Genes & Immunity

Study questionWhat are the molecular characteristics during the maturation process of the human fetal immune system in the third trimester of pregnancy? Summary answerBoth the diversity and length of complementarity determining region 3 (CDR3s) in the fetal TCRB repertoire were less than those of adult CDR3s, and the fetal CDR3 length increased with gestation weeks in late pregnancy. What is known alreadyThe adaptive immune system recognizes various pathogens based on a large repertoire of T-cell receptors (TCR repertoire), but the maturation dynamics of the fetal TCR repertoire in the third trimester are largely unknown. The CDR3is the most diversified segment in the T-cell receptor {beta} chain (TCRB) that binds and recognizes the antigen. Study design, size, and durationThis was a basic research to assess the composing characteristics of TCRBs in core blood and the dynamic pattern with fetal development in the third trimester of pregnancy. Participants/materials, setting methodsHigh-throughput TCRB-enrichment sequencing was utilized to characterize the TCRB repertoire of cord blood at 24~38 weeks of gestational age (WGA) with nonpreterm fetuses and to investigate their difference compared with that of adult peripheral blood. Main results and the role of chanceCompared to the adult control, the fetal TCRB repertoire had a 4.8-fold lower number of unique CDR3s, a comparable Shannon diversity index (p=0.7387), a lower mean top clone rate (p < 0.001) and a constrictive top 1000 unique clone rates. Although all kinds of TCRBV and TCRBJ genes present in adult CDR3s were identified in fetuses, nearly half of these fragments showed a significant difference in usage. Moreover, the fetal TCRB repertoire held a shorter CDR3 length, and the CDR3 length showed a progressive increase with fetal development. Jensen-Shannon (JS) divergences of TCRBV and TCRBJ gene usage in dizygotic twins were much lower than those in unrelated pairs. In the parental-fetal pair, JS divergence of TCRBV gene usage was not obviously different, while that of TCRBJ gene usage was only slightly lower. Limitations, reasons for cautionThe sample size is limited due to the limited accessibility to cord blood in late pregnancy with healthy nonpreterm fetuses. Wider implications of the findingsOur findings reveal the unique properties of fetal TCRB repertoires in the third trimester, fill the gap in our understanding of the maturation process of prenatal fatal immunity, and deepen our understanding of the immunologically relevant problems in neonates. Study funding/competing interest(s)This work was supported by the National Natural Science Foundation of China (82171661) and Tianjin Municipal Science and Technology Special Funds for Enterprise Development (NO. 14ZXLJSY00320). The authors declare that they have no competing interests.

BackgroundThe inborn errors of immunity (IEI) that include defective antibody responses are clinically heterogenous, especially the common variable immunodeficiency (CVID) phenotype that includes low immunoglobulin levels and impaired humoral responses to antigens. Beyond recurrent infections, many with the CVID phenotype develop non-infectious complications (NICs), including autoimmunity and lymphoproliferation, that confer a high rate of morbidity and mortality. At present, it is unknown what genetic and functional factors predispose patients to NICs. ObjectiveWe aimed to discover the pathobiology underlying complicated CVID (CVIDc). MethodsIn a heterogenous group of 12 CVIDc patients, we conducted whole exome sequencing and high-throughput signaling assays by multiplexed phospho-mass cytometry. The immune deficiency and dysregulation activity (IDDA) score was used to determine the burden of NICs in individual patients. We integrated polygenic risk scores to determine the role of common background variants in the pathogenesis of CVIDc. ResultsIn CVID patients with high IDDA scores, there was aberrant increased phosphorylation of STAT1 and STAT3 upon stimulation with IL-10 or IL-21. Furthermore, common variants related to high eosinophil count and allergy/eczema confer a higher likelihood of autoimmunity in CVID. ConclusionVariants in loci related to high eosinophil count/function and over-reactive IL-10 signaling are associated with the development of autoimmune disease and NICs in CVID. Clinical implicationsIt may be possible to manage CVIDc through modulating IL-10 and IL-21 signaling pathways. Polygenic risk scoring may predict the development of autoimmune complications in CVID patients.

