genetic variants can predict clinical response to PD-1 blockade for non-small cell lung cancer patients
Authors: Dutta Nikita , Rohlin Anna , Eklund Ella Äng , Magnusson Maria , Nilsson Frida , Akyürek Levent , Torstensson Per , Sayin Volkan , Lundgren Anna , Hallqvist Andreas , Raghavan Sukanya 
Published: August 2023

Abstract
Blockade of PD-1/PDL1 (PD-1 blockade) with antibodies has revolutionized treatment options for non-small cell lung cancer (NSCLC) patients with tumors without targetable mutations. The benefit of PD-1 blockade is limited only to a subset of the patients. This study aims to identify biological markers of clinical response in a discovery cohort (n=15) of patients early during treatment to distinguish responders from nonresponders using immunological and genetic markers. Immune subsets identified in the blood are characterized to establish a panel of immune markers that could distinguish the two. Blood drawn from NSCLC patients before and after PD-1 blockade was analyzed by clinical flow cytometric assay for changes in the frequencies and concentration of immune cell populations. Next generation sequencing was performed on the extracted DNA from archival tumor biopsies from the same patients. irRECIST criteria was used to evaluate the clinical responses with cut-off at 10 months. Responders had a significantly increased frequency of activated effector memory CD4 & CD8 T cells & decreased frequency of central memory CD4 & CD8 T cells in circulation post-treatment compared to pre-treatment. In a separate cohort we validate initial findings in a cohort of n=29 & observe that effector memory CD8 T cells in responders produced high TNFα at pretreatment. Pathogenic & likely-pathogenic mutations in TP53, KRAS, KEAP1, NOTCH-1 and STK11 in the patients that responded to PD-1 blockade are observed. A multivariate analysis combining immune and genetic parameters could discriminate responders from non-responders. We report that combined analyses of selected immune cell & genetic parameters could predict early clinical response to PD-1 blockade.
Dendritic cell expansion and activation enhances the adaptive immune response against TNBC brain metastases
Authors: Conarroe Claire Ann , Bullock Timothy N 
Published: August 2023

Abstract
Despite initial control by chemotherapy, Triple Negative Breast Cancer (TNBC) quickly acquires resistance and metastasizes to distal organs, including the brain. Median survival following diagnosis of TNBC brain metastases is a meager 7.3 months—indicative of a substantial unmet clinical need, with only a small subpopulation responding to checkpoint immunotherapy. As suboptimal antigen presentation can contribute to the weak T lymphocyte response to intracranial tumors, we hypothesized that enhancing dendritic cell (DC) presence in tumors may support intracranial T cell responses to tumors. Using a murine model of intracranial metastasis, we assessed immune cell frequency and function and in vivo cytokine staining for flow cytometry to test whether Flt3L can be used to promote DC presence within tumors, and whether the addition of polyIC further enhances subsequent T cell responses.
Flt3L treatment effectively increases the number of DC within the brains and meninges of mice, however these newly expanded populations exhibit lower proportions of the costimulatory molecule CD86 than the untreated control group, indicative of an immature phenotype. 24 hours after polyIC treatment, a higher percentage of DCs in brain tumors express CD86 but do not produce IL-12. Despite the lack of intratumoral IL-12, the combination of Flt3L and polyIC treatments led to a higher presence of T cells within tumors and their production of IFN-γ in the TME than either treatment alone. In conclusion, simply increasing the presence of DC within intracranial tumors is insufficient to promote T cell immunity; rather, deliberate activation of de novo DC is required for this full effect.
Supported by grants from NIH (2T32CA009109-46 and 1R21CA226607-01A1) and the Schiff Foundation
Androgen signaling shapes the sexual differences of skin immunity by regulating ILC2 and dendritic cells
Authors: Chi Liang , Gribonika Inta , Corral Dan , Gschwend Julia , Han Seong-Ji , Lim Ai Ing , Link Verena , Wells Alex , Collins Nicholas , Bouladoux Nicolas , Schneider Christoph , Belkaid Yasmine 
Published: August 2023

