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PURPOSE Multiple myeloma (MM) is characterized by copy number abnormalities (CNAs), some of which influence patient outcomes and are sometimes observed only at relapse(s), suggesting their acquisition during tumor evolution. However, the presence of micro-subclones may be missed in bulk analyses. Here, we use single-cell genomics to determine how often these high-risk events are missed at diagnosis and selected at relapse. MATERIALS AND METHODS We analyzed 81 patients with plasma cell dyscrasias using single-cell CNA sequencing. Sixty-six patients were selected at diagnosis, nine at first relapse, and six in presymptomatic stages. A total of 956 newly diagnosed patients with MM and patients with first relapse MM have been identified retrospectively with required cytogenetic data to evaluate enrichment of CNA risk events and survival impact. RESULTS A total of 52,176 MM cells were analyzed. Seventy-four patients (91%) had 2-16 subclones. Among these patients, 28.7% had a subclone with high-risk features (del(17p), del(1p32), and 1q gain) at diagnosis. In a patient with a subclonal 1q gain at diagnosis, we analyzed the diagnosis, postinduction, and first relapse samples, which showed a rise of the high-risk 1q gain subclone (16%, 70%, and 92%, respectively). In our clinical database, we found that the 1q gain frequency increased from 30.2% at diagnosis to 43.6% at relapse (odds ratio, 1.78; 95% CI, 1.58 to 2.00). We subsequently performed survival analyses, which showed that the progression-free and overall survival curves were superimposable between patients who had the 1q gain from diagnosis and those who seemingly acquired it at relapse. This strongly suggests that many patients had 1q gains at diagnosis in microclones that were missed by bulk analyses. CONCLUSION These data suggest that identifying these scarce aggressive cells may necessitate more aggressive treatment as early as diagnosis to prevent them from becoming the dominant clone.

Background Relatives of patients with inflammatory bowel disease (IBD) have a higher risk to develop IBD than the general population. In some families, even a remarkably high prevalence of disease is found. Here, we aim to determine the role of the known IBD risk loci in familial aggregation of disease, as well as to study if there are common variants specific to familial IBD. Methods Imputed immunochip genotypes of 55 families [157 Crohn’s disease (CD), 29 ulcerative colitis (UC) and 138 unaffected relatives] that have at least three affected, first-degree relatives were used. A sporadic dataset (1705 CD, 917 UC, 873 controls) was used for comparison. For each individual, a polygenic risk score (PRS) was calculated with PRSice based on the IBD summary statistics of de Lange et al (2017), a p-value threshold ≤0.01 and MAF≥0.01. The mean PRS of all relatives of one family is denoted the familial PRS. Family-based association analyses were performed with SAIGE. The significance threshold for association used was p Results As a group, unaffected relatives have a lower PRS than affected relatives (p=1.36e-5, β(se)=-0.60(0.14)), but still higher than unrelated controls (p=2.07e-4, β(se)=0.39(0.11))(fig 1). Twenty-four families have a familial PRS that is higher than the mean PRS of sporadic cases, and seven families have a familial PRS that is lower than the mean PRS of unrelated controls, the low PRS families (fig 2A). In most families, the affected members have a higher mean PRS than the unaffected members (fig 2B). This relationship however is sometimes reversed, especially in the low PRS families. SAIGE found nine variants to be associated with familial IBD (fig 3A, table 1). Two independently associated variants, rs2241130 in IL1RL2 (p=1.19 e-5, β(se)=1.21(0.28)) and rs144641193 in IL1RL1 (p=8.23e-5, β(se)=1.29(0.33)) reside in a known IBD locus (IL18RAP). Some other identified variants were also located in genes previously implicated in IBD, either through GWAS [rs72781786 in PRKCQ (p=2.93e-5, β(se)= -0.95(0.23))], or via functional studies (rs2242601 in EPHA1 and rs2272766 in CTSB). A restricted analysis of the low PRS families identified only one significant variant: rs11579543, located between RPE65 and DEPDC1 (p=6.12e-5, β(se)=-2.71(0.68))(fig 3B, table 1). Conclusion Our analysis indicates that common risk variants play an important role in familial aggregation of disease in many multiplex families. Some families however have a very low polygenic risk, indicating shared environmental factors might be relatively more important, or genetic factors not captured by the score, e.g. rare variants, may have contributed. Also, a few loci are specifically implicated in familial IBD, some related to the immune system, e.g. CLECL1 and CD69.

