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SummaryDrug resistance threatens the effective control of infections,including parasitic diseases such as leishmaniases. Neutrophils are essential players in antimicrobial control,but their role in drug-resistant infections is poorly understood. Here,we evaluated human neutrophil response to clinical parasite strains having distinct natural drug susceptibility. We found that Leishmania antimony drug resistance significantly altered the expression of neutrophil genes,some of them transcribed by specific neutrophil subsets. Infection with drug-resistant parasites increased the expression of detoxification pathways and reduced the production of cytokines. Among these,the chemokine CCL3 was predominantly impacted,which resulted in an impaired ability of neutrophils to attract myeloid cells. Moreover,decreased myeloid recruitment when CCL3 levels are reduced was confirmed by blocking CCL3 in a mouse model. Collectively,these findings reveal that the interplay between naturally drug-resistant parasites and neutrophils modulates the infected skin immune microenvironment,revealing a key role of neutrophils in drug resistance. Graphical abstract Highlights•Drug-resistant parasites induce distinct neutrophil transcriptional programs•Meglumine-antimoniate-resistant (MAR) Leishmania limits neutrophil chemokine release•Infection with MAR parasites impairs CCL3-driven early myeloid cell recruitment Immunology; Parasitology View Publication

SummaryHispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups,yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses,we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals,but not in non-Hispanic White individuals,with an effect size of ∼1.44 (95% confidence interval = 1.33–1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry,showed evidence of selection in human history,and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children. Graphical abstract Highlights•IKZF1 variants contribute to the increased risk of ALL in Hispanic/Latino children•Risk allele is associated with Indigenous American ancestry and underwent selection•Risk variant impacts IKZF1 enhancer that is selectively active in B cell development•Risk allele reduces enhancer activity,chromatin accessibility,and IKZF1 expression Genetic fine-mapping across the IKZF1 gene revealed a variant associated with childhood ALL that contributes to the increased risk of this disease in Hispanic/Latino individuals. The ALL risk allele reduces enhancer activity and IKZF1 expression specifically in B cell progenitors,likely resulting in stalled B cell development and an increased risk of ALL. View Publication

α-Defensin 1-3 (DEFA1A3) are host antimicrobial peptides with potent innate immune functions during infectious diseases. Differential UTI risk has been linked to DEFA1A3 DNA polymorphisms. This study elucidates mechanisms of DEFA1A3 gene dose–dependent protection against UTI pathogenesis. Antimicrobial peptides (AMPs) are host defense effectors with potent neutralizing and immunomodulatory functions against invasive pathogens. The AMPs α-Defensin 1-3/DEFA1A3 participate in innate immune responses and influence patient outcomes in various diseases. DNA copy-number variations in DEFA1A3 have been associated with severity and outcomes in infectious diseases including urinary tract infections (UTIs). Specifically,children with lower DNA copy numbers were more susceptible to UTIs. The mechanism of action by which α-Defensin 1-3/DEFA1A3 copy-number variations lead to UTI susceptibility remains to be explored. In this study,we use a previously characterized transgenic knock-in of the human DEFA1A3 gene mouse to dissect α-Defensin 1-3 gene dose–dependent antimicrobial and immunomodulatory roles during uropathogenic Escherichia coli (UPEC) UTI. We elucidate the relationship between kidney neutrophil– and collecting duct intercalated cell–derived α-Defensin 1-3/DEFA1A3 expression and UTI. We further describe cooperative effects between α-Defensin 1-3 and other AMPs that potentiate the neutralizing activity against UPEC. Cumulatively,we demonstrate that DEFA1A3 directly protects against UPEC meanwhile impacting pro-inflammatory innate immune responses in a gene dosage–dependent manner. View Publication

