Abstract Tuberculosis (TB) remains the leading cause of infectious mortality. The limited efficacy of the only TB vaccine, Bacille Calmette–Guérin (BCG) against pulmonary disease necessitates improved vaccines. Host factors such as malnutrition and microbiome composition shape immune responses in humans, though these factors are overlooked in preclinical vaccine evaluation. Here we show that a recombinant BCG strain, BCG::ESAT-6-PE25SS, confers superior protection compared to BCG across murine models of malnutrition, antibiotic-induced dysbiosis and environmentally enriched microbiota. Unexpectedly, malnourished mice displayed reduced Mycobacterium tuberculosis (Mtb) burden, associated with altered host metabolism and immune composition. Microbiome disruption increased TB susceptibility, whereas diversification of microbiota enhanced resistance and immune heterogeneity. Vaccine efficacy correlated with enrichment of known immunomodulatory microbial taxa. These findings suggest diet-microbiome-immunity interactions as potential key determinants of TB pathogenesis and provide evidence for the importance of vaccine candidate evaluation under physiologically relevant co-morbid conditions

Abstract Background Refractory coeliac disease type 1 (RCD1) lacks defining molecular markers, and the immune and epithelial mechanisms sustaining intestinal injury remain poorly understood. Objective To define the clonal immune and epithelial states that distinguish RCD1 from active coeliac disease (ACD) and determine their spatial organisation in the duodenal mucosa. Design We integrated single-cell RNA sequencing, CITE-seq surface proteomics and paired T-cell receptor sequencing of duodenal immune and epithelial compartments from Healthy controls (n = 6), ACD (n = 7), RCD1 (n = 9) and RCD2 (n = 2), with spatial transcriptomics in a subset of biopsies. Results RCD1 showed widespread TCRαβ and TCRγδ clonal expansion across multiple IEL states, extending beyond previously defined mutation-bearing aberrant clones. Distinct IEL populations converged on a shared programme of adaptive persistence, innate-like signalling, metabolic fitness and cytoskeletal remodelling; GZMK expression marked both clonally expanded and non-clonal disease-associated states. In parallel, RCD1 epithelium showed loss of mature absorptive cell states and expansion of stress-associated, immune-interacting and regenerative programmes. Transit-amplifying cells acquired differentiation and tissue-remodelling signatures, while enteroendocrine cells expanded and developed a sensory-neurosecretory programme involving TRPA1, TRPV1 , vesicle trafficking and NEUROD1 regulon activity. Spatial transcriptomics localised regenerative and enteroendocrine-associated epithelial programmes adjacent to immune-visible epithelial regions and KLRK1 / GZMK -expressing IEL-rich niches in refractory tissue. Conclusion RCD1 represents a distinct mucosal state characterised by coordinated clonal IEL adaptation and epithelial remodelling, rather than simple amplification of ACD, providing a cellular framework for persistent tissue injury and disease stratification.

Crocodilians possess a unique and robust immune system, offering a valuable model for studying vertebrate antiviral responses and informing zoonotic disease surveillance and therapeutic discovery. Building on our previous work that characterized crocodilian immune responses to synthetic viral mimics, this study investigates the innate immune dynamics of Crocodylus porosus liver (LV-1) cells infected with the Kunjin2011 virus, a genetically and antigenically related member of the West Nile virus (WNV) complex. A time-course infection assay was conducted up to 192 h post-infection (hpi), combining viral infectivity analysis with transcriptomic profiling. Delayed Kunjin2011 viral replication was confirmed via qRT-PCR, revealing a clear exponential phase after 48 hpi and peaking at 192 hpi. RNA sequencing demonstrated progressive transcriptional reprogramming in LV-1 cells, with early gene expression changes modest but becoming pronounced by 192 hpi. Differential expression analysis identified 1428 upregulated and 1308 downregulated genes, with temporal shifts from early activation to late-stage suppression. Principal component analysis and hierarchical clustering further supported a time-dependent divergence in host transcriptional responses. Notably, CXCL10, a key immune-associated chemokine, exhibited a biphasic expression pattern, with an early peak at 8 hpi, suppression at intermediate time points, and renewed induction from 72 hpi onwards. Together, these results demonstrate that Kunjin2011 infection elicits a dynamic and time-dependent transcriptional response in C. porosus liver cells, characterized by early activation of innate immune pathways followed by extensive transcriptional remodeling during prolonged infection. This study provides new insights into crocodilian host responses to flavivirus infection and establishes a foundation for future investigations of antiviral immunity and host-virus interactions in reptiles.