Leukocyte Immunoglobulin (Ig)-like Receptors (LILR) LILRB1 and LILRB2 play a pivotal role in maintaining self-tolerance and modulating the immune response through interaction with classical and non-classical Human Leukocyte Antigen (HLA) molecules. Although both diversity and natural selection patterns over HLA genes have been extensively evaluated, little information is available concerning the genetic diversity and selection signatures on the LIRB1/2 regions. Therefore, we identified the LILRB1/2 genetic diversity using next-generation sequencing in a population sample comprising 528 healthy control individuals from Sao Paulo State, Brazil. We identified 58 LILRB1 Single Nucleotide Variants (SNVs), which gave rise to 13 haplotypes with at least 1% of frequency. For LILRB2, we identified 41 SNVs arranged into 11 haplotypes with frequencies above 1%. We found evidence of either positive or purifying selection on LILRB1/2 coding regions. Some residues in both proteins showed to be under the effect of positive selection, suggesting that amino acid replacements in these proteins resulted in beneficial functional changes. Finally, we have shown that allelic variation (six and five amino acid exchanges in LILRB1 and LILRB2, respectively) affects the structure and/or stability of both molecules. Nonetheless, LILRB2 has shown higher average stability, with no D1/D2 residue affecting protein structure. Taken together, our findings demonstrate that LILRB1 and LILRB2 are highly polymorphic and provide strong evidence supporting the directional selection regime hypothesis.

BackgroundInflammatory bowel disease (IBD), which is characterised by genetic predispositions and dysregulated immune responses, is rapidly emerging as a global health challenge. Genetic variations in the human leukocyte antigen (HLA) region are strongly associated with IBD; nonetheless, the functional consequences of this variation on the composition of T-cell receptors remain poorly understood. MethodsWe conducted comprehensive CDR3-QTL mapping using T-cell receptor beta (TRB) repertoires paired with HLA allotypes from 1,973 individuals, including 1,201 individuals with IBD and 772 healthy controls (HCs), to explore the role of the HLA allelic variants on TRB composition. Using network analyses, we defined key CDR3 motifs of public clones that were linked to risk HLA alleles for chronic inflammatory diseases. ResultsWe identified novel sites within both HLA class I and class II proteins that were strongly linked to TRB amino acid composition - cdr3QTLs, in both HCs and individuals with IBD. Those sites in HLA-DRB1 and HLA-DQ had stronger effects on CDR3 composition than did the disease in the IBD cohort. In HCs, but not in UC or CD, the strongest HLA signals that affected expanded clones, overlapped with primary CD risk loci from GWAS, e.g., DRB1 site 70 and DQA1 site 25. The strongest CD-specific effects on TRB composition were found in HLA-B, especially at sites that modulate viral responses (e.g., HLA-B sites 9, 67). Finally, the main risk HLA alleles for chronic inflammatory diseases clustered together based on the physicochemical properties of residues mapped to cdr3QTLs, suggesting that risk alleles might exert similar effects on the TRB repertoire. ConclusionStructurally, the main cdr3QTLs in both HLA class I/II are located in peptide-binding sites or sites contacting TCRs, highlighting their direct and antigen-mediated influences on TRB repertoires. Our findings suggest that cdr3QTLs in HLA class I exert IBD-specific effects on the TRB composition, influencing the dysregulated T cell responses implicated in IBD pathogenesis, possibly on the earlier stages of T cell development. While HLA class II cdr3QTLs show universal effects and strong associations with T-cell receptors, irrespective of disease.