AbstractBacillus anthracis peptidoglycan (PGN) is a major component of the bacterial cell wall and a key pathogen-associated molecular pattern contributing to anthrax pathology,including organ dysfunction and coagulopathy. Increases in apoptotic leukocytes are a late-stage feature of anthrax and sepsis,suggesting there is a defect in apoptotic clearance. In this study,we tested the hypothesis that B. anthracis PGN inhibits the capacity of human monocyte-derived macrophages (MΦ) to efferocytose apoptotic cells. Exposure of CD163+CD206+ MΦ to PGN for 24 h impaired efferocytosis in a manner dependent on human serum opsonins but independent of complement component C3. PGN treatment reduced cell surface expression of the proefferocytic signaling receptors MERTK,TYRO3,AXL,integrin αVβ5,CD36,and TIM-3,whereas TIM-1,αVβ3,CD300b,CD300f,STABILIN-1,and STABILIN-2 were unaffected. ADAM17 is a major membrane-bound protease implicated in mediating efferocytotic receptor cleavage. We found multiple ADAM17-mediated substrates increased in PGN-treated supernatant,suggesting involvement of membrane-bound proteases. ADAM17 inhibitors TAPI-0 and Marimastat prevented TNF release,indicating effective protease inhibition,and modestly increased cell-surface levels of MerTK and TIM-3 but only partially restored efferocytic capacity by PGN-treated MΦ. We conclude that human serum factors are required for optimal recognition of PGN by human MΦ and that B. anthracis PGN inhibits efferocytosis in part by reducing cell surface expression of MERTK and TIM-3. View Publication

SummaryFollicular lymphoma (FL) is an indolent non-Hodgkin lymphoma of germinal center origin,which presents with significant biologic and clinical heterogeneity. Using RNA-seq on B cells sorted from 87 FL biopsies,combined with machine-learning approaches,we identify 3 transcriptional states that divide the biological ontology of FL B cells into inflamed,proliferative,and chromatin-modifying states,with relationship to prior GC B cell phenotypes. When integrated with whole-exome sequencing and immune profiling,we find that each state was associated with a combination of mutations in chromatin modifiers,copy-number alterations to TNFAIP3,and T follicular helper cells (Tfh) cell interactions,or primarily by a microenvironment rich in activated T cells. Altogether,these data define FL B cell transcriptional states across a large cohort of patients,contribute to our understanding of FL heterogeneity at the tumor cell level,and provide a foundation for guiding therapeutic intervention. Graphical abstract Highlights•B cells from follicular lymphoma exhibit 3 distinct transcriptional states•FL B cells differ by enhanced inflammation,proliferation,or chromatin remodeling•Tumor cell states correlate with unique immune-microenvironment features•Unique mutation and CNV profiles highlight potential genetic causes of heterogeneity Krull et al. analyzed bulk transcriptional,genomic,and immune profiles of B cells from follicular lymphoma and reveal 3 distinct transcriptional states. These cell states underscore the inherent variability of FL tumors,independent of stroma,and implicate intrinsic differences as an underpinning to FL heterogeneity. View Publication

IntroductionBAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes,through its direct catalytic activity on the repressive epigenetic mark histone H2AK119ub,as well as on several other substrates. BAP1 is also a highly important tumor suppressor,expressed and functional across many cell types and tissues. In recent work,we demonstrated a cell intrinsic role of BAP1 in the B cell lineage development in murine bone marrow,however the role of BAP1 in the regulation of B cell mediated humoral immune response has not been previously explored. Methods and resultsIn the current study,we demonstrate that a B-cell intrinsic loss of BAP1 in activated B cells in the Bap1 fl/fl Cγ1-cre murine model results in a severe defect in antibody production,with altered dynamics of germinal centre B cell,memory B cell,and plasma cell numbers. At the cellular and molecular level,BAP1 was dispensable for B cell immunoglobulin class switching but resulted in an impaired proliferation of activated B cells,with genome-wide dysregulation in histone H2AK119ub levels and gene expression. Conclusion and discussionIn summary,our study establishes the B-cell intrinsic role of BAP1 in antibody mediated immune response and indicates its central role in the regulation of the genome-wide landscapes of histone H2AK119ub and downstream transcriptional programs of B cell activation and humoral immunity. View Publication