Abstract
The skin immune system mediates the skin health status, but the sex differences of the skin immune system are still unclear. This study aims to investigate sex differences in the skin immune system and decipher the underlying regulatory factors. We found that female mice have a higher magnitude of adaptive immune responses during commensal bacteria association and pathogen infection. Correspondingly, females have a higher level of skin dendritic cells (DCs), which play a fundamental role in commensal-induced adaptive immune responses. These sex differences were regulated by male sex hormones, that castration of males normalized the sex differences in the level of skin immune cells as well as the adaptive immune responses to bacteria. However, our scRNA-seq data reveals that androgen receptor is not expressed in DCs, but highly expressed in skin ILC2. Females have a significantly higher level of ILC2 than males and ILC2 from females also have a more activating gene expression signature than ILC2 from males. Females also have a significantly higher level of ILC2-produced IL-13 and GM-CSF than male mice. In addition, our data reveal that IL-13 and GM-CSF play a critical role to maintain the level of skin DCs, that IL-13/GM-CSF deficient mice have a remarkable decrease of skin DCs, and the sex differences of DCs are also largely impaired. Therefore, based on these findings, we suggest that androgen signaling negatively regulates the level of skin ILC2 and DCs, thereby shaping sex-specific skin immunity to commensals, pathogens, and/or other stimuli. Collectively our work proposes a mechanism for the heighten immunity observed in female and have important implication for our understanding of tissue immunity in the context of infection and cancer.
Impaired mTOR Signaling Causes Immune Suppression in Diabetes
Authors: Genito Christopher J , Darwitz Benjamin , Thurlow Lance R 
Published: August 2023

Abstract
It is estimated that over 11% of the U.S. population has diabetes and that 38% of the adult population is pre-diabetic. Diabetes carries increased risk and severity of many infections, which has been attributed to defects in the innate immune system. Despite the high impact of diabetes on infection, the underlying mechanisms of immune dysfunction in the diabetic host have yet to be fully elucidated. We have recently shown that innate immune cells in a diabetic host environment cannot undergo respiratory burst of reactive oxygen species and nitric oxide in response to infection with Staphylococcus aureus, the most common pathogen associated with frequently severe and invasive skin and soft tissue infection (SSTI) in patients with diabetes. The inhibition of respiratory burst was due to defects in the activation-dependent expression of the glucose transporter GLUT1, which is required for respiratory burst in neutrophils and macrophages. We therefore sought to further elucidate the specific mechanisms by which phagocytes in a diabetic environment are impaired in their ability to control S. aureus SSTI. We observed that mTOR signaling is impaired in a diabetic mouse model of S. aureus SSTI, which is upstream of both respiratory burst and GLUT-1 expression. Inhibition of mTOR signaling with rapamycin phenocopies the higher bacterial burden during diabetic infection, as well as the inhibition of respiratory burst and GLUT-1 expression. We further observed that mTOR activity upon macrophage activation is impaired in the absence of insulin and growth factor signaling. These findings begin to elucidate a role for mTOR signaling in the mechanism of immune suppression caused by diabetes.
CD4 co-receptor regulates sexual dimorphic NK cell responses to T. gondii infection
Authors: Roy Tathagato 
Published: August 2023

