Several studies examined host and pathogen genetic influences on tuberculosis (TB) susceptibility separately, but relatively few studied their combined effects. However, host-pathogen interactions or co-evolution may explain the inability to replicate many reported human genetic effects across global populations and provide additional insight into TB risk. In this study, we address such possible interactions by focusing on the outcome of infection with L4-Uganda M. tuberculosis sub-lineage and human genetic variants as independent variables. This is possible because the L4-Uganda sub-lineage is both restricted to Uganda and nearby locations and is recent there, compared to other more ancestral L4 lineages. Our study consisted of 276 culture-confirmed adult TB cases from a long-standing household contact study. Multiple loci with results suggestive of association (p<10 -5 ) also demonstrated convergent relevant evidence for strain specific infection via: evidence of gene expression in relevant cells and lung tissue, signatures of natural selection, eQTL expression, and CRISPR screens for immunity-related genes. We also replicated previously published host-pathogen interaction effects, demonstrating that effects seen for other sub-lineages were also present for L4-Uganda. These results provide evidence for host-pathogen co-evolution in TB and indicate these interactions involve genes highly relevant to the host immune response to Mycobacterium infection.

Exposure to Mycobacterium tuberculosis (Mtb) leads to a spectrum of outcomes, from latent infection to active disease, but limited insight into protective immune correlates has hampered vaccine development. Using a proteome-wide Mtb microarray, we mapped antibody specificities across individuals with varying Mtb exposure, including humans with controlled latent tuberculosis infection, uncontrolled active TB, or that resist IGRA conversion as well as non-human primates with near sterilized Mtb infection following intravenous BCG. While current TB vaccine antigens were poorly immunogenic across most populations, striking overlap in antibody binding was observed to surface and secreted proteins, all associated with enhanced antibody functions and some also robustly targeted by T cells. Collectively, these data provide an atlas of antibody protein binding across the spectrum of Mtb infection, and further point to a handful of promising Mtb protein candidates to guide the design of antibody-based TB interventions aimed at mitigating disease globally.

Immune and clinical outcomes to Mycobacterium tuberculosis (Mtb) infection vary greatly between individuals, yet the underlying genetic and cellular mechanisms driving this heterogeneity remain poorly understood. We performed a cellular genome-wide association study to identify genetic variants associated with Mtb-induced monocyte transcriptional expression of IL1B, IL6, TNF, and IFNB1 via RNA-Seq in a Ugandan cohort. Significantly associated variants were assessed for transferability in an independent Seattle cohort, further validated in vitro, and assessed for clinical phenotype associations. We identified 77 loci suggestively associated with Mtb-induced cytokine expression in monocytes in Uganda. SNPs associated with Mtb-induced TNF were enriched within α-linolenic acid metabolism pathway genes, which was validated in vitro using PLA2 inhibitors. Four loci maintained significant associations in Seattle. We validated a cytokine effect with siRNA knockdown for two of these loci, which mapped to the genes SLIT3 and SLC1A1. Furthermore, exogenous treatment of macrophages with SLIT3 enhanced Mtb intracellular replication. Finally, SLC1A1 and SLIT3 variants were associated with susceptibility to tuberculous meningitis and subsequent survival, respectively, in a Vietnamese cohort. In summary, we identified multiple variants and pathways associated with Mtb-induced cytokine transcriptional responses that were validated in vitro and were associated with clinical tuberculosis susceptibility.