Graves disease (GD) is the leading cause of hyperthyroidism and is often treated with antithyroid drugs (ATDs). Although ATD therapy is effective, it might cause a rare but serious adverse effect called ATD-induced agranulocytosis (TiA), which can lead to severe neutropenia and life-threatening infections. Previous studies have shown that certain human leukocyte antigen (HLA) alleles, including HLA-B*38:02 and HLA-DRB1*08:03 in Asian populations, have been associated with TiA susceptibility. However, the underlying mechanisms remain unclear, highlighting the need to investigate the TiA-related immune alterations to better understand its pathogenesis and mechanisms. In this study, we investigated the immune receptor repertoire in TiA patients. Global repertoire diversity, VJ gene usage, and V-J pairing remained preserved across phenotypes and disease phases. Notably, TiA patients exhibited several upregulated complementarity-determining regions 3 (CDR3) clonotypes compared to GD patients, suggesting their role in disease progression and pathogenesis. Single-cell immune repertoire analysis revealed that TiA-associated risk CDR3 sequences were predominantly expressed on CD8+ effector memory T cells (CD8 TEM) in patients with HLA-B*38:02, while CD4+ central memory T cells (TCM) showed increased expression of risk CDR3 sequences in patients with HLA-DRB1*08:03, suggesting distinct cellular mechanisms underlying HLA-associated TiA pathogenesis. In conclusion, this study sheds light on the adaptive immunoprofile associated with TiA development and provides insights into the adaptive immune profile of TiA and HLA-mediated disease susceptibility.

Structured AbstractO_ST_ABSBackgroundC_ST_ABSIndividuals with common variable immunodeficiency (CVID) are at increased risk of respiratory infections such as SARS-CoV-2 infection due to poorly understood defects within the memory B cell (MBC) compartment. The COVID-19 pandemic presented a unique opportunity to investigate the effects of a novel pathogen and vaccination on the immune system of patients with CVID. MethodsA cross-sectional, single-center, cohort study was used to evaluate the immunologic effect of SARS-CoV-2 vaccination and/or disease on the immune system. We examined the antibody levels, neutralization capacity, MBC, and CD4+ T follicular helper cell (TFH) response against two SARS-CoV-2 variants in 23 CVID patients and 51 age- and sex-matched healthy individuals with both vaccine-induced and hybrid immunity across multiple immunization events. ResultsOur study shows that while CVID patients mount a sufficient CD4+ TFH response against both ancestral and Omicron variants, and some levels of neutralizing antibodies, Spike-specific MBC formation is severely inhibited. Only CVID patients with hybrid immunity were able to generate switched MBCs against both variants. These MBCs were transient however, as Spike-specific switched MBCs did not persist over time in CVID patients. We found that the level of switched MBCs correlated with both CD21 and BAFF-R expression in patients, many of whom expressed low levels of either receptor. ConclusionTaken together, our study shows that CVID patients generate a sufficient CD4+ TFH response against SARS-CoV-2 but rarely cross-reactive MBCs, and suggest that this effect is correlated with CD21 and BAFF-R dysregulation which might cause switched MBC obsolescence. Trial registration21/54057. FundingLundbeck Foundation, Novo Nordisk Foundation and Odense University Hospital.

Killer-cell immunoglobulin-like receptors (KIRs) are essential components of the innate immune system found on the surfaces of natural killer (NK) cells. The KIRs encoding genes are located on chromosome 19q13.4 and are genetically diverse across populations. KIRs are associated with various disease states including HIV progression, and are linked to transplantation rejection and reproductive success. However, there is limited knowledge on the diversity of KIRs from Uganda and Botswana HIV-infected paediatric cohorts, with high endemic HIV rates. We used next-generation sequencing technologies on 312 (246 Uganda, 66 Botswana) samples to generate KIR allele data and employed customised bioinformatics techniques for allelic, allotype and disease association analysis. We show that these sample sets from Botswana and Uganda have different KIRs of different diversities. In Uganda, we observed 147 vs 111 alleles in the Botswana cohort, which had a more than 1 % frequency. We also found significant deviation towards homozygosity for the KIR3DL2 gene for both rapid (RPs) and long-term non-progressors (LTNPs)in the Ugandan cohort. The frequency of the bw4-80I ligand was also significantly higher among the LTNPs than RPs (8.9 % Vs 2.0%, P-value: 0.032). In the Ugandan cohort, KIR2DS4*001 (OR: 0.671, 95 % CI: 0.481-0.937, FDR adjusted Pc=0.142) and KIR2DS4*006 (OR: 2.519, 95 % CI: 1.085-5.851, FDR adjusted Pc=0.142) were not associated with HIV disease progression after adjustment for multiple testing. Our study results provide additional knowledge of the genetic diversity of KIRs in African populations and provide evidence that will inform future immunogenetics studies concerning human disease susceptibility, evolution and host immune responses.