Abstract
Immunity to Toxoplasma gondii is sexually dimorphic in humans and mice with females having higher morbidity and mortality during immune dysfunction and HIV/AIDS. The mechanisms underlying these sex differences are unclear. Since CD4+ T cells are very low during HIV/AIDS and females are more susceptible to Toxoplasmic encephalitis (TE) when they have AIDS, we investigated how a lack of CD4 co-receptor expression (CD4KO) and CD4+ T cells (MHCIIKO) impacted T. gondii survival and innate immune responses in mice. Female CD4KO mice succumbed to T. gondii much faster than male CD4KO mice. To dissect why female CD4KO mice died faster we tested their NK cell responses to acute T. gondii infection compared to male CD4KO mice. Although in wild type (WT) animals both sexes had similar increases in NK cell numbers and IFNg production, infected CD4KO female mice had 50% fewer IFNg+ NK cells than infected WT female mice. However, infected male CD4KO had the same number of NK cells producing IFNg compared to WT male mice. Since CD4 co-receptor deficient mice still have functional helper T cells that are CD4-we next tested survival and NK cell responses in female and male MHCII deficient (MHCIIKO) animals, which have very few helper CD4+T cells. To our surprise survival, NK cell numbers, and IFNg+ NK cells were not significantly different between WT or MHCIIKO female and male mice. These results suggest only in female mice and not in male mice, CD4 co-receptor expression is required for survival via optimal NK cell responses during acute T. gondii infection. Our findings reveal an unappreciated sexual dimorphic role of CD4 co-receptor expression in regulation of NK cell responses to acute T. gondii infection.
National Institute of General Medical Sciences (P20GM103432)
Brief IL-12, IL-15, IL-18 activation drives the acquisition of two distinct memory-like NK cell states
Authors: Foltz Jennifer Ann , Tran Jennifer , Fisk Bryan , Wong Pamela , Khan Saad M , Berrien-Elliott Melissa M , Becker-Hapak Michelle , Russler-Germain David A , Marsala Lynne , Bednarski Jeffrey J , Zimmerman Clare , Cubitt Celia C , Marin Nancy D , Zhou Alice Y , Jacobs Miriam T , Foster Mark , Schappe Timothy , Pence Patrick , Cashen Amanda , Griffith Obi L , Griffith Malachi , Petti Allegra A , Fehniger Todd A 
Published: August 2023

Abstract
IL-12/15/18 activation induces natural killer (NK) cell differentiation into cytokine-induced memory-like (ML) NK cells with enhanced IFNγ and killing of tumor targets that is antigen independent, rendering them distinct from conventional (cNK) and CMV-induced adaptive NK cells. In leukemia patients, ML NK cells have an excellent safety profile and 47% CR rate (PMID: 32826231). Despite their clinical promise, little is known about the biology underlying ML NK cells. Based on individual variability of human ML NK cell function, we hypothesized that ML NK cells manifest molecular heterogeneity. To this end, we applied Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) to profile RNA and protein expression on the single-cell level, and evaluated NK cell function.
Overnight IL-12/15/18 stimulation induced broad activation with distinct transcriptional programs evident in CD56bright compared to CD56dim NK cells. In contrast, following in vitro differentiation for 7 days, IL-12/15/18 activated NK cells acquired a unique transcriptional and protein signature, and manifest one of two ML NK cell states (ML-1, ML-2), or remained similar to cNK cells. ML-1 was marked by increased activating receptor expression (NKp46, NKp30, NKp44) while ML-2 had increased expression of inhibitory receptors, CD25, HLA-DR, MKI67, and IFNG. In functional assays, ML-2 cells produced more IFNγ following cytokine stimulation than ML-1 cells. Further, ML-1 and ML-2 had divergent transcription factor profiles suggesting distinct mechanisms of regulation. Collectively, our findings reveal molecular and functional heterogeneity of ML NK cells, and investigations into ML subsets in patients receiving ML NK cell therapy are ongoing.
AAI Intersect Fellowship for Computational Scientists & Immunologists (JAF, TAF, AAP), T32GM139799 (JAF), P50CA171963 (TAF, MMB-E), R01CA205239 (TAF), P30CA91842 (TAF)
Mycobacterium tuberculosis induces immune evasion in macrophages through RNA-binding protein tristetraprolin
Authors: Liu Jianguo , Wei Jiawei , Huan Ning , Ramos-Espinosa Octavio , Eickhoff Christopher , Liu Ethan , Hoft Daniel , Liu Jianguo 
Published: August 2023