Identification of young children with Mycobacterium tuberculosis (Mtb) infection is critical to curb pediatric morbidity and mortality. The optimal test to identify young children with Mtb infection remains controversial. Using a tuberculosis (TB) household contact (HHC) study design among 130 Ugandan children less than 5 years of age with Mtb exposure, this study was conducted to determine the following: (1) the prevalence of Mtb immune sensitization in young children heavily exposed to TB using both the tuberculin skin test (TST) and QuantiFERON Gold Plus (QFT-Plus) interferon gamma release assay, and to examine the concordance of these two tests; and (2) the diagnostic accuracy of TST and QFT-plus for confirmed and unconfirmed TB in young children. Prevalence of Mtb immune sensitization was determined using TST at both 5 mm and 10 mm thresholds for positivity; manufacturer’s thresholds were utilized to establish QFT-Plus positivity. Concordance analysis between TST and QFT-Plus results was performed, including correlation between QFT-Plus tube TB.1 and tube TB.2. The sensitivity and specificity of TST and QFT-Plus for confirmed and unconfirmed TB was determined, and a logistic regression model was utilized to estimate the odds of TB. A 5 mm TST threshold identified the most children with Mtb sensitization (49.2%) and had moderate agreement with QFT-Plus (Cohen’s Kappa 0.59). The odds of TB were two times higher among children with a positive TST using a 5 mm threshold. Concordance between 10 mm TST threshold and QFT-Plus was substantial (Cohen’s Kappa 0.65), with higher concordance observed among older children (2–5 years). The QFT-Plus tube TB.1 and tube TB.2 results were highly correlated. Positive TST using a 5 mm threshold demonstrated the highest sensitivity for TB (60%), whereas QFT-Plus testing demonstrated the highest specificity (72%). Overall, our findings support that among a population of young, BCG-vaccinated children with heavy household exposure to TB, the TST using a 5 mm threshold identified more children with evidence of Mtb immune sensitization, and children with TB disease, than the QFT-Plus. These findings are highly relevant for children who are TB HHCs in endemic settings, and most at risk for TB following an exposure. We recommend that TST testing continue to be performed to assess for Mtb sensitization in young, TB-exposed children in TB-endemic settings to both prioritize provision of preventive therapy and to aide in diagnosis of pediatric TB.

Despite heavy exposure to Mycobacterium tuberculosis (Mtb), some individuals are resistant to TST and IGRA conversion (RSTRs). The functional and immunological mechanisms governing resistance are poorly understood. We hypothesized that RSTR and LTBI alveolar macrophages (AMs) respond differently to Mtb infection with transcriptional programs that are distinct from peripheral blood monocytes. We examined media and Mtb-infected AMs from bronchoalveolar lavage fluid collected from a RSTR cohort in Uganda with over 10 years of clinical follow-up. With transcriptional profiles of BAL cells analyzed immediately after collection, gene set enrichment analysis (GSEA) revealed 13 differentially expressed gene sets between RSTR (n = 19) and LTBI (n = 26) groups, including one (Hallmark E2F targets) which was positively enriched in the RSTR group (FDR < 0.3). In a subset of this cohort (n = 7 RSTR and 8 LTBI), AMs were examined with and without Mtb infection. When comparing the RSTR and LTBI groups, we identified 52 DEGs including 22 in the media condition, 15 with Mtb stimulation, and 11 with the interaction term (FDR < 0.2, Log 2-fold change > 1/<-1). Notably, RSTR AMs appear to upregulate inflammation more strongly than LTBI counterparts, including Hallmark inflammatory response (FDR < 0.2), IFNγ response (FDR < 0.1), and IFNα response (FDR < 0.1) while existing in a more non-inflammatory state at baseline (Hallmark TNF signaling via NF-kB (down, FDR < 0.1), inflammatory response (down, FDR < 0.1). In a comparison of peripheral blood monocyte gene expression profiles from the same cohort, there were both shared and AM-specific RSTR profiles detected. Together, these results suggest that RSTR and LTBI AMs have different basal and Mtb-induced transcriptional profiles, including some that differ from peripheral blood monocytes.

Understanding the mechanisms of early clearance of Mycobacterium tuberculosis (Mtb) may illuminate new therapeutic strategies for tuberculosis (TB). We previously found genetic, epigenetic, and transcriptomic signatures associated with resistance (resister, RSTR) to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion among highly exposed TB contacts. We hypothesized that integration of these datasets with multi-omic latent factor methods would detect pathways differentiating RSTR patients from those with asymptomatic TB infection (TBI, also known as latent TB infection or LTBI) that were not detected in individual dataset analyses. We pre-filtered and scaled features with the largest change between TBI and RSTR groups for 126 patients with data in at least two of five data modalities: single nucleotide polymorphisms (SNP), monocyte RNAseq (baseline and Mtb-stimulated conditions), and monocyte epigenetics (methylation and ATAC-seq). Using multiomic latent factor analysis (MOFA), we generated ten latent factors on the subset of 33 patients with all five datasets available, four of which differed by RSTR status (FDR < 0.1). Factor 4 showed the greatest difference between RSTR and TBI groups (FDR < 0.001). Three additional latent factor integration methods also distinguished the RSTR and TBI groups and identified overlapping features with MOFA. Using pathway analysis and a cluster-based enrichment method, we identified functions associated with latent factors and found that MOFA Factors 2–4 include functions related to cell-cell adhesion, cell shape, and multicellular structure development. In summary, latent variable integration methods uncovered signatures associated with resistance to TST/IGRA conversion that were not detected by individual dataset analyses and included pathways associated with cellular interactions and multicellular structures.