Additional file 2: Supplementary Table 1. APOE4 follow-up versus baseline significant differentially expressed genes. Supplementary Table 2. APOE4 non-carriers follow-up versus baseline significant differentially expressed genes. Supplementary Table 3. Cell deconvolution contributions generated using CIBERSORT. Supplementary Table 4. Amyloid non-accumulators follow-up versus baseline significant differentially expressed genes. Supplementary Table 5. Follow-up versus baseline significant differentially expressed genes in amyloid negative-positive and amyloid positive-positive individuals. Supplementary Table 6. Follow-up versus baseline significant differentially expressed genes in amyloid negative individuals. Supplementary Table 7. Direct association scores of significant differentially expressed genes at follow-up versus baseline in APOE4 carriers. Supplementary Table 8. Direct association scores of significant differentially expressed genes at follow-up versus baseline in amyloid negativepositive and amyloid positive-positive individuals. Supplementary Table 9. APOE4 carriers gene set enrichment analysis gene ontology upregulated. Supplementary Table 10. APOE4 non-carriers gene set enrichment analysis gene ontology upregulated. Supplementary Table 11. APOE4 carriers gene set enrichment analysis gene ontology downregulated. Supplementary Table 12. APOE4 non-carriers gene set enrichment analysis gene ontology downregulated. Supplementary Table 13. Amyloid non-accumulators gene set enrichment analysis gene ontology upregulated. Supplementary Table 14. Amyloid non-accumulators gene set enrichment analysis gene ontology downregulated. Supplementary Table 15. Amyloid negative-positive/positive-positive gene set enrichment analysis gene ontology upregulated. Supplementary Table 16. Amyloid negative-negative gene set enrichment analysis gene ontology upregulated. Supplementary Table 17. Amyloid negative-positive/positive-positive gene set enrichment analysis gene ontology downregulated. Supplementary Table 18. Amyloid negative-negative gene set enrichment analysis gene ontology downregulated. Supplementary Table 19. Baseline Blue module enrichment. Supplementary Table 20. Follow-up Blue module enrichment. Supplementary Table 21. Follow-up Turquoise module enrichment.

Additional file 1: Supplementary Figure 1. Differentially expressed genes at follow-up compared to baseline in amyloid non-accumulators. Data points are based coloured on significance: grey = non-significant, blue = non-significant but with FDR p-value < 0.05, red = significant with FDR p-value < 0.05 and log2FoldChange ± 1. N = 53. Pval on y-axis represents the uncorrected p-value < 0.05 threshold for visualisation. Supplementary Figure 2. Detection of modules using baseline expression data. (A) Scale independence and (B) mean connectivity used to derive the soft power threshold. (C) Clustering of module eigengenes, where similar clusters were merged using a cutHeight =0.25 (red line). (D) Cluster dendrogram of co-expression modules shown, both with the 28 dynamic modules (top row) and final merged 17 modules (bottom row). Supplementary Figure 3. Top 20 general cell types derived from cell-specific enrichment of the highly interconnected genes from the baseline blue WGCNA module. The genes are displayed from left to right ranked by the most significant human tissue-cell-type. The red dotted line is the Bonferronicorrected significance (p = 3.69 × 10 × 10−5) by 1355 tissue-cell types. The grey line is the nominal significance (p = 1 × 10 × 10−3). The Y-axis indicates the tissue-cell-type specificity (–log10 (combined p value)) for each tissue-cell-type from the cell-specific enrichment. Supplementary Figure 4. Detection of modules using follow-up expression data. (A) Scale independence and (B) mean connectivity used to derive the soft power threshold. (C) Clustering of module eigengenes, where similar clusters were merged using a cutHeight =0.25 (red line). (D) Cluster dendrogram of co-expression modules shown, both with the 32 dynamic modules (top row) and final merged 35 modules (bottom row). Supplementary Figure 5. Top 20 general cell types derived from cell-specific enrichment of the highly interconnected genes from the follow-up blue WGCNA module. The genes are displayed from left to right ranked by the most significant human tissue-cell-type. The red dotted line is the Bonferronicorrected significance (p = 3.69 × 10 × 10−5) by 1355 tissue-cell types. The grey line is the nominal significance (p = 1 × 10 × 10−3). The Y-axis indicates the tissue-cell-type specificity (–log10 (combined p value)) for each tissue-cell-type from the cell-specific enrichment. Supplementary Figure 6. Top 20 general cell types derived from cell-specific enrichment of the highly interconnected genes from the follow-up turquoise WCGNA module. The genes are displayed from left to right ranked by the most significant human tissue-cell-type. The red dotted line is the Bonferroni-corrected significance (p = 3.69 × 10 × 10−5) by 1355 tissue-cell types. The grey line is the nominal significance (p = 1 × 10 × 10−3). The Y-axis indicates the tissue-cell-type specificity (–log10 (combined p-value)) for each tissue-cell-type from the cell-specific enrichment. Supplementary Figure 7. Detection of modules using follow-up expression data. (A) Scale independence and mean connectivity used to derive the soft power threshold. (B) Cluster dendrogram of consensus modules.

Identifying copy-number alteration with prognostic impact is typically done in a supervised approach, were candidate regions are user-selected (chomosome arms, oncogenes, etc). Yet CNA events may range from whole chromosome alterations to small focal amplifications or deletions, with no available approach to combine the potential prognostic impact of different aberration ranges. We propose and compare different statistical models to integrate the effects of multi-scale CNA events by exploiting the longitudinal structure of the genome, and assume that the survival distribution follows a Cox-proportional hazard model. These methods are adaptable to any cohorts screened for CNA by genome-wide assays such as CGH-array or whole-genome sequencing technologies, and with sufficient follow-up time. We show that combining a segmentation in the survival odds strategy with a lasso-regularization selection approach provides the best results in terms of recovering the true significant CNA regions as well as predicting survival outcomes. In particular, as shown on a 551 Multiple Myeloma patient cohort, this method allows to refine previously identified regions to exhibit potential novel driver genes.