Intestinal inflammation continues in a subset of patients with celiac disease despite a gluten-free diet. Here, by applying multi-omic single-cell analysis to duodenal biopsies, we found that low-grade malignancies with lymphoma driver mutations in patients with refractory celiac disease type 2 (RCD2) are comprised by surface CD3-negative (sCD3 − ) lymphocytes stalled at an innate lymphoid cell (ILC)–progenitor T cell stage undergoing extensive TRA , TRB , and TRD TCR recombination. In people with refractory celiac disease type 1 (RCD1), a disease currently lacking explanation, we identified sCD3 + T cells with lymphoma driver mutations in 6 of 10 individuals with RCD1 and in one of the patients with active, recently diagnosed celiac disease. Furthermore, the mutant T cells formed large TCRαβ clones and displayed inflammatory and cytotoxic molecular profiles. Thus, accumulation of lymphoma driver–mutated T cells and sCD3 − progenitors may contribute to chronic, nonresponsive celiac disease.

Sabah, Malaysia, has amongst the highest burden of human Plasmodium knowlesi infection in the world, associated with increasing encroachment on the parasite's macaque host habitat. However, the genomic make-up of P. knowlesi in Sabah was previously poorly understood. To inform on local patterns of transmission and putative adaptive drivers, we conduct population-level genetic analyses of P. knowlesi human infections using 52 new whole genomes from Sabah, Malaysia, in combination with publicly available data. We identify the emergence of distinct geographical subpopulations within the macaque-associated clusters using identity-by-descent-based connectivity analysis. Secondly, we report on introgression events between the clusters, which may be linked to differentiation of the subpopulations, and that overlap genes critical for survival in human and mosquito hosts. Using village-level locations from P. knowlesi infections, we also identify associations between several introgressed regions and both intact forest perimeter-area ratio and mosquito vector habitat suitability. Our findings provide further evidence of the complex role of changing ecosystems and sympatric macaque hosts in Malaysia driving distinct genetic changes seen in P. knowlesi populations. Future expanded analyses of evolving P. knowlesi genetics and environmental drivers of transmission will be important to guide public health surveillance and control strategies.

BACKGROUND:In autoimmune disease it is not understood how self-reactive B cells escape immune tolerance checkpoints to produce pathogenic autoantibodies. OBJECTIVE:In patients with demyelinating polyneuropathy caused by IgM autoantibodies against myelin associated glycoprotein (MAG) and the sulphated trisaccharide CD57, we aimed to test the hypothesis that B cells making the autoantibody escaped tolerance by acquiring lymphoma driver somatic mutations. METHODS:Deep single-cell RNA, DNA, flow cytometric and antibody specificity analysis of blood from three patients with MAG neuropathy. RESULTS:MAG autoantibody-producing B cell clones exhibited extensive intraclonal immunoglobulin V(D)J hypermutation. In many of the sub-clonal branches, the replacement:silent ratio of V-region mutations was not different from that expected for unselected mutations, although in some branches the mutations either increased or eliminated binding to MAG and CD57 autoantigens. Prior to intraclonal V(D)J diversification, each clone had acquired a gain-of-function MYD88p.L265P mutation, and some branches had acquired additional somatic mutations in CXCR4, IGLL5 and BTG2. Whilst all MAG-binding clones harboured the MYD88p.L265P mutation, the same mutation was also found in some control, polyclonal B cells. Deep sequencing of different blood cell subsets indicated MYD88p.L265P was confined to B cells. CONCLUSION:In three MAG neuropathy patients we find evidence that the self-reactive B cells responsible for their disease acquired a classical lymphoma driver somatic mutation early in their clonal expansion.