Abstract
Immune evasion of Mycobacterium tuberculosis (Mtb) facilitates intracellular bacterial growth. The mechanisms of immune evasion, however, are still not fully understood. In this study, we reveal that tristetraprolin (TTP), one of the best characterized RNA-binding proteins controlling stability of the target mRNAs, mediates innate immune evasion of mycobacteria. We found that TTP knockout mice displayed reduced bacterial burden in the early stage after Mtb aerosol challenge. Macrophages deficient in TTP also showed an inhibition in mycobacterial growth. Live mycobacteria induced TTP protein expression in macrophages, which was blocked by mTOR inhibitor rapamycin. Rapamycin promoted TTP protein degradation. Proteasome inhibitor MG-132 recovered the shortened TTP protein half-life induced by rapamycin. Ubiquitination mediated TTP protein degradation triggered by rapamycin in infected macrophages. TTP induction suppressed the expression of iNOS/TNF-α/IL-12/IL-23, and weakened the bactericidal effects in infected macrophages, whereas blocking mTOR pathway with rapamycin enhanced the bactericidal effects of infected macrophages through TTP inhibition. Overall, this study reveals a novel role for RNA-binding protein TTP in Mtb immune evasion mechanisms and provides a potential target for host-directed therapy against TB.
R21AI171734 & R21AI151936
Hyperglycemia facilitates dengue virus infection and host immune alteration
Authors: Lin Chiou-Feng , Shen Ting-Jing , Chen Chia-Ling 
Published: August 2023

Abstract
Patients with diabetes mellitus are highly comorbid with severe dengue diseases caused by the dengue virus (DENV). In search of possible host factors involved in DENV infection under hyperglycemic stress, cells and murine treated with high glucose (HG) increase viral protein expression and virion release but have no effects on antiviral interferon responses as well as viral early infectious stage. Following HG stimulation, a cellular replicon-based assay displays an increased viral translation while the glucose uptake inhibitor phloretin treatment blocks such an effect. Treating HG causes increases in the protein and gene expression of translational factor poly(A)-binding protein (PABP) in a glucose transporter-associated PI3K/AKT-regulated manner. PABP silence further causes a significant decrease in HG-increased virion production. In addition, HG treatment enhances the formation of the PABP-eukaryotic translation initiation factor 4G complex, regulated by protein-disulfide isomerase. Furthermore, streptozotocin-treated hyperglycemic mice reveal increased mortality, brain viral protein expression, and viral loads under DENV infection. This study demonstrates that hyperglycemic stress facilitates DENV infection by strengthening PABP-mediated viral translation.
This work is supported by the grants from the National Science and Technology Council (NSTC109-2327-B-006-010 and 110-2320-B-038-064-MY3), Taipei, Taiwan.
Brd4 regulates metabolic reprogramming of macrophages upon H. pylori infection
Authors: Modi Nikita , Chen Yanheng , Chen Lin-feng 
Published: August 2023

Abstract
Metabolic reprogramming plays an important role in the regulation of several macrophage functions, including bacterial killing and cytokine production. Brd4 has emerged as a key innate immune response regulator by modulating the inflammatory cytokine expression in macrophages. However, the potential role of Brd4 in metabolic reprograming of macrophage activation remains unknown. Here, we showed that Brd4 facilitated a HIF-1α-dependent glycolytic shift for macrophage activation in response to H. pylori infection. H. pylori infection triggered Brd4-dependent polarization of macrophages to the M1 phenotype, which was associated with an increase in glycolysis and the upregulation of glycolytic genes, glucose transporter 1 (Glut1) and Hexokinase II (HK2). Mechanistically, Brd4 was recruited to the promoters of Glut1 and Hk2 by HIF-1α and regulated glycolysis by facilitating HIF-1α-dependent expression of Glut1 and Hk2. Furthermore, we found that Brd4-mediated glycolysis was essential for M1 macrophage activation since the expression of iNOS, a marker of M1 polarization, was down-regulated in Brd4-deficient macrophages and could be rescued by the addition of pyruvate. Consistently, the iNOS-mediated killing of H. pylori was decreased in Brd4-deficient macrophages and also in mice with myeloid-specific deletion of Brd4. Our study identified a novel function of Brd4 in metabolic reprograming of macrophages through glycolysis and iNOS expression in response to bacterial infection.
Supported by grant from NIH R03 AI163932
Inhibition of the mevalonate pathway causes accumulation of CD14 in the endoplasmic reticulum of macrophages
Authors: Frey Tiffany A , Heine Grace , Howe Andrew 
Published: August 2023