Tuberculosis (TB) outcomes vary widely, from asymptomatic infection to mortality, yet most animal models do not recapitulate human phenotypic and genotypic variation. The genetically diverse Collaborative Cross mouse panel models distinct facets of TB disease that occur in humans and allows identification of genomic loci underlying clinical outcomes. We previously mapped a TB susceptibility locus on mouse chromosome 2. Here, we identify cathepsin Z (Ctsz) as a lead candidate underlying this TB susceptibility and show that Ctsz ablation leads to increased bacterial burden, pulmonary inflammation and decreased survival in mice. Ctsz disturbance within murine macrophages enhances production of chemokine (C-X-C motif) ligand 1 (CXCL1), a known biomarker of TB severity. From a Ugandan household contact study, we identify significant associations between CTSZ variants and TB disease severity. Finally, we examine patient-derived TB granulomas and report CTSZ localization within granuloma-associated macrophages, placing human CTSZ at the host-pathogen interface. These findings implicate a conserved CTSZ-CXCL1 axis in humans and genetically diverse mice that mediates TB disease severity.

T cells are required for protective immunity against Mycobacterium tuberculosis. We recently described a cohort of Ugandan household contacts of tuberculosis cases who appear to "resist" M. tuberculosis infection (resisters; RSTRs) and showed that these individuals harbor IFN-γ-independent T cell responses to M. tuberculosis-specific peptide antigens. However, T cells also recognize nonprotein antigens via antigen-presenting systems that are independent of genetic background, known as donor-unrestricted T cells (DURTs). We used tetramer staining and flow cytometry to characterize the association between DURTs and "resistance" to M. tuberculosis infection. Peripheral blood frequencies of most DURT subsets were comparable between RSTRs and latently infected controls (LTBIs). However, we observed a 1.65-fold increase in frequency of MR1-restricted T (MR1T) cells among RSTRs in comparison with LTBIs. Single-cell RNA sequencing of 18,251 MR1T cells sorted from 8 donors revealed 5,150 clonotypes that expressed a common transcriptional program, the majority of which were private. Sequencing of the T cell receptor α/T cell receptor δ (TCRα/δ) repertoire revealed several DURT clonotypes were expanded among RSTRs, including 2 MR1T clonotypes that recognized mycobacteria-infected cells in a TCR-dependent manner. Overall, our data reveal unexpected donor-specific diversity in the TCR repertoire of human MR1T cells as well as associations between mycobacteria-reactive MR1T clonotypes and resistance to M. tuberculosis infection.

BACKGROUND:Tuberculosis vaccine trials using disease as the primary endpoint are large, time consuming, and expensive. An earlier immunological measure of the protection against disease would accelerate tuberculosis vaccine development. We aimed to assess whether the effectiveness of the Bacillus Calmette-Guérin (BCG) vaccine for prevention of Mycobacterium tuberculosis infection was consistent with that for prevention of tuberculosis disease. METHODS:We conducted an individual participant data (IPD) meta-analysis on experimental and observational longitudinal studies before April 6, 2018, identified through systematic reviews, known to us through expert knowledge in the field, reporting on BCG vaccination status, M tuberculosis infection test (QuantiFERON IFN-γ release assay [IGRA] and tuberculin skin test [TST]), and tuberculosis incidence. Cohort studies were included only for countries with a mandatory neonatal BCG vaccination policy. Exclusion criteria were previous or current tuberculosis disease, HIV infection, tuberculosis preventive treatment usage, and for household contacts, a positive baseline IGRA or TST test and young children aged 0-2 years; for randomised controlled trials, TST results within 2 years after random assignation were excluded. We contacted the investigators of the identified studies to provide IPD. We compared the protective efficacy of the BCG vaccine against M tuberculosis infection with that against tuberculosis disease using mixed-effects, multivariable proportional hazards modelling, by study type, M tuberculosis infection test (IGRA and TST), cutoff for defining test positivity, age, sex, and latitude. FINDINGS:We identified 79 studies eligible for full screening and of these, IPD datasets from 14 studies were included in our analysis: 11 household contact studies (29 147 participants), two adolescent cohort studies (11 368 participants), and one randomised controlled trial (2963 participants). Among 28 188 participants we found no protection by the BCG vaccine against TST conversion regardless of cutoff in any type of study. Among 1491 household contacts, but not among 5644 adolescents, the BCG vaccine protected against QuantiFERON conversion at the primary cutoff of 0·7 IU/mL or more with the adjusted hazard ratio (0·65, 95% CI 0·51-0·82) being consistent with that for protection against disease (0·68, 0·18-2·59). Protection against QuantiFERON conversion at cutoff of 0·35 IU/mL or more (0·64, 0·51-0·81) was similar. INTERPRETATION:Protection from the BCG vaccination against M tuberculosis infection, measured as QuantiFERON conversion, is inconsistent across different groups. Among groups with recent household exposure, QuantiFERON conversion is consistent with protection against disease and could be evaluated as a proxy for disease in tuberculosis vaccine trials. We found that TST lacks value for prevention in phase 2b proof-of-concept trials. FUNDING:Bill & Melinda Gates Foundation.