Background: Inflammatory Bowel Disease (IBD), including Ulcerative Colitis and Crohn’s Disease, is a multifactorial inflammatory condition of the intestinal tract driven by a complex interplay of genetic factors, immune system dysfunction, and gut microbiota alterations. This review aims to synthesize current advancements in modern drug development strategies for IBD. It emphasizes the integration of computational modelling, cell-based experiments, and animal model studies to enhance translational outcomes. Methods: To compile this review, an extensive literature search was performed utilizing PubMed, Scopus, and Google Scholar databases for English-language research and review articles published between 2000 and 2025 using keywords such as “IBD,” “molecular docking,” “bioinformatics,” “organoids,” “animal models,” and “network pharmacology,” among others. A total of 199 peer-reviewed studies were identified for inclusion based on relevance, transparency, and methodological robustness. Results: The review outlines a range of cutting-edge approaches to IBD drug discovery. These include computer modelling, molecular docking, and network analysis to accelerate early-stage target prediction and drug screening. The review further highlights the critical importance of utilizing 2D and 3D cell culture systems in parallel with advanced animal models. It emphasizes the critical integration of computational predictions with biologically relevant in vitro and in vivo validations to improve the reliability and efficiency of drug development. Conclusions: The integration of computer modelling, cell culture systems, and animal studies provides a revolutionary paradigm for accelerating drug discovery to IBD and other diseases enabling personalized and more effective treatment approaches.

Background: The precise mechanism by which autoantibody-producing clones develop in patients with autoimmune diseases is incompletely understood. Somatic mutations in lymphoma driver genes that accrue in self-reactive clones have been described by our group in patients with cryoglobulinaemic vasculitis [1], as an explanation for how these clones overcome the tolerance checkpoints that usually prevent autoimmunity. It is uncertain if this applies to autoimmune diseases more broadly. We sought to test this hypothesis in the autoimmune disease myelin-associated glycoprotein (MAG) neuropathy, in which pathogenic autoantibodies targeting MAG leading to a demyelinating polyneuropathy that is often refractory to immune therapies. Almost all patients harbour IgM kappa B-cell clones and somatic mutations in MYD88 [2,3] and CXCR4 [3] have been identified in these bulk clonal populations. However, it has not been definitively shown that the expanded, somatically mutated clones are the MAG autoantibody-producing clones, and they have not been interrogated at single cell level, nor have their immunoglobulin sequences been published. Objectives: To test the hypothesis that somatic mutations in both immunoglobulin and lymphoma driver genes converge on the same B cell to produce expanded, pathogenic clones in MAG neuropathy. Methods: Peripheral blood mononuclear cells from the blood of three MAG neuropathy patients were analysed, and single B-lymphocytes were sorted from IgM kappa expansions, along with control B cells. Immunoglobulin sequences, both mutant and germline-reverted, were expressed and tested for MAG-specificity by ELISA. MAG-specific and control B-cells were then interrogated using single-cell multi-omic analysis for cell surface protein expression, gene expression and gDNA sequences [4,5]. Results: Multiple, expanded, IgM kappa clones and subclones were identified in all three patients, and at least one MAG-specific clone was confirmed in each patient. All clonal immunoglobulin sequences exhibited high levels of somatic hypermutation with unique V(D)J gene usage specific to each clone. Germline-reverted sequences demonstrated variable MAG binding. All clones harboured a somatic MYD88L265P gain-of-function mutation, irrespective of MAG-specificity. Strikingly, this mutation was also present in control, non-clonal B cells in all three patients, albeit at a lower frequency. Two different somatic non-sense mutations in CXCR4 were also identified in the MAG-specific clones in two patients. Additionally, there were also somatic mutations in IGLL5 and BTG2 present in some of the clones. There were no differences in gene expression or cell surface protein expression between the clones across all three patients, nor between MAG-positive and MAG-negative clones. Our results reveal unexpectedly diverse clonal evolutionary trees and place MYD88L265P acquisition at the root of these trees, at or before the processes of V(D)J recombination and V-region hypermutation that conferred antibody binding to MAG. Conclusion: In this cohort of MAG neuropathy patients, the first published study of interrogation of this disease at a single-cell level, the acquisition of a mutation in a key lymphoma drive gene occurs early in B-cell development, prior to V(D)J rearrangement or acquisition of self-reactivity. This contrasts with our findings in patients with cryoglobulinaemic vasculitis, suggesting that B cells may traverse more than one route of somatic mutagenesis in their evolution towards pathogenic clones. REFERENCES: [1] M. Singh, et al. Cell, 180 (5) (2020), pp. 878-894.e19. [2] Vos JM et al. J Neurol Neurosurg Psychiatry. 2018 Sep;89(9):1007-1009. [3]Allain et al. Haematologica. 2018 May;103(5):e207-e210. [4] I.C. Macaulay, et al. Nat. Methods, 12 (6) (2015), pp. 519-522. [5] Ruff, D.W. et al. Methods Mol Biol. 2022:2386:171-188. Acknowledgements: National Health and Medical Research Council (NHMRC) grants; APP2010134 & APP1113904, the UNSW Cellular Genomics Futures Institute. Disclosure of Interests: None declared.