Recurrent somatic mutation in the ECSIT gene encoding p.V140A was reported in 19.3% (17/88) extranodal natural-killer/T cell lymphoma (ENKTL) and was associated with hemophagocytic syndrome (HPS). However, another cohort of similar geographical descent also had the ECSITV140A mutation as germline in 20.0% (5/25) of ENKTL and none were somatic. The reanalysis of published data revealed that the reported somatic ECSITV140A could be germline as well. First-digit analysis on the IDs of sequencing read also found irregularity among the data that initially reported the somatic ECSITV140A mutation. As such, this study questions the only somatic genetic link of HPS in ENKTL and also introduces a simple well-known algorithm to detect data irregularity in voluminous genomic sequencing data.

Human Leukocyte Antigen (HLA) loci have been implicated in several diseases from different world populations, including HIV-1. It is necessary to characterize HLA allele variation at the population level prior to investigating associations linked to human diseases. In global databases, limited high-resolution HLA allele types generated by next-generation sequencing (NGS) have been described for populations from African countries. We sought to expand our HLA NGS database to include a total of 1023 participants from multiple HIV clinical studies using full-length HLA genotyping by NGS. Collectively we describe HLA genotypes of individuals from Kenya (n=375), Uganda (n=338), Nigeria (n=139), Tanzania (n=89), and Mozambique (n=82). Overall, we identified 371 unique HLA alleles across 11 loci with the most frequent at each locus being A*02:01:01, B*53:01:01, C*04:01:01, C*06:02:01, DPA1*01:03:01, DPB1*01:01:01, DQA1*01:02:01, DQB1*06:02:01, DRB1*15:03:01, DRB3*02:02:01, DRB4*01:03:01, and DRB5*01:01:01. A total of 25 novel alleles were identified, including 4 with non-synonymous changes affecting the peptide binding groove of HLA molecules. This expansion of NGS based HLA data at the African population level will improve our understanding of human genetic variation and provide insights for vaccine development and targeted personalized therapies.

BackgroundNonhuman primates are valuable experimental models for human disease pathology and vaccine design. However, the vast and mostly uncatalogued immunogenomic diversity of typical species adds complexity to the interpretation of experiments and hinders reproducibility. Mauritian cynomolgus macaques (MCM) offer a unique opportunity to circumvent these difficulties, due to their restricted genetic diversity. ResultsWe assembled high-quality immunoglobulin heavy chain (IGH) haplotypes from long-read genomic sequencing of 13 MCM. Four animals were homozygous for IGH, yielding 3 distinct haplotypes, termed H1, H2, and H3. IGH haplotype H1 was observed in two of the homozygotes and 5 additional heterozygous animals, accounting for half of the assemblies recovered. H1 shares only 83% average sequence identity with the IGH locus of the rhesus macaque reference genome, in addition to numerous large structural variations. The other two homozygous haplotypes exhibited considerable variation, including a 60 kilobase (Kbp) deletion and 200 Kbp insertion relative to H1. Furthermore, we annotated the IG gene content from all complete MCM IGH assemblies and found 288 functional IGHV alleles, of which 94 (33%) were not in existing databases. We also identified 68 functional IGHD alleles, 11 functional IGHJ alleles, and 33 functional constant gene alleles across all 5 isotypes. ConclusionsWe identified multiple common and genetically diverse IGH haplotypes within MCM and provide high-quality reference assemblies and annotations for these to facilitate future work with this important animal model.