Human milk oligosaccharides (HMOs) can modulate the intestinal barrier and regulate immune cells to favor the maturation of the infant intestinal tract and immune system,but the precise functions of individual HMOs are unclear. To determine the structure-dependent effects of individual HMOs (representing different structural classes) on the intestinal epithelium as well as innate and adaptive immune cells,we assessed fucosylated (2′FL and 3FL),sialylated (3′SL and 6′SL) and neutral non-fucosylated (LNT and LNT2) HMOs for their ability to support intestinal barrier integrity,to stimulate the secretion of chemokines from intestinal epithelial cells,and to modulate cytokine release from LPS-activated dendritic cells (DCs),M1 macrophages (MØs),and co-cultures with naïve CD4+ T cells. The fucosylated and neutral non-fucosylated HMOs increased barrier integrity and protected the barrier following an inflammatory insult but exerted minimal immunomodulatory activity. The sialylated HMOs enhanced the secretion of CXCL10,CCL20 and CXCL8 from intestinal epithelial cells,promoted the secretion of several cytokines (including IL-10,IL-12p70 and IL-23) from LPS-activated DCs and M1 MØs,and increased the secretion of IFN-γ and IL-17A from CD4+ T cells primed by LPS-activated DCs and MØs while reducing the secretion of IL-13. Thus,3′SL and 6′SL supported Th1 and Th17 responses while reducing Th2 responses. Collectively,our data show that HMOs exert structure-dependent effects on the intestinal epithelium and possess immunomodulatory properties that confer benefits to infants and possibly also later in life. View Publication

PurposeIsolating circulating tumour cells (CTCs) from the blood is challenging due to their low abundance and heterogeneity. Limitations of conventional CTC detection methods highlight the need for improved strategies to detect and isolate CTCs. Currently,the Food and Drug Administration (FDA)-approved CellSearch™ and other RUO techniques are not available in India. Therefore,we wanted to develop a flexible CTC detection/isolation technique that addresses the limitation(s) of currently available techniques and is suitable for various downstream applications.MethodsWe developed a novel,efficient,user-friendly CTC isolation strategy combining density gradient centrifugation and immuno-magnetic hematogenous cell depletion with fluorescence-activated cell sorting (FACS)-based positive selection using multiple CTC-specific cell-surface markers. For FACS,a stringent gating strategy was optimised to exclude debris and doublets by side scatter/forward scatter (SSC/FSC) discriminator,remove dead cells by 4′,6-diamidino-2-phenylindole (DAPI) staining,and eliminate non-specific fluorescence using a “dump” channel. APC-labelled anti-CD45mAB was used to gate remaining hematogenous cells,while multiple epithelial markers (EpCAM,EGFR,and Pan-Cytokeratin) and an epithelial–mesenchymal transition (EMT) marker (Vimentin) labelled with fluorescein isothiocyanate (FITC) were used to sort cancer cells. The technique was initially developed by spiking Cal 27 cancer cells into the blood of healthy donors and then validated in 95 biopsy-proven oral squamous cell carcinoma (OSCC) patients. CTCs isolated from patients were reconfirmed by Giemsa staining,immuno-staining,and whole transcriptome amplification (WTA),followed by qRT-PCR. In vitro culture and RNA sequencing (RNA-Seq) were also performed to confirm their suitability for various downstream applications.ResultsThe mean detection efficiency for the Cal 27 tongue cancer cells spiked in the whole blood of healthy donors was 32.82% ± 12.71%. While ~75% of our patients (71/95) had detectable CTCs,the CTC positivity was independent of the TNM staging. The isolated potential cancer cells from OSCC patients were heterogeneous in size. They expressed different CTC-specific markers in various combinations as identified by qRT-PCR after WTA in different patients. Isolated CTCs were also found to be suitable for downstream applications like short-term CTC culture and RNA-Seq.ConclusionWe developed a sensitive,specific,flexible,and affordable CTC detection/isolation technique,which is scalable to larger patient cohorts,provides a snapshot of CTC heterogeneity,isolates live CTCs ready for downstream molecular analysis,and,most importantly,is suitable for developing countries. View Publication