A subset of individuals exposed to Mycobacterium tuberculosis (Mtb) that we refer to as 'resisters' (RSTR) show evidence of IFN-γ- T cell responses to Mtb-specific antigens despite serially negative results on clinical testing. Here we found that Mtb-specific T cells in RSTR were clonally expanded, confirming the priming of adaptive immune responses following Mtb exposure. RSTR CD4+ T cells showed enrichment of TH17 and regulatory T cell-like functional programs compared to Mtb-specific T cells from individuals with latent Mtb infection. Using public datasets, we showed that these TH17 cell-like functional programs were associated with lack of progression to active tuberculosis among South African adolescents with latent Mtb infection and with bacterial control in nonhuman primates. Our findings suggested that RSTR may successfully control Mtb following exposure and immune priming and established a set of T cell biomarkers to facilitate further study of this clinical phenotype.

Mycobacterium tuberculosis (Mtb) exposure leads to a range of outcomes including clearance, latent TB infection (LTBI), and pulmonary tuberculosis (TB). Some heavily exposed individuals resist tuberculin skin test (TST) and interferon-gamma (IFNγ) release assay (IGRA) conversion (RSTR), which suggests that they employ IFNγ-independent mechanisms of Mtb control. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. Chromatin accessibility did not differ between uninfected RSTR and LTBI monocytes. By contrast, methylation significantly differed at 174 CpG sites and across 63 genomic regions. Consistent with previous transcriptional findings in this cohort, differential methylation was enriched in lipid- and cholesterol-associated pathways including the genes APOC3, KCNQ1, and PLA2G3. In addition, methylation was enriched in Hippo signaling, which is associated with cholesterol homeostasis and includes CIT and SHANK2. Lipid export and Hippo signaling pathways were also associated with gene expression in response to Mtb in RSTR as well as IFN stimulation in monocyte-derived macrophages (MDMs) from an independent healthy donor cohort. Moreover, serum-derived high-density lipoprotein from RSTR had elevated ABCA1-mediated cholesterol efflux capacity (CEC) compared to LTBI. Our findings suggest that resistance to TST/IGRA conversion is linked to regulation of lipid accumulation in monocytes, which could facilitate early Mtb clearance among RSTR subjects through IFNγ-independent mechanisms.IMPORTANCETuberculosis (TB) remains an enduring global health challenge with millions of deaths and new cases each year. Despite recent advances in TB treatment, we lack an effective vaccine or a durable cure. While heavy exposure to Mycobacterium tuberculosis often results in latent TB latent infection (LTBI), subpopulations exist that are either resistant to infection or contain Mtb with interferon-gamma (IFNγ)-independent mechanisms not indicative of LTBI. These resisters provide an opportunity to investigate the mechanisms of TB disease and discover novel therapeutic targets. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. We identify methylation signatures in host lipid and cholesterol pathways with potential relevance to early TB clearance before the sustained IFN responses indicative of LTBI. This adds to a growing body of literature linking TB disease outcomes to host lipids.

Childhood apraxia of speech (CAS) is a severe and rare form of speech sound disorder (SSD). CAS is typically sporadic, but may segregate in families with broader speech and language deficits. We hypothesize that genetic changes may be involved in the etiology of CAS. We conduct whole-genome sequencing in 27 families with CAS, 101 individuals in all. We identify 17 genomic regions including 19 unique copy number variants (CNVs). Three variants are shared across families, but the rest are unique; three events are de novo. In four families, siblings with milder phenotypes co-inherited the same CNVs, demonstrating variable expressivity. We independently validate eight CNVs using microarray technology and find many of these CNVs are present in children with milder forms of SSD. Bioinformatic investigation reveal four CNVs with substantial functional consequences (cytobands 2q24.3, 6p12.3-6p12.2, 11q23.2-11q23.3, and 16p11.2). These discoveries show that CNVs are a heterogeneous, but prevalent, cause of CAS. Copy number variations identified in families with childhood apraxia of speech and other speech sound disorders provide a deeper understanding of the genetic basis for naturally acquired speech.