The reduced prevalence of insulin resistance and type 2 diabetes in countries with endemic parasitic worm infections suggests a protective role for worms against metabolic disorders, however clinical evidence has been non-existent. This 2-year randomised, double-blinded clinical trial in Australia of hookworm infection in 40 male and female adults at risk of type 2 diabetes assessed the safety and potential metabolic benefits of treatment with either 20 ( n = 14) or 40 ( n = 13) Necator americanus larvae (L3) or Placebo ( n = 13) (Registration ACTRN12617000818336). Primary outcome was safety defined by adverse events and completion rate. Homoeostatic model assessment of insulin resistance, fasting blood glucose and body mass were key secondary outcomes. Adverse events were more frequent in hookworm-treated participants, where 44% experienced expected gastrointestinal symptoms, but completion rates were comparable to Placebo. Fasting glucose and insulin resistance were lowered in both hookworm-treated groups at 1 year, and body mass was reduced after L3-20 treatment at 2 years. This study suggests hookworm infection is safe in people at risk of type 2 diabetes and associated with improved insulin resistance, warranting further exploration of the benefits of hookworms on metabolic health.

Cancer is a heterogeneous disease with a strong genetic component making it suitable for precision medicine approaches aimed at identifying the underlying molecular drivers within a tumour. Large scale population-level cancer sequencing consortia have identified many actionable mutations common across both cancer types and sub-types, resulting in an increasing number of successful precision medicine programs. Nonetheless, such approaches fail to consider the effects of mutations unique to an individual patient and may miss rare driver mutations, necessitating personalised approaches to driver-gene prioritisation. One approach is to quantify the functional importance of individual mutations in a single tumour based on how they affect the expression of genes in a gene interaction network (GIN). These GIN-based approaches can be broadly divided into those that utilise an existing reference GIN and those that construct de novo patient-specific GINs. These single-tumour approaches have several limitations that likely influence their results, such as use of reference cohort data, network choice, and approaches to mathematical approximation, and more research is required to evaluate the in vitro and in vivo applicability of their predictions. This review examines the current state of the art methods that identify driver genes in single tumours with a focus on GIN-based driver prioritisation.