Graphical abstract Summary of the study. Peripheral blood neutrophils from >200 hospitalised patients across three patient groups (coronavirus disease 2019 (COVID-19),non-COVID-19 lower respiratory tract infection (LRTI) and matched controls) were comprehensively profiled using mass spectrometry,revealing novel proteomic changes in acute and convalescent COVID-19. DIA: data-independent acquisition; TLR: Toll-like receptor; ARG: arginase; TGF: transforming growth factor; IFN: interferon. BackgroundNeutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19),but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not fully understood. We used quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes immediately following acute SARS-CoV-2 infection and during recovery.MethodsProspective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May to December 2020). Patients were enrolled within 96 h of admission,with longitudinal sampling up to 29 days. Control groups comprised non-COVID-19 acute lower respiratory tract infection (LRTI) and age-matched noninfected controls. Neutrophils were isolated from peripheral blood and analysed using mass spectrometry. COVID-19 severity and recovery were defined using the World Health Organization ordinal scale.ResultsNeutrophil proteomes from 84 COVID-19 patients were compared to those from 91 LRTI and 42 control participants. 5800 neutrophil proteins were identified,with >1700 proteins significantly changed in neutrophils from COVID-19 patients compared to noninfected controls. Neutrophils from COVID-19 patients initially all demonstrated a strong interferon signature,but this signature rapidly declined in patients with severe disease. Severe disease was associated with increased abundance of proteins involved in metabolism,immunosuppression and pattern recognition,while delayed recovery from COVID-19 was associated with decreased granule components and reduced abundance of metabolic proteins,chemokine and leukotriene receptors,integrins and inhibitory receptors.ConclusionsSARS-CoV-2 infection results in the sustained presence of circulating neutrophils with distinct proteomes suggesting altered metabolic and immunosuppressive profiles and altered capacities to respond to migratory signals and cues from other immune cells,pathogens or cytokines. Tweetable abstractHigh-resolution mass spectrometry analysis of peripheral blood neutrophils from >200 individuals provides novel insights into neutrophil phenotypes during acute COVID-19 and reveals that altered neutrophils persist in convalescent COVID-19 patients https://bit.ly/3QSSq9W View Publication

SummaryMesenchymal stromal cells (MSCs) have been modified via genetic or pharmacological engineering into potent antigen-presenting cells-like capable of priming responding CD8 T cells. In this study,our screening of a variant library of Accum molecule revealed a molecule (A1) capable of eliciting antigen cross-presentation properties in MSCs. A1-reprogrammed MSCs (ARM) exhibited improved soluble antigen uptake and processing. Our comprehensive analysis,encompassing cross-presentation assays and molecular profiling,among other cellular investigations,elucidated A1’s impact on endosomal escape,reactive oxygen species production,and cytokine secretion. By evaluating ARM-based cellular vaccine in mouse models of lymphoma and melanoma,we observe significant therapeutic potency,particularly in allogeneic setting and in combination with anti-PD-1 immune checkpoint inhibitor. Overall,this study introduces a strong target for developing an antigen-adaptable vaccination platform,capable of synergizing with immune checkpoint blockers to trigger tumor regression,supporting further investigation of ARMs as an effective and versatile anti-cancer vaccine. Graphical abstract Highlights•Treatment with A1/antigen mix reprograms MSCs into antigen-presenting cells•The antigen cross-presenting ability of ARM cells require ROS and UPR•ARMs synergize with immune-checkpoint inhibitors in priming potent antitumoral activity Classification Description: Immunology; Pharmaceutical engineering; Cancer View Publication