Reductions in tuberculosis (TB) incidence require identification of individuals at high risk of developing active disease, such as those with recent Mycobacterium tuberculosis (Mtb) infection. Using a prospective household contact (HHC) study in Kampala, Uganda, we diagnosed new Mtb infection using both the tuberculin skin test (TST) and interferon-gamma release assay (IGRA). Our study aimed to determine if the TST adds additional value to the characterization of IGRA converters. We identified 13 HHCs who only converted the IGRA (QFT-only converters), 39 HHCs who only converted their TST (TST-only converters), and 24 HHCs who converted both tests (QFT/TST converters). Univariate analysis revealed that TST-only converters were older. Additionally, increased odds of TST-only conversion were associated with older age (p = 0.02) and crowdedness (p = 0.025). QFT/TST converters had higher QFT quantitative values at conversion than QFT-only converters and a bigger change in TST quantitative values at conversion than TST-only converters. Collectively, these data indicate that TST conversion alone likely overestimates Mtb infection. Its correlation to older age suggests an “environmental” boosting response due to prolonged exposure to environmental mycobacteria. This result also suggests that QFT/TST conversion may be associated with a more robust immune response, which should be considered when planning vaccine studies.

We introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling of RNA-seq including covariates, weights, random effects, covariance matrices, and fit metrics. In simulated datasets, kimma detects differentially expressed genes (DEGs) with similar specificity, sensitivity, and computational time as limma unpaired and dream paired models. Unlike other software, kimma supports covariance matrices as well as fit metrics like AIC. Utilizing genetic kinship covariance, kimma revealed that kinship impacts model fit and DEG detection in a related cohort. Thus, kimma equals or outcompetes current DEG pipelines in sensitivity, computational time, and model complexity.

Purpose: The study's primary aims were to describe the long-term speech outcomes for adolescents and young adults with a history of childhood apraxia of speech (CAS) and to examine the association of persistent speech sound errors with measures of literacy skills, phonological processing, motor speech production, and parent report of early motor difficulty. Method: Data from a large longitudinal 25-year study were used to explore outcomes for 32 individuals with a history of CAS, ages 12;6 (years;months) to 25 years ( M = 17.4, SD = 4.7). Persistent and nonpersistent groups were compared on decoding, phonological processing, multisyllabic word repetition, diadochokinetic rate, and parent report of motor involvement. Parametric (Welch's t tests) and nonparametric tests (Wilcoxon and Fisher exact tests) were used to identify differences between the groups' distributions. Developmental trajectories of speech production were plotted. Results: Outcomes for individuals with CAS are highly variable, with some demonstrating speech sound errors into adolescence and young adulthood. Speech sound errors were primarily on later developing sounds. Persistence was significantly associated with early motor difficulties. Difficulties with multisyllabic words, phonological processing, and literacy were often present regardless of persistence or nonpersistence of speech errors. Conclusions: Children with CAS are at risk for persistent speech sound errors into adulthood. For children showing limited progress with more traditional speech therapy, alternative interventions should be explored. Individuals with persistent speech sound errors are more likely to have a history of early motor deficits. Regardless of persistence, participants with CAS demonstrated ongoing weaknesses in literacy, phonological processing skills, and complex speech production tasks.

IntroductionThe heterogeneity of outcomes after Mycobacterium tuberculosis (Mtb) exposure is a conundrum associated with millennia of host-pathogen co-evolution. We hypothesized that human myeloid cells contain genetically encoded, Mtb-specific responses that regulate critical steps in tuberculosis (TB) pathogenesis.MethodsWe mapped genome-wide expression quantitative trait loci (eQTLs) in Mtb-infected monocytes with RNAseq from 80 Ugandan household contacts of pulmonary TB cases to identify monocyte-specific, Mtb-dependent eQTLs and their association with cytokine expression and clinical resistance to tuberculin skin test (TST) and interferon-γ release assay (IGRA) conversion.Resultscis-eQTLs (n=1,567) were identified in Mtb-infected monocytes (FDR<0.01), including 29 eQTLs in 16 genes which were Mtb-dependent (significant for Mtb:genotype interaction [FDR<0.1], but not classified as eQTL in uninfected condition [FDR≥0.01]). A subset of eQTLs were associated with Mtb-induced cytokine expression (n=8) and/or clinical resistance to TST/IGRA conversion (n=1). Expression of BMP6, an Mtb-dependent eQTL gene, was associated with IFNB1 induction in Mtb-infected and DNA ligand-induced cells. Network and enrichment analyses identified fatty acid metabolism as a pathway associated with eQTL genes.DiscussionThese findings suggest that monocyte genes contain Mtb-dependent eQTLs, including a subset associated with cytokine expression and/or clinical resistance to TST/IGRA conversion, providing insight into immunogenetic pathways regulating susceptibility to Mtb infection and TB pathogenesis.