Background Early detection of individuals at risk for Alzheimer’s disease (AD) is highly important. Amyloid accumulation is an early pathological AD event, but the genetic association with known AD risk variants beyond the APOE4 effect is largely unknown. We investigated the association between different AD polygenic risk scores (PRS) and amyloid accumulation in the Flemish Prevent AD Cohort KU Leuven (F-PACK). Methods We calculated PRS with and without the APOE region in 90 cognitively healthy F-PACK participants (baseline age 67.8 (52–80) years, 41 APOE4 carriers), with baseline and follow-up amyloid-PET (time interval 6.1 (3.4–10.9) years). Individuals were genotyped using Illumina GSA and imputed. PRS were calculated using three p-value thresholds (pT) for variant inclusion: 5 × 10−8, 1 × 10−5, and 0.1, based on the stage 1 summary statistics from Kunkle et al. (Nat Genet 51:414–30, 2019). Linear regression models determined if these PRS predicted amyloid accumulation. Results A score based on PRS excluding the APOE region at pT = 5 × 10−8 plus the weighted sum of the two major APOE variants (rs429358 and rs7412) was significantly associated with amyloid accumulation (p = 0.0126). The two major APOE variants were also significantly associated with amyloid accumulation (p = 0.0496). The other PRS were not significant. Conclusions Specific PRS are associated with amyloid accumulation in the asymptomatic phase of AD.

ObjectiveDysfunctional resolution of intestinal inflammation and altered mucosal healing are essential features in the pathogenesis of inflammatory bowel disease (IBD). Intestinal macrophages are vital in the process of inflammation resolution, but the mechanisms underlying their mucosal healing capacity remain elusive.DesignWe investigated the role of the prostaglandin E2 (PGE2) receptor PTGER4 on the differentiation of intestinal macrophages in patients with IBD and mouse models of intestinal inflammation. We studied mucosal healing and intestinal epithelial barrier regeneration in Csf1r-iCre Ptger4fl/fl mice during dextran sulfate sodium (DSS)-induced colitis. The effect of PTGER4+ macrophage secreted molecules was investigated on epithelial organoid differentiation.ResultsHere, we describe a subset of PTGER4-expressing intestinal macrophages with mucosal healing properties both in humans and mice. Csf1r-iCre Ptger4fl/fl mice showed defective mucosal healing and epithelial barrier regeneration in a model of DSS colitis. Mechanistically, an increased mucosal level of PGE2 triggers chemokine (C-X-C motif) ligand 1 (CXCL1) secretion in monocyte-derived PTGER4+ macrophages via mitogen-activated protein kinases (MAPKs). CXCL1 drives epithelial cell differentiation and proliferation from regenerating crypts during colitis. Specific therapeutic targeting of macrophages with liposomes loaded with an MAPK agonist augmented the production of CXCL1 in vivo in conditional macrophage PTGER4-deficient mice, restoring their defective epithelial regeneration and favouring mucosal healing.ConclusionPTGER4+ intestinal macrophages are essential for supporting the intestinal stem cell niche and regeneration of the injured epithelium. Our results pave the way for the development of a new class of therapeutic targets to promote macrophage healing functions and favour remission in patients with IBD.

Background Patients with inflammatory bowel disease [IBD] are considered immunosuppressed, but do not seem more vulnerable for COVID-19. Nevertheless, intestinal inflammation has shown to be an important risk factor for SARS-CoV-2 infection and prognosis. Therefore, we investigated the role of intestinal inflammation on the viral intestinal entry mechanisms, including ACE2, in IBD. Methods We collected inflamed and uninflamed mucosal biopsies from Crohn’s disease [CD] [n = 193] and ulcerative colitis [UC] [n = 158] patients, and from 51 matched non-IBD controls for RNA sequencing, differential gene expression, and co-expression analysis. Organoids from UC patients were subjected to an inflammatory mix and processed for RNA sequencing. Transmural ileal biopsies were processed for single-cell [sc] sequencing. Publicly available colonic sc-RNA sequencing data, and microarrays from tissue pre/post anti-tumour necrosis factor [TNF] therapy, were analysed. Results In inflamed CD ileum, ACE2 was significantly decreased compared with control ileum [p = 4.6E-07], whereas colonic ACE2 was higher in inflamed colon of CD/UC compared with control [p = 8.3E-03; p = 1.9E-03]. Sc-RNA sequencing confirmed this ACE2 dysregulation and exclusive epithelial ACE2 expression. Network analyses highlighted HNF4A as key regulator of ileal ACE2, and pro-inflammatory cytokines and interferon regulating factors regulated colonic ACE2. Inflammatory stimuli upregulated ACE2 in UC organoids [p = 1.7E-02], but not in non-IBD controls [p = 9.1E-01]. Anti-TNF therapy restored colonic ACE2 regulation in responders. Conclusions Intestinal inflammation alters SARS-CoV-2 coreceptors in the intestine, with opposing dysregulations in ileum and colon. HNF4A, an IBD susceptibility gene, seems an important upstream regulator of ACE2 in ileum, whereas interferon signalling might dominate in colon.

Multiple investigations are available to aid the diagnosis and monitoring of disease activity in inflammatory bowel disease (IBD). Fecal calprotectin (FC) is an established surrogate for intestinal inflammatory activity. Therapeutic drug monitoring (TDM) including thiopurine metabolites, anti-tumor necrosis factor (TNF) levels and antidrug antibody measurements are a step toward personalized medicine in IBD, but face access barriers. We aimed to assess test availability and barriers for these investigations in European practice.Five-hundred questionnaires were distributed to workshop participants at the 11th Congress of the European Crohn's and Colitis Organisation (ECCO). Access to FC, TDM for thiopurines and anti-tumor necrosis factor agents, as well as factors associated with usage and barriers to access were recorded.Responses were obtained from 195 attendees from 38 countries across a range of practices, healthcare settings and levels of experience. FC was available to 92.3% while access to anti-TNF (78.9%, P = 0.02 vs. thiopurine TDM, P = 0.0002 vs. FC) and thiopurine TDM (67.7%, P = 0.0001) were less widespread. Cost was a frequently cited barrier to test access or usage, with access having a significant West-East and North-South divide across all three investigations. The strongest independent predictor of access to all tests was healthcare spending per capita (P = 0.005 for FC; P 0.0001 for both TDM).FC, anti-TNF and thiopurine TDM are increasingly incorporated as part of routine practice in IBD care across Europe and have the potential to impact positively on patient care. However, access barriers remain of which we found test cost the most significant with the investment required to reduce these barriers.