AimsGestational diabetes mellitus (GDM) is the most common pregnancy-related medical complication. GDM is linked to aberrant immune responses in both mothers and offsprings, specifically, the subsequent development of inflammatory diseases. Whereas prior research has focused on specific immune cell subsets, a comprehensive overview of the impacts of GDM on maternal and fetal immune landscape is lacking. Here, we aim to comprehensively decipher how GDM modulates various immune cell populations in mothers and offsprings. MethodsA prospective, longitudinal case-control study was carried out. Maternal blood from GDM-affected (GDM, n=18) and non-GDM-affected (Ctrl, n=21) mothers were collected at ante-(36-38 weeks of gestation) and post-partum (6-8 weeks post-partum) timepoints. Cord blood from GDM (n=7) and Ctrl (n=11) pregnancies were collected upon C-section. They were analyzed with the state-of-the-art cytometry by time of flight (CyTOF) with a 40-marker panel. Additionally, a publicly available RNA-seq dataset for cord blood mononuclear cells was re-analyzed to confirm results from CyTOF experiments. ResultsCompared to Ctrl, GDM was associated with more activated maternal T cell subsets ante-partum, including increased CD45RO+ and Ki67+ CD4+ T cell populations, which reverted post-partum. GDM-affected maternal innate lymphoid cell (ILC) also exhibited increased granzyme B production ante-partum. On the other hand, in GDM-impacted cord blood, fetal T and B cells were more activated, displaying less naive and more effector phenotypes, further supported by RNA-seq analyses. ConclusionsOur comprehensive analyses revealed that GDM is linked to profound changes in the immune landscapes of the mothers (ante-/post-partum) and foetuses (at birth), casting novel insights towards GDM pathophysiology. Longitudinal immune profiling might be warranted for early detection and stratification of risk, and development of targeted interventions to prevent inflammatory disorders in GDM mothers and their offspring. Research in contextO_LIWhat is already known about this subject? O_LIThe maternal and intrauterine environments are important contributors to long-term health outcomes of mothers and offsprings. C_LIO_LISome maternal and fetal immunity changes have been observed in gestational diabetes mellitus (GDM)-affected pregnancies. C_LIO_LIGDM is associated with increased risk of later-life metabolic and inflammatory diseases in mothers as well as offsprings. C_LI C_LIO_LIWhat is the key question? O_LIWhat are the longitudinal alterations in maternal and fetal immune landscapes in GDM-affected pregnancies? C_LI C_LIO_LIWhat are the new findings? O_LIHigh-dimensional immune profiling provided the most comprehensive overview of alterations in maternal and fetal immune landscapes associated with GDM. C_LIO_LIGDM is associated with skewing of maternal CD4+ T cell and ILC towards activated phenotypes ante-partum. C_LIO_LIGDM is linked to more activated fetal T and B cell profiles. C_LI C_LIO_LIHow might this impact on clinical practice in the foreseeable future? O_LIUnderstanding the complex alterations in the maternal and fetal immune landscape in GDM-affected pregnancy provides insights into the long-term impacts of GDM on the mother and offspring. C_LI C_LI

Red blood cell (RBC) alloimmunization is a clinically significant complication in transfused patients whose immunological determinants remain incompletely understood. Type I interferon (IFN-I) signaling drives RBC alloimmunization in murine models, and systemic lupus erythematosus (SLE) is characterized by constitutive IFN-I hyperactivation alongside elevated alloimmunization rates. We analyzed three publicly available SLE RNA-seq cohorts (GSE72509, GSE112087, GSE122459; whole blood and PBMC; total n = 150 SLE) in a pre-specified discovery-replication-validation design. A 14-gene IFN-I signature score was computed per sample; differential expression, gene set enrichment analysis, and Spearman correlation were performed independently per cohort. IFN-I scores were significantly elevated in SLE versus healthy controls in all three cohorts (p < 0.01 each). IFN-high SLE patients showed 665 differentially expressed genes, with enrichment of alloimmunization-associated and plasmablast differentiation gene sets confirmed by GSEA. The alloimmunization signature score correlated significantly with IFN-I score across all three independent cohorts ({rho} = +0.77, +0.51, +0.60; all FDR q < 0.05); Tfh differentiation showed no association in any cohort. To our knowledge, this represents the first human transcriptomic evidence that IFN-I pathway activity in SLE is coupled to alloimmunization-associated immune programs in vivo. These findings identify IFN-I score as a candidate biomarker of alloimmunization susceptibility in SLE and provide translational rationale for prospective studies incorporating transfusion outcome data.