A decline in the prevalence of parasites such as hookworms appears to be correlated with the rise in non-communicable inflammatory conditions in people from high- and middle-income countries. This correlation has led to studies that have identified proteins produced by hookworms that can suppress inflammatory bowel disease (IBD) and asthma in animal models. Hookworms secrete a family of abundant netrin-domain containing proteins referred to as AIPs (Anti-Inflammatory Proteins), but there is no information on the structure-function relationships. Here we have applied a downsizing approach to the hookworm AIPs to derive peptides of 20 residues or less, some of which display anti-inflammatory effects when co-cultured with human peripheral blood mononuclear cells and oral therapeutic activity in a chemically induced mouse model of acute colitis. Our results indicate that a conserved helical region is responsible, at least in part, for the anti-inflammatory effects. This helical region has potential in the design of improved leads for treating IBD and possibly other inflammatory conditions.

Scleractinian corals are crucially important to the health of some of the world's most biodiverse, productive, and economically important marine habitats. Despite this importance, analysis of coral peptidomes is still in its infancy. Here we show that the tentacle extract from the stony coral Heliofungia actiniformis is rich in peptides with diverse and novel structures. We have characterized the sequences and three-dimensional structures of four new peptides, three of which have no known homologues. We show that a 2 kDa peptide, Hact-2, promotes significant cell proliferation on human cells and speculate this peptide may be involved in the remarkable regenerative capacity of corals. We found a 3 kDa peptide, Hact-3, encoded within a fascin-like domain, and homologues of Hact-3 are present in the genomes of other coral species. Two additional peptides, Hact-4 and Hact-SCRiP1, with limited sequence similarity, both contain a beta-defensin-like fold and highlight a structural link with the small cysteine-rich proteins (SCRiP) family of proteins found predominantly in corals. Our results provide a first glimpse into the remarkable and unexplored structural diversity of coral peptides, providing insight into their diversity and putative functions and, given the ancient lineage of corals, potential insight into the evolution of structural motifs.

Background and aims Lupus nephritis (LN) is a clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Although proteinuria is highly correlated with disease progression in LN, the composition of the LN urinary proteome remains poorly characterised. To address this issue, complementary mass spectrometry (MS)-based approaches were used to identify candidate urinary biomarkers and a targeted proteomics panel was developed to further assess levels in LN samples. Methods LN urine samples were profiled using three MSbased methods: 2D SDS-PAGE, chemical labelling using isobaric mass tags, and data-independent acquisition (DIA). A quantitative, multiple reaction monitoring method was developed to further evaluate levels of these candidate peptide biomarkers in a larger cohort. Results Using these discovery proteomic approaches>2600 proteins were identified, 290 of which are up-regulated in LN samples. While chemical labelling enabled identification of more total proteins, DIA outperformed chemical labelling in identification of proteins significantly up-regulated in LN samples. Further evaluation of a selected panel revealed increases in the majority of candidate peptide biomarkers in LN samples compared to healthy controls, including peptides from proteins involved in inflammation and adaptive immunity. Conclusions These results indicate that peptides from proteins involved in inflammation and adaptive immunity can be quantified in urine of LN patients using a multiplexed MS-based method. Results from this study will be used to inform longitudinal and interventional studies focused on understanding the biological implications of these candidate biomarkers and to direct development of novel tools to evaluate disease progression and treatment efficacy of current and future LN therapeutics.

Background The suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings. Methodology/Principal findings High copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings. Conclusions/Significance This newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests.