Background and Aims Early treatment of Crohn’s disease [CD] is required in order to optimize patient outcomes. To this end, we need to gain a better understanding of the molecular changes at the onset of CD. Methods As a model for the earliest mucosal CD lesions, we study post-operative recurrent CD [Rutgeerts score ≥ i2b]. We are the first to analyse gene and microRNA [miRNA] expression profiles in ileal biopsies from these patients, and compare them with those of newly diagnosed [≤18 months] and late-stage [>10 years after diagnosis] CD patients. Results Except for one gene [WNT5A], there are no differential genes in CD patients without post-operative recurrence [i0], showing that previous disease did not influence gene expression in the neoterminal ileum, and that this model can be used to study early mucosal CD lesions. Gene expression and co-expression network dysregulation is more pronounced in newly diagnosed and late-stage CD than in post-operative recurrent CD, with most important modules associated with [a]granulocyte adhesion/diapedesis, and cholesterol biosynthesis. In contrast, we found a role for snoRNAs/miRNAs in recurrent CD, highlighting the potential importance of regulatory RNAs in early disease stages. Immunohistochemistry confirmed the expression of key dysregulated genes in damaged/regenerating epithelium and immune cells in recurrent CD. Conclusions Aside from regulatory RNAs, there are no clear gene signatures separating post-operative recurrent, newly diagnosed, and late-stage CD. The relative contribution of dysregulated genes and networks differs, and suggests that surgery may reset the disease at the mucosal site, and therefore post-operative recurrent CD might be a good model a good model to study to study early mucosal CD lesions.

We consider a change-point detection problem for a simple class of Piecewise Deterministic Markov Processes (PDMPs). A continuous-time PDMP is observed in discrete time and through noise, and the aim is to propose a numerical method to accurately detect both the date of the change of dynamics and the new regime after the change. To do so, we state the problem as an optimal stopping problem for a partially observed discrete-time Markov decision process taking values in a continuous state space and provide a discretization of the state space based on quantization to approximate the value function and build a tractable stopping policy. We provide error bounds for the approximation of the value function and numerical simulations to assess the performance of our candidate policy.

Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.

Genome-wide association studies (GWAS) have identified hundreds of loci associated with Crohns disease (CD), however, as with all complex diseases, deriving pathogenic mechanisms from these non-coding GWAS discoveries has been challenging. To complement GWAS and better define actionable biological targets, we analysed sequenced data from more than 30,000 CD patients and 80,000 population controls. We observe rare coding variants in established CD susceptibility genes as well as ten genes where coding variation directly implicates the gene in disease risk for the first time.

Background and Aims Inflammatory bowel disease [IBD] phenotypes are very heterogeneous between patients, and current clinical and molecular classifications do not accurately predict the course that IBD will take over time. Genetic determinants of disease phenotypes remain largely unknown but could aid drug development and allow for personalised management. We used genetic risk scores [GRS] to disentangle the genetic contributions to IBD phenotypes. Methods Clinical characteristics and imputed genome-wide genetic array data of patients with IBD were obtained from two independent cohorts [cohort A, n = 1097; cohort B, n = 2156]. Genetic risk scoring [GRS] was used to assess genetic aetiology shared across traits and IBD phenotypes. Significant GRS–phenotype (false-discovery rate [FDR] corrected p

The bridging integrator 1(TheForty-four percent of F-PACK participants wereWe could not confirm the association between

Designing efficient and rigorous numerical methods for sequential decision-making under uncertainty is a difficult problem that arises in many applications frameworks. In this paper we focus on the numerical solution of a subclass of impulse control problem for piecewise deterministic Markov process (PDMP) when the jump times are hidden. We first state the problem as a partially observed Markov decision process (POMDP) on a continuous state space and with controlled transition kernels corresponding to some specific skeleton chains of the PDMP. Then we proceed to build a numerically tractable approximation of the POMDP by tailor-made discretizations of the state spaces. The main difficulty in evaluating the discretization error come from the possible random or boundary jumps of the PDMP between consecutive epochs of the POMDP and requires special care. Finally we extensively discuss the practical construction of discretization grids and illustrate our method on simulations.