BackgroundImmunocompromised people, including those with Inborn Errors of Immunity (IEI), are at increased risk of severe disease from viral infections. Therefore, regular booster vaccinations are recommended for SARS-CoV-2 and influenza, but it is unclear if these elicit protective immunity. ObjectiveComprehensive evaluation of adaptive immune responses, including SARS-COV-2 specific antibodies, memory B-(Bmem) and memory T-cells (Tmem), to COVID-19 vaccination in IEI patients. MethodsBlood samples were collected at 1-month post doses 2 and 3 of the ancestral COVID-19 vaccine, SARS-CoV-2 neutralizing antibodies (NAb) and Spike receptor binding domain (RBD) specific IgG were determined in 25 IEI patients and 29 controls. Ancestral Spike specific Tmem, and ancestral and Omicron subvariant RBD-specific Bmem were evaluated with flow cytometry. ResultsAfter dose 2, IEI patients had significantly lower Nab, RBD-specific IgG and Bmem against ancestral and Omicron subvariants. Third dose vaccination boosted NAb, IgG and Bmem levels, but these remained lower than healthy controls. Especially IgG1+ Bmem were lower in the IEI patients, while they carried higher frequencies of CD71+ ancestral RBD-specific Bmem. IEI patients and controls had similar numbers of Spike-specific CD4+ and CD8+ Tmem after both doses. However, patients Tmem had lower CD69 expression and reduced cytokine co-expression. While 9/25 IEI patients did not have NAb after dose 3, all had detectable SARS-CoV-2 specific IgG, Bmem- and/or Tmem. ConclusionPatients with IEI form lower levels of antibodies and immune memory cells to COVID-19 vaccination than controls. Still, all patients displayed formation of adaptive immune memory. This suggests a beneficial effect of vaccination, and supports the strategy for offering regular booster vaccinations to limit severe COVID-19 in this at-risk population. KEY MESSAGESO_LIWhilst antibody-deficient patients fail to generate NAb, all evaluated IEI patients could form spike-specific Tmem after COVID-19 vaccination. C_LIO_LIA 3-dose regimen boosted humoral and/or cellular responses in 60% of IEI patients, reinforcing the importance of prioritizing this population for early and repeated vaccination. C_LIO_LIComprehensive analysis of Bmem and Tmem responses revealed COVID-19 vaccination elicited adaptive immunity, underscoring the need for monitoring of immune cells in addition to serology in immunodeficient populations. C_LI CAPSULE SUMMARYFollowing 3-dose COVID-19 vaccination, all adult patients with inborn errors of immunity formed memory B- and/or memory T cells regardless of whether neutralizing antibodies are elicited. Therefore, IEI patients generate adaptive immunity to COVID-19 vaccination.

ObjectiveThe heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. MethodsWe performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. ResultsIn a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel potential drug targets for SLE. ConclusionThis study expands the number of genes associated with SLE and reveals novel pathways of disease. The findings reveal possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and the genetic architecture of DNAm in different molecular contexts. Finally, novel targets for drug development were discovered.

COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. Since innate and adaptive immune responses are elicited in COVID-19 patients, we genotyped 94 Florida patients with confirmed COVID-19 and 89 healthy controls. We identified an HLA gene, HLA-DPA1, in which specific alleles were associated with the risk of SARS-CoV-2 positivity and COVID-19 disease. HLA-DPA1*01:03 was associated with reduced incidence of SARS-CoV-2 positivity, whereas HLA-DPA1*03:01 was associated with increased risk of SARS-CoV-2 positivity. These data suggest a model in which COVID-19 severity is influenced by immunodominant peptides derived from SARS-CoV-2 preferentially presented by specific HLA-DP molecules to either protective (for asymptomatic COVID-19) or pathogenic T cells (in severe COVID-19). Although this study is limited to comparing SARS-CoV-2 positive and negative subjects, these data suggest that HLA typing of COVID-19 patients stratified for disease severity may be informative for identifying biomarkers and disease mechanisms in high-risk individuals.