The symbiotic relationships shared between humans and their gastrointestinal parasites present opportunities to discover novel therapies for inflammatory diseases. A prime example of this phenomenon is the interaction of humans and roundworms such as the hookworm, Necator americanus. Epidemiological observations, animal studies and clinical trials using experimental human hookworm infection show that hookworms can suppress inflammation in a safe and well-tolerated way, and that the key to their immunomodulatory properties lies within their secreted proteome. Herein we describe the identification of 2 netrin domain-containing proteins from the N. americanus secretome, and explore their potential in treating intestinal inflammation in mouse models of ulcerative colitis. One of these proteins, subsequently named Na-AIP-1, was effective at suppressing disease when administered prophylactically in the acute TNBS-induced model of colitis. This protective effect was validated in the more robust CD4 T cell transfer model of chronic colitis, where prophylactic Na-AIP-1 reduced T-cell-dependent type-1 cytokine responses in the intestine and the associated intestinal pathology. Mechanistic studies revealed that depletion of CD11c+ cells abrogated the protective anticolitic effect of Na-AIP-1. Next generation sequencing of colon tissue in the T-cell transfer model of colitis revealed that Na-AIP-1 induced a transcriptomic profile associated with the downregulation of metabolic and signaling pathways involved in type-1 inflammation, notably TNF. Finally, co-culture of Na-AIP-1 with a human monocyte-derived M1 macrophage cell line resulted in significantly reduced secretion of TNF. Na-AIP-1 is now a candidate for clinical development as a novel therapeutic for the treatment of human inflammatory bowel diseases. (Translational Research 2021; 232:88-102)

Global statistics show that prostate cancer (PrCa) is the second most common non-cutaneous cancer diagnosed in men, and currently, it is the most commonly diagnosed cancer in Australian men [ [1] Australian Institute of Health and WelfareCancer in Australia 2017. AIHW, Canberra, Australia2017 Google Scholar ]. While PrCa is a clinically complex, heterogeneous disease, it is one of the most heritable common cancers, with family history a strong predictor of susceptibility [ [2] Benafif S. Eeles R. Genetic predisposition to prostate cancer. Br Med Bull. 2016; 120: 75-89https://doi.org/10.1093/bmb/ldw039 Crossref PubMed Scopus (33) Google Scholar ]. However, the identification of rare, high-risk germline variants for PrCa has lagged significantly behind other heritable cancers [ [3] Mancuso N. Rohland N. Rand K.A. Tandon A. Allen A. Quinque N. et al. The contribution of rare variation to prostate cancer heritability. Nat Genet. 2016; 48: 30-35https://doi.org/10.1038/ng.3446 Crossref PubMed Scopus (99) Google Scholar ]. Massively parallel sequencing (MPS) applied to large families with a dense aggregation of disease, where genetic complexity is reduced and rare variants are enriched, has proven successful for rare variant discovery [ [4] Cirulli E.T. Goldstein D.B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet. 2010; 11: 415-425https://doi.org/10.1038/nrg2779 Crossref PubMed Scopus (903) Google Scholar ]. Here, we performed whole-genome sequencing (WGS) in a large Australian PrCa family (PcTas72: Fig. 1) of Northern European ancestry. Rare variants (frequency <1%) were prioritised using an established pipeline (Supplementary Methods). Two rare heterozygous variants were identified, a known PrCa risk mutation in HOXB13 (G84E), which has been previously reported [ [5] FitzGerald L.M. Raspin K. Marthick J.R. Field M.A. Malley R.C. Thomson R.J. et al. Impact of the G84E variant on HOXB13 gene and protein expression in formalin-fixed, paraffin-embedded prostate tumours. Sci Rep. 2017; 7: 17778https://doi.org/10.1038/s41598-017-18217-w Crossref PubMed Scopus (7) Google Scholar ]; and a variant in the DNA damage repair (DDR) gene, RAD51C (rs61758784; A126T). After additional genotyping of extended family members, the RAD51C A126T variant was found to segregate with disease in a further eight individuals, including three affected and five unaffected relatives (one unaffected son [64 years of age] and four daughters of cases). One affected carrier was a married-in spouse, and to the best of our knowledge, not a blood relative. Notably, the HOXB13 G84E mutation was confined to a single branch of the family, and no individuals carried both mutations (Fig. 1). The clinicopathological characteristics of all available PcTas72 PrCa cases are shown in Supplementary Table S1. Subsequently, the RAD51C variant was genotyped in additional Australian familial (n = 786) and case-control (n = 807) datasets of Northern European ancestry (described in the Supplementary Methods). Genotyping revealed a further 19 carriers (four families with multiple carriers and three families with a single carrier; Supplementary Fig. S2A). In addition, four sporadic cases and two unaffected controls were identified as carriers. Association analysis was performed using MQLS [ [5] FitzGerald L.M. Raspin K. Marthick J.R. Field M.A. Malley R.C. Thomson R.J. et al. Impact of the G84E variant on HOXB13 gene and protein expression in formalin-fixed, paraffin-embedded prostate tumours. Sci Rep. 2017; 7: 17778https://doi.org/10.1038/s41598-017-18217-w Crossref PubMed Scopus (7) Google Scholar ], which permits the inclusion of both familial and case–control genotypes (Supplementary Methods). A significant association between the RAD51C A126T variant and PrCa risk was identified (OR = 3.05; p = 1.68 × 10−3), which remained significant after removal of the eight discovery PcTas72 individuals (OR = 2.46; p = 4.13 × 10−3; Supplementary Table S2).