Abstract State-of-the-art technologies for wind and tidal energy exploitation focus mostly on axial turbines. However, cross-flow hydrokinetic tidal turbines possess interesting features, such as higher area-based power density in array installations and shallow water, as well as a generally simpler design. Up to now, the highly unsteady flow conditions and cyclic blade stall have hindered deployment at large scales because of the resulting low single-turbine efficiency and fatigue failure challenges. Concepts exist which overcome these drawbacks by actively controlling the flow, at the cost of increased mechatronical complexity. Here, we propose a bioinspired approach with hyperflexible turbine blades. The rotor naturally adapts to the flow through deformation, reducing flow separation and stall in a passive manner. This results in higher efficiency and increased turbine lifetime through decreased structural loads, without compromising on the simplicity of the design. Graphic abstract

A numerical approach for assessing the injury risk of fish during turbine passages is introduced. The approach combines computational fluid dynamics (CFD) coupled with the discrete element method (DEM), and extends it with fish behaviour models. The fish behaviour is achieved by an additional force term acting on the particles. Based on ethohydraulic observations three rules of conduct were defined and combined via weighting factors. These rules represent 1) the aim to follow the main flow direction, 2) the instinct of downstream migration, and 3) an avoidance reaction towards moving objects. It is shown that the behavior of the fish surrogates can be actively tuned and adapted. This allows for the expression of both individual and collective behavior with the implementation of instantaneous reactions to the local, unsteady flow conditions in a trade-off with global behavior rules. Therefore, the approach allows for the investigation of a large bandwidth of tasks related to etho- and ecohydraulics and is not limited to the case at hand. In this study, the model is deployed on an example case of a water vortex power plant (WVPP) that allows for the presentation of the general mechanisms and advantages of the method.

Extracellular vesicles are nanovesicles released by many cell types into the extracellular space. They are important mediators of intercellular communication, enabling the functional transfer of molecules from one cell to another. Moreover, their molecular composition reflects the physiological status of the producing cell and tissue. Consequently, these vesicles have been involved in many [patho]physiological processes such as immunomodulation and intestinal epithelial repair, both key processes involved in inflammatory bowel disease. Given that these vesicles are present in many body fluids, they also provide opportunities for diagnostic, prognostic, and therapeutic applications. In this review, we summarise functional roles of extracellular vesicles in health and disease, with a focus on immune regulation and intestinal barrier integrity, and review recent studies on extracellular vesicles and inflammatory bowel disease. We also elaborate on their clinical potential in inflammatory bowel disease. ispartof: JOURNAL OF CROHNS & COLITIS vol:15 issue:3 pages:499-510 ispartof: location:England status: published

Inflammatory bowel disease and Parkinson's disease are chronic progressive disorders that mainly affect different organs: the gut and brain, respectively. Accumulating evidence has suggested a bidirectional link between gastrointestinal inflammation and neurodegeneration, in accordance with the concept of the 'gut-brain axis'. Moreover, recent population-based studies have shown that inflammatory bowel disease might increase the risk of Parkinson's disease. Although the precise mechanisms underlying gut-brain interactions remain elusive, some of the latest findings have begun to explain the link. Several genetic loci are shared between both disorders with a similar direction of effect on the risk of both diseases. The most interesting example is LRRK2 (leucine-rich repeat kinase 2), initially identified as a causal gene in Parkinson's disease, and recently also implicated in Crohn's disease. In this review, we highlight recent findings on the link between these seemingly unrelated diseases with shared genetic susceptibility. We discuss supporting and conflicting data obtained from epidemiological and genetic studies along with remaining questions and concerns. In addition, we discuss possible biological links including the gut-brain axis, microbiota, autoimmunity, mitochondrial function and autophagy. ispartof: GUT vol:70 issue:2 pages:408-417 ispartof: location:England status: published

Patients with IBD are considered immunosuppressed, but do not seem more vulnerable for COVID-19. Nevertheless, intestinal inflammation has shown an important risk factor for SARS-CoV-2 infection and prognosis. Therefore, we investigated the effect of intestinal inflammation on the viral intestinal entry mechanisms, includingACE2, in IBD.We collected (un)inflamed mucosal biopsies from CD (n=193) and UC (n=158) patients, and 51 matched non-IBD controls for RNA sequencing, differential gene expression and co-expression analysis. Organoids from UC patients were subjected to an inflammatory mix and processed for RNA sequencing. Transmural ileal biopsies were processed for single-cell (sc) sequencing. Publicly available colonic sc-RNA sequencing data, and microarrays from tissue pre/post anti-TNF therapy, were analyzed.In inflamed CD ileum,ACE2was significantly decreased compared to control ileum (p=4.6E-07), whereas colonicACE2expression was higher in inflamed colon of CD/UC compared to control (p=8.3E-03; p=1.9E-03). Sc-RNA sequencing confirmed thisACE2dysregulation, and exclusive epithelialACE2expression. Network analyses highlightedHNF4Aas key regulator of ilealACE2, while pro-inflammatory cytokines and interferon regulating factors regulated colonicACE2.Inflammatory stimuli upregulatedACE2in UC organoids (p=1.7E-02), not in non-IBD controls (p=9.1E-01). Anti-TNF therapy restored colonicACE2dysregulation in responders.Intestinal inflammation alters SARS-CoV-2 coreceptors in the intestine, with opposing effects in ileum and colon.HNF4A, an IBD susceptibility gene, is an important upstream regulator ofACE2in ileum, whereas interferon signaling dominates in colon. Our data support the importance of adequate control of IBD in order to reduce risk of (complicated) COVID-19.