CD19-directed chimeric antigen receptor (CAR) T cells have greatly improved the prognosis of relapsed/refractory large B-cell lymphoma (rrLBCL), yet treatment failure occurs in more than half of patients, usually in the first 3 months after treatment. While they primarily act through CAR-dependent, HLA-independent recognition of tumor targets, CAR-T cells may also indirectly contribute to long-term tumor immunosurveillance by stimulating endogenous immunity. We hypothesized that HLA diversity, measured by the HLA evolutionary divergence (HED) metric which reflects the breadth of the immunopeptidome presented to host T cells, could influence antitumor response after CAR T-cell therapy, as seen after immune chekpoint inhibitor treatment. We studied 127 rrLBCL patients treated with commercial CAR-T cells in our center, of whom 50 % achieved durable response. We observed no impact of diversity at any HLA locus, except for HED-DQA1 that was surprisingly negatively associated with response. Analysis of the distribution of HLA-DQ alleles according to clustering of HED values pointed to the DQ1/DQ1 genotype as an independent predictor of durable response and lower incidence of relapse/progression. These findings highlight the unsuspected role of germline HLA-DQ molecules in the response to CAR-T cells and suggest an important contribution of cross-talk between CAR-T cells and endogenous immune cells. Key PointsO_LIGermline HLA-DQ genotype is an independent predictor of durable response and lower incidence of relapse/progression after CAR T-cell therapy in rrLBCL C_LIO_LIHLA-DQ1/DQ1 genotype could influence the host immune response after CAR T-cell therapy and increase the chances of a durable response C_LI

Inhibitory killer cell immunoglobulin-like receptors (iKIRs) are a family of inhibitory receptors that are expressed by natural killer cells and late-stage differentiated T cells. There is accumulating evidence that iKIRs regulate T cell-mediated immunity. Recently, we reported that T cell-mediated control was enhanced by iKIRs in chronic viral infections. We hypothesized that in the context of autoimmunity, where an enhanced T cell response might be considered detrimental, iKIRs would have an opposite effect. We studied Type 1 diabetes (T1D) as a paradigmatic example of autoimmunity. In T1D, variation in the Human Leucocyte Antigen (HLA) genes explains up to 50% of the genetic risk, indicating that T cells have a major role in T1D etiopathogenesis. To investigate if iKIRs affect this T cell response we asked whether HLA associations were modified by iKIR genes. We conducted an immunogenetic analysis of a case-control T1D dataset (N= 11,961) and found that iKIR genes, in the presence of genes encoding their ligands, have a consistent and significant effect on protective HLA class II genetic associations. Our results were validated in an independent data set. We conclude that iKIRs significantly decrease HLA class II protective associations and suggest that iKIRs regulate CD4+ T cell responses in T1D.