Objective: To determine whether Mycobacterium tuberculosis (Mtb)-induced monocyte transcriptional responses differ in people with HIV (PWH) who do (RSTR) or do not (LTBI) resist tuberculin skin test/interferon-γ (IFN-γ) release assay (TST/IGRA) conversion after exposure. Design: We compared ex-vivo Mtb-induced monocyte transcriptional responses in a Ugandan tuberculosis (TB) household contact study of RSTR and LTBI individuals among PWH. Methods: Monocytes were isolated from peripheral blood mononuclear cells from 19 household contacts of pulmonary TB patients, and their transcriptional profiles were measured with RNA-Seq after a 6 h infection with Mtb (H37Rv) or media. Differentially expressed genes (DEGs) were identified by a linear mixed effects model and pathways by gene set enrichment analysis that compared RSTR and LTBI phenotypes with and without Mtb stimulation. Results: Among PWH, we identified 8341 DEGs that were dependent on Mtb stimulation [false discovery rate (FDR) <0.01]. Of these, 350 were not significant (FDR >0.2) in individuals without HIV. Additionally, we found 26 genes that were differentially expressed between RSTR and LTBI monocytes in PWH, including 20 which were Mtb-dependent (FDR <0.2). In unstimulated monocytes, several gene sets [TGF-β signaling, TNF-α signaling via NF-κB, NOTCH signaling, coagulation, and epithelial mesenchymal transition (EMT)] were enriched in RSTR relative to LTBI monocytes (FDR <0.1). These patterns were not observed in individuals without HIV. Conclusion: RSTR monocytes in PWH show different gene expressions in response to Mtb infection when compared with those with LTBI and RSTR without HIV. These differential expression patterns are enriched in inflammatory pathways.

T-cells are a critical facet of the adaptive immune system and have been shown in both human and animal studies to be essential for control of Mycobacterium tuberculosis (Mtb) infection. T-cells recognize foreign antigens presented by infected cells via a unique T-cell receptor (TCR). Understanding the specific TCRs that mediate recognition and clearance of Mtb-infected cells is essential to inform vaccine design. We recently described a cohort of Ugandan household contacts of tuberculosis cases that appear to ‘resist’ Mtb infection (RSTRs) and showed that these individuals harbor IFN-γ independent T-cell responses to Mtb peptide antigens. The role of unconventional T-cells that recognize non-peptide antigens, such as gd T-cells, CD1-restricted and MR1-restricted T-cells (MR1T), in “resistance” is unknown. In this study, we aimed to characterize the frequencies, functional programs, and repertoire of unconventional T-cells in RSTRs in comparison with latently infected (LTBI) controls. We used multi-parameter flow cytometry, single cell RNA and TCR sequencing and immunosequencing to address these gaps. We observed a 1.65-fold increase in frequency of circulating MR1T cells among RSTRs in comparison with LTBI (p=0.03). Single-cell RNA-sequencing of 18,251 sorted MR1T cells revealed 5,150 clonotypes expressing a common transcriptional program, the majority of which were private. Immunosequencing of the TCR-α/d repertoire revealed several TCRα clonotypes that were expanded in RSTRs (p <0.01), including at least two MR1T clonotypes. Overall, our data reveal unexpected donor-specific diversity in the TCR repertoire of human MR1T cells as well as associations between MR1 clonotypes and ‘resistance’ to Mtb infection. This work was supported by grants from the NIH (R01-AI124348 to Boom, Stein, and Hawn; R01-AI125189 and R01-AI146072 to Seshadri) and the Bill & Melinda Gates Foundation (OPP1151836 and OPP1109001 to Hawn and GH-VAP-IS-ID5 to Seshadri).

Background A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype). Objective Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype. Materials and methods Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M . tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis. Results We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2 , which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR. Conclusion and limitations Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study.