Ulcerative colitis is a chronic inflammatory disease confined to the colon. Although the etiopathogenesis remains unknown, small bowel dysfunctions like histological and permeability alterations have been described in ulcerative colitis. We evaluated the molecular gene signature in the non-inflamed terminal ileum of 36 ulcerative colitis patients (7 active, with Mayo endoscopic subscore &ge, 2, and 29 inactive) as compared to 15 non-inflammatory bowel disease controls. Differential gene expression analysis with DESeq2 showed distinct expression patterns depending on disease activity and maximal disease extent. We found 84 dysregulated genes in patients with active extensive colitis and 20 in inactive extensive colitis, compared to controls. There was an overlap of 5 genes: REG1B, REG1A, MUC4, GRAMD2, and CASP10. In patients with left-sided colitis, ileal gene expression levels were similar to controls. Based on gene co-expression analysis, ileal changes in active ulcerative colitis patients were related to immune functions. The ileal changes in the inactive ulcerative colitis subjects converged into the maintenance of the intestinal barrier through increased mitochondrial function and dampened immune functions. In conclusion, we identified molecular changes in the non-inflamed ileum of ulcerative colitis that are dependent on colonic inflammation.

Dysfunctional resolution of intestinal inflammation and altered mucosal healing are essential features in the pathogenesis of inflammatory bowel disease (IBD). Intestinal macrophages are vital in the process of inflammation resolution, but the mechanisms underlying their mucosal healing capacity remain elusive.We investigated the role of the prostaglandin EHere, we describe a subset of PTGER4-expressing intestinal macrophages with mucosal healing properties both in humans and mice. Csf1r-iCre Ptger4PTGER4

Abstract The characteristics of the fluid–structure interaction on the flexible blades of a horizontal-axis water turbine are studied; this bioinspired technology features mechanical simplicity, performance and lifetime improvement, and low fish impact risk, all characteristics of a truly sustainable renewable energy exploitation. A surface-tracking method synchronized with force measurements was applied on a surrogate model of single-bladed, vertical-axis water turbine in a water channel. This allows for the characterization of the structural deformations and their link to the hydrodynamic forces, over a large range of turbine designs and operating points. It is shown that the phase angles of the maxima in blade deformation coincide with those of the load maxima on a rigid blade in identical flow conditions. The influence of the turbine’s tip/speed ratio on the blade deformation and blade load is investigated. With the chosen blade design, hydrofoil deformation is found to be maximum in the operating points where the performance improvement is maximized ($$k_o=0.3$$ko=0.3). With lower values of reduced frequency (corresponding to lower rotation speed), fluid-induced forces dominate the fluid–structure interaction. Conversely, at higher frequencies, structural inertia dominates the interaction, and blade deformation is again reduced. Results suggest that the optimal blade rigidity may depend on the operating point; nevertheless the potential of the flexible-blade design is demonstrated through clear linking of fluid-induced forces and blade deformation in the complex flow conditions of the Darrieus water turbine. Graphic abstract

Dysfunctional resolution of intestinal inflammation and altered mucosal healing are essential features in the pathogenesis of inflammatory bowel disease (IBD). Intestinal macrophages are vital in the process of resolution of inflammation but the mechanisms underlying their mucosal healing capacity remains elusive. Here, we describe a subset of E prostanoid receptor 4 (EP4) expressing intestinal macrophages with mucosal healing properties both in human and mice. Notably, Csf1r-iCre EP4-fl/fl mice showed defective mucosal healing and intestinal epithelial barrier regeneration in a dextran sodium sulfate-induced colitis model. Mechanistically, an increased mucosal level of prostaglandin E2 (PGE2) triggers the secretion of chemokine (C-X-C motif) ligand 1 (CXCL1) in monocyte-derived EP4+ macrophages via MAPKs. Subsequently, CXCL1 drives epithelial cell differentiation and proliferation from regenerating crypts during the resolution phase of colitis. Thus, EP4+ intestinal macrophages are essential for the support of the intestinal stem cell niche and for the regeneration of the injured epithelium.One Sentence SummaryProstaglandin E2 licenses E-type prostanoid receptor 4 intestinal macrophage regenerative capacity promoting mucosal healing via the secretion of CXCL1

International audience; The characteristics of a vortex power plant integrated in a weir have been investigated using computational fluid dynamics, with a special focus on all flow properties relevant to fish migration and energy conversion. The numerical model relies on a Reynolds-averaged, unsteady description using the volume-of-fluid method to describe the free surface. Several monitors are implemented, quantifying, in particular, the distribution of water velocities within the plant, and the probability of impact between drifting objects and turbine blades. Parameters, such as volume flow rate, turbine clearance, turbine speed and number of turbine blades have been varied. The systematic observation of the distribution of velocities and power density help assess the ecological impact of those modifications. It is found that a moderate increase of the turbine clearance and a reduction of the number of blades provide an attractive compromise between power output and opportunity for easy migration. Finally, it is predicted that the hazard associated with a fish hitting turbine blades can be greatly reduced by a careful adaptation of the turbine rotation velocity. Those developments are a first step towards a systematic numerical assessment of the fish-friendliness of machines operating under stringent ecological regulations.