IntroductionWe have reanalyzed the genomic data from the International Collaboration for the Genomics of HIV (ICGH), focusing on HIV-1 Elite Controllers (EC). MethodsA genome-wide association study (GWAS) was performed, comparing 543 HIV-1 EC individuals with 3,272 uninfected controls (CTR) of European ancestry. 8 million single nucleotide polymorphisms (SNPs) and HLA class I and class II gene alleles were imputed to compare EC and CTR. Results2,626 SNPs were associated with EC (p<5.10-8), all located within the Major Histocompatibility Complex (MHC) region. Stepwise regression analysis narrowed this list to 17 SNPs. In parallel, 22 HLA class I and II alleles were associated with EC. Through meticulous mapping of the LD between all identified signals and employing reciprocal covariate analyses, we delineated a final set of 6 independent SNPs and 3 HLA class I gene alleles that accounted for most of the associations observed with EC. Our study revealed the presence of cumulative haploblock effects (SNP rs9264942 contributing to the HLA-B*57:01 effect) and that several HLA allele associations were in fact caused by SNPs in linkage disequilibrium (LD). Upon investigating SNPs in LD with the selected 6 SNPs and 3 HLA class I alleles for their impact on protein function (either damaging or differential expression), we identified several compelling mechanisms potentially explaining EC among which: a multi-action mechanism of HLA-B*57:01 involving MICA mutations and MICB differential expression overcoming the HIV-1 blockade of NK cell response, and overexpression of ZBTB12 with a possible anti-HIV-1 effect through HERV-K interference; a deleterious mutation in PPP1R18 favoring viral budding associated with rs1233396. ConclusionOur results show that MHC influence on EC likely extends beyond traditional HLA class I or class II allele associations, encompassing other MHC SNPs with various biological impacts. They point to the key role of NK cells in preventing HIV-1 infection. Our analysis shows that HLA-B*57:01 is indeed associated with a partially functional NK cell response which could also explain this markers involvement in other diseases such as psoriasis. More broadly, our findings suggest that within any HLA class I and II association in diseases, there may exist distinct causal SNPs within this crucial, gene-rich, and LD-rich MHC region.

BackgroundGiven its high mortality and broad societal impacts, the COVID-19 pandemic is a particularly notable global outbreak of a respiratory illness in the 21st century. Although previous studies have identified several genes associated with COVID-19 susceptibility, relatively little is known about the genes contributing to severe COVID-19, including their evolutionary histories. In the current study, we analyzed IL-4, TLR2, CCL2, and SLC11A1--four immunity genes that have been implicated in severe COVID-19 and other immune-related diseases--in globally diverse populations from the 1000 Genomes Project. We also tested for associations between genetic variation in these genes and clinical COVID-19 phenotypes in more than 4,000 laboratory-confirmed COVID-19-positive individuals from Italy. ResultsBased on our analyses, we identified 72 single nucleotide polymorphisms (SNPs) across these genes as targets of positive selection, including several derived alleles shared with archaic Neanderthal and/or Denisovan genomes--a finding not previously reported in the literature. Furthermore, we found that common SNPs--implicated in respiratory diseases such as tuberculosis and chronic obstructive pulmonary disorder--were also under selection. Functional predictions based on in silico analyses revealed that a subset of selected alleles map to transcription factor binding sites and are predicted to affect binding affinity. In addition, our genetic association analyses uncovered significant correlations between derived alleles in the coding region of TLR2 and COVID-19 severity. Interestingly, these candidate alleles occurred at relatively low frequency in western European and East Asian populations but were absent in populations of African and South Asian descent. ConclusionsOverall, our study provides new insights into the evolution of biologically relevant immunity genes in the modern human lineage and highlights genetic variants that may underlie differential risk for severe COVID-19.

Polymorphisms of human leukocyte antigen (HLA) genes confer risks for many human diseases. For predisposing effects relating to T-cell receptor (TCR) recognition of peptide-HLA, the effect can be both selection of the TCR repertoire and preferential presentation of disease-driving epitopes. In celiac disease (CeD) HLA-DQ2.5 predisposes by presenting deamidated gluten peptides to CD4+ T cells that typically employ stereotyped TCRs. Here we analyzed whether genetic variants within the HLA and TR loci shape the naive TCR repertoire. We sequenced the {beta} TCR repertoires of naive CD4+ T cells of 103 CeD subjects and 103 controls and performed gene usage quantitative trait loci analyses. The naive CD4+ TCR repertoire was significantly affected by HLA and TRA and TRB polymorphisms. Individuals carrying the HLA-DQ2.5 allotype exhibited increased frequencies of TCR genes involved in stereotyped recognition of gluten epitopes thus demonstrating a disease-predisposing effect of HLA by selection of a disease-relevant TCR repertoire.