We identify an intronic deletion in VANGL1 that predisposes to renal injury in high risk populations through a kidney-intrinsic process. Half of all SLE patients develop nephritis, yet the predisposing mechanisms to kidney damage remain poorly understood. There is limited evidence of genetic contribution to specific organ involvement in SLE.(1,2) We identify a large deletion in intron 7 of Van Gogh Like 1 (VANGL1), which associates with nephritis in SLE patients. The same deletion occurs at increased frequency in an indigenous population (Tiwi Islanders) with 10-fold higher rates of kidney disease compared with non-indigenous populations. Vangl1 hemizygosity in mice results in spontaneous IgA and IgG deposition within the glomerular mesangium in the absence of autoimmune nephritis. Serum transfer into B cell-deficient Vangl1(+/-) mice results in mesangial IgG deposition indicating that Ig deposits occur in a kidney-intrinsic fashion in the absence of Vangl1. These results suggest that Vangl1 acts in the kidney to prevent Ig deposits and its deficiency may trigger nephritis in individuals with SLE.

The human hookworm Necator americanus infects more than 400 million people worldwide, contributing substantially to the poverty in these regions. Adult stage N. americanus live in the small intestine of the human host where they inject excretory/secretory (ES) products into the mucosa. ES products have been characterized at the proteome level for a number of animal hookworm species, but until now, the difficulty in obtaining sufficient live N. americanus has been an obstacle in characterizing the secretome of this important human pathogen. Herein we describe the ES proteome of N. americanus and utilize this information along with RNA Seq data to conduct the first proteogenomic analysis of a parasitic helminth, significantly improving the available genome and thereby generating a robust description of the parasite secretome. The genome annotation resulted in a revised prediction of 3,425 fewer genes than initially reported, accompanied by a significant increase in the number of exons and introns, total gene length and the percentage of the genome covered by genes. Almost 200 ES proteins were identified by LC-MS/MS with SCP/TAPS proteins, hypothetical proteins and proteases among the most abundant families. These proteins were compared to commonly used model species of human parasitic infections, including Ancylostoma caninum, Nippostrongylus brasiliensis and Heligmosomoides polygyrus. SCP/TAPS proteins are immunogenic in nematode infections, so we expressed four of those identified in this study in recombinant form and showed that they are all recognized to varying degrees by serum antibodies from hookworm-infected subjects from a disease-endemic area of Brazil. Our findings provide valuable information on important families of proteins with both known and unknown functions that could be instrumental in host-parasite interactions, including protein families that might be key for parasite survival in the onslaught of robust immune responses, as well as vaccine and diagnostic targets.