Background Successful personalized treatment in inflammatory bowel disease (IBD) is critically dependent on identifying those patients at greater risk of a complicated disease course and who therefore may benefit from early advanced therapies. To this end, prospective inception cohorts integrating medical records with multi-omics data are needed. The Belgian Prognostic biobANk of paTients witH Early cRohn’s or colitis (PANTHER) was therefore initiated in 2015. We here present the initial disease course of this cohort. Methods The PANTHER cohort is an inception cohort of adult IBD patients from 3 Belgian, tertiary IBD referral centres. Patients are included within 3 months after diagnosis, are naïve for immunosuppressives and biologicals, and without previous IBD-related surgery. Clinical data are prospectively collected; and DNA, serum, feces and intestinal biopsies are taken at predefined time points. Patients are treated according to routine clinical management. Log-rank tests, and univariate and multivariate analyses were performed in R 3.6.2. Results A total of 289 newly-diagnosed IBD patients were recruited (median [IQR] follow-up of 2.9 [1.4–4.2] years), of whom 161 (56%) had Crohn’s disease (CD), 122 (42%) had ulcerative colitis, and 6 (2%) had IBD type unclassified (Table 1). Thus far, 242 of these patients (83%) are minimally at 1-year follow-up. Twenty-two patients (9%) already needed surgery (n=5 for colectomy and n=17 for ileocecal or small bowel resection) and 124 patients (51%) received biological therapy within the 1st year after diagnosis. Time series analysis showed a clear trend for increase in biological use within the 1st year after diagnosis when comparing 2015–2017 (42%) to 2018–2020 (54%) (p=0.06) (Fig.1). Being exposed to a biological within the 1st year was associated with age (OR=0.98 [95%CI: 0.96–0.99]), CD diagnosis (OR=3.7 (95% CI: 2.2–6.3) and more recent diagnosis (2018–2020 as opposed to previous years) (OR=1.2 [95% CI: 1.2–3.4]). Within CD, perianal disease was the strongest driver for early biological use (OR=4.4 [95% CI: 1.8–12.8]). Early biological exposure led to clear trends in decreased surgery rates one year later (2/99 [2%]) as compared to non-exposed patients (8/108 [7%]) (p=0.07), while hospitalization rates significantly decreased (4% versus 12%, p=0.04). Conclusion In this Belgian inception cohort, an increase in early biological use is observed in recent years and is associated with reduced IBD-related surgery and -hospitalization.

Background and aim Transmural inflammation in Crohn's disease [CD] leads to stricturing or penetrating complications. Factors impacting on the need and timing of surgery in ileal stricturing CD [IS-CD] are understudied. Our aim was to identify risk factors in IS-CD associated with the need for surgery over time. Methods All cross-sectional imaging [XSI] performed for CD between 2006 and 2015 in a tertiary referral centre was analysed. The electronic charts of patients with IS-CD were reviewed for demographic, clinical, biochemical, imaging, genetic, and endoscopic factors. An independent cohort was used for validation. Results A total of 1803 XSI were performed in 957 patients with CD. IS-CD was diagnosed in 235 patients, and 161 of these [69%] needed surgery. Prestenotic dilation (hazard ratio [HR] 2.05, 95% confidence interval [CI] 1.22-3.45, p = 0.007], C-reactive protein at diagnosis of IS-CD > 11 mg/L [HR 1.53, 95% CI 1.05-2.24, p = 0.026], Montreal B3 phenotype [HR 1.58, 95% CI 1.06-2.36, p = 0.023], previous/current anti-tumour necrosis factor [TNF] exposure [HR 1.44, 95% CI 1.00-2.06, p = 0.048], and presence of at least one NOD2 rs2066844 risk allele [HR 1.51, 95% CI 1.02-2.23, p = 0.038] significantly impacted on the need for surgery in multivariate analysis. The risk stratification model [BACARDI] yielded a surgery-free survival after 5 years of 77%, 38%,19%, and 0% for the low, medium, high, and all risk groups, respectively. Based on an independent cohort of 27 patients, the results were validated and demonstrated adequate performance. Conclusions This risk model can facilitate therapeutic decisions in IS-CD and suggest the correct time for surgery in daily clinical practice.

Whole exome sequencing (WES) data are allowing researchers to pinpoint the causes of many Mendelian disorders. In time, sequencing data will be crucial to solve the genome interpretation puzzle, which aims at uncovering the genotype-to-phenotype relationship, but for the moment many conceptual and technical problems need to be addressed. In particular, very few attempts at the in-silico diagnosis of oligo-to-polygenic disorders have been made so far, due to the complexity of the challenge, the relative scarcity of the data and issues such as batch effects and data heterogeneity, which are confounder factors for machine learning (ML) methods. Here, we propose a method for the exome-based in-silico diagnosis of Crohn's disease (CD) patients which addresses many of the current methodological issues. First, we devise a rational ML-friendly feature representation for WES data based on the gene mutational burden concept, which is suitable for small sample sizes datasets. Second, we propose a Neural Network (NN) with parameter tying and heavy regularization, in order to limit its complexity and thus the risk of over-fitting. We trained and tested our NN on 3 CD case-controls datasets, comparing the performance with the participants of previous CAGI challenges. We show that, notwithstanding the limited NN complexity, it outperforms the previous approaches. Moreover, we interpret the NN predictions by analyzing the learned patterns at the variant and gene level and investigating the decision process leading to each prediction. ispartof: NAR GENOMICS AND BIOINFORMATICS vol:2 issue:1 ispartof: location:England status: published

Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Susceptibility to AD is considerably determined by genetic factors which hitherto were primarily identified using case-control designs. Elucidating the genetic architecture of additional AD-related phenotypic traits, ideally those linked to the underlying disease process, holds great promise in gaining deeper insights into the genetic basis of AD and in developing better clinical prediction models. To this end, we generated genome-wide single-nucleotide polymorphism (SNP) genotyping data in 931 participants of the European Medical Information Framework Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) sample to search for novel genetic determinants of AD biomarker variability. Specifically, we performed genome-wide association study (GWAS) analyses on 16 traits, including 14 measures derived from quantifications of five separate amyloid-beta (A beta) and tau-protein species in the cerebrospinal fluid (CSF). In addition to confirming the well-established effects of apolipoprotein E (APOE) on diagnostic outcome and phenotypes related to A beta 42, we detected novel potential signals in the zinc finger homeobox 3 (ZFHX3) for CSF-A beta 38 and CSF-A beta 40 levels, and confirmed the previously described sex-specific association between SNPs in geminin coiled-coil domain containing (GMNC) and CSF-tau. Utilizing the results from independent case-control AD GWAS to construct polygenic risk scores (PRS) revealed that AD risk variants only explain a small fraction of CSF biomarker variability. In conclusion, our study represents a detailed first account of GWAS analyses on CSF-A beta and -tau-related traits in the EMIF-AD MBD dataset. In subsequent work, we will utilize the genomics data generated here in GWAS of other AD-relevant clinical outcomes ascertained in this unique dataset.

Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Susceptibility to AD is considerably determined by genetic factors which hitherto were primarily identified using case-control designs. Elucidating the genetic architecture of additional AD-related phenotypic traits, ideally those linked to the underlying disease process, holds great promise in gaining deeper insights into the genetic basis of AD and in developing better clinical prediction models. To this end, we generated genome-wide single-nucleotide polymorphism (SNP) genotyping data in 931 participants of the European Medical Information Framework Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) sample to search for novel genetic determinants of AD biomarker variability. Specifically, we performed genome-wide association study (GWAS) analyses on 16 traits, including 14 measures derived from quantifications of five separate amyloid-beta (A beta) and tau-protein species in the cerebrospinal fluid (CSF). In addition to confirming the well-established effects of apolipoprotein E (APOE) on diagnostic outcome and phenotypes related to A beta 42, we detected novel potential signals in the zinc finger homeobox 3 (ZFHX3) for CSF-A beta 38 and CSF-A beta 40 levels, and confirmed the previously described sex-specific association between SNPs in geminin coiled-coil domain containing (GMNC) and CSF-tau. Utilizing the results from independent case-control AD GWAS to construct polygenic risk scores (PRS) revealed that AD risk variants only explain a small fraction of CSF biomarker variability. In conclusion, our study represents a detailed first account of GWAS analyses on CSF-A beta and -tau-related traits in the EMIF-AD MBD dataset. In subsequent work, we will utilize the genomics data generated here in GWAS of other AD-relevant clinical outcomes ascertained in this unique dataset.

Objective Although anti-tumour necrosis factor alpha (anti-TNFα) therapies represent a major breakthrough in IBD therapy, their cost–benefit ratio is hampered by an overall 30% non-response rate, adverse side effects and high costs. Thus, finding predictive biomarkers of non-response prior to commencing anti-TNFα therapy is of high value. Design We analysed publicly available whole-genome expression profiles of colon biopsies obtained from multiple cohorts of patients with IBD using a combined computational deconvolution—meta-analysis paradigm which allows to estimate immune cell contribution to the measured expression and capture differential regulatory programmes otherwise masked due to variation in cellular composition. Insights from this in silico approach were experimentally validated in biopsies and blood samples of three independent test cohorts. Results We found the proportion of plasma cells as a robust pretreatment biomarker of non-response to therapy, which we validated in two independent cohorts of immune-stained colon biopsies, where a plasma cellular score from inflamed biopsies was predictive of non-response with an area under the curve (AUC) of 82%. Meta-analysis of the cell proportion-adjusted gene expression data suggested that an increase in inflammatory macrophages in anti-TNFα non-responding individuals is associated with the upregulation of the triggering receptor expressed on myeloid cells 1 (TREM-1) and chemokine receptor type 2 (CCR2)-chemokine ligand 7 (CCL7) –axes. Blood gene expression analysis of an independent cohort, identified TREM-1 downregulation in non-responders at baseline, which was predictive of response with an AUC of 94%. Conclusions Our study proposes two clinically feasible assays, one in biopsy and one in blood, for predicting non-response to anti-TNFα therapy prior to initiation of treatment. Moreover, it suggests that mechanism-driven novel drugs for non-responders should be developed.

Whole exome sequencing (WES) data are allowing researchers to pinpoint the causes of many Mendelian disorders. In time, sequencing data will be crucial to solve the genome interpretation puzzle, which aims at uncovering the genotype-to-phenotype relationship, but for the moment many conceptual and technical problems need to be addressed. In particular, very few attempts at the in-silico diagnosis of oligo-to-polygenic disorders have been made so far, due to the complexity of the challenge, the relative scarcity of the data and issues such as batch effects and data heterogeneity, which are confounder factors for machine learning (ML) methods. Here, we propose a method for the exome-based in-silico diagnosis of Crohn’s disease (CD) patients which addresses many of the current methodological issues. First, we devise a rational ML-friendly feature representation for WES data based on the gene mutational burden concept, which is suitable for small sample sizes datasets. Second, we propose a Neural Network (NN) with parameter tying and heavy regularization, in order to limit its complexity and thus the risk of over-fitting. We trained and tested our NN on 3 CD case-controls datasets, comparing the performance with the participants of previous CAGI challenges. We show that, notwithstanding the limited NN complexity, it outperforms the previous approaches. Moreover, we interpret the NN predictions by analyzing the learned patterns at the variant and gene level and investigating the decision process leading to each prediction.

The intestinal mucosa is a difficult environment to maintain homeostasis as it is constantly challenged by microbial and food antigens. Maintaining an intact epithelial barrier, a continuous turnover