Abstract
Mevalonate kinase deficiency (MKD) is an autoinflammatory disease caused by mutations in the mevalonate kinase enzyme, which acts early in the mevalonate pathway to produce sterol and non-sterol isoprenoid compounds. Patients with MKD have episodes of inflammatory symptoms accompanied by increased plasma levels of pro-inflammatory cytokines. CD14 is a receptor that binds to lipopolysaccharide (LPS) and induces the release of cytokines. Isoprenoid depletion was previously shown to increase cellular and decrease extracellular levels of CD14 in macrophages after LPS stimulation. The objective of this study is to characterize the cellular localization of CD14 following isoprenoid depletion. RAW 264.7 macrophages were treated with lovastatin to deplete isoprenoids and CD14 localization was examined using immunofluorescence and western blotting after LPS stimulation. CD14 co-localized with the endoplasmic reticulum (ER) protein calnexin following lovastatin treatment. To quantitate ER CD14, cell lysates were digested with endoglycosidase (Endo) H, which removes high mannose glycans found on ER proteins, but not complex glycans added in the Golgi apparatus. Western blot results showed that the level of Endo H sensitive CD14 was higher in lovastatin as compared to carrier-treated cells. Co-incubation of lovastatin-treated cells with mevalonate or geranylgeranyl pyrophosphate (GGPP), but not cholesterol, prevented the ER accumulation of CD14 indicating that GGPP depletion may cause this effect. Understanding how mevalonate pathway products contribute to protein trafficking in macrophages will expand our understanding of inflammatory diseases.
Evolutionary signatures of host-virus conflict reveal a family of micropeptides regulating mito-immune functions
Authors: Herrera Natalia E , Chang Tyron , Alemu Samrawit , Pinkham Chelsea , Hancks Dustin 
Published: August 2023

Abstract
Genomics has led to an expansive set of predicted genes; yet, functional annotation is rate-limiting. To drive discovery of immune functions, we exploit genomic scars of pathogen-conflict like rapid evolution and virologs. Virologs are host-coding sequences stolen and repurposed by viruses to rewire cells. Classic examples include master regulators SRC, IL-10, and IL-17. To identify novel immune activities, we screened all viral genomes in the database for factors displaying sequence similarity to cellular factors. Subsequent filtering using motif analysis and expression paired with our functional analysis of our top hit - a micropeptide named C15ORF48 - revealed a vertebrate specific MItochondrial STress Response (MISTR) circuit. MISTR consists of related micropeptides that interface with the electron transport chain (ETC). MISTR factors – MISTR1, MISTR Antiviral(AV)/C15ORF48, and MISTR (H)ypoxia are regulated by ultraconserved miRNAs and stress signals such as cytokines, infection, and hypoxia. MISTR factors are encoded by diverse viruses that infect a range of hosts from squirrels to algae; they are shown to be ancient as they are encoded by yeast but ill-defined in any system. We find that cellular MISTR factors shape chemical- and virus-triggered apoptosis, which is counteracted by a viral-MISTR. Emerging data link MISTR functions to inflammatory signaling via modulation of ETC Complex IV. We show that viral-MISTRs antagonize higher-order configurations of the ETC termed supercomplexes – whose precise function has remained of debate. Using viral systems to seed discovery, we identified new dimensions for textbook functions which implicate supercomplexes as an unappreciated battleground in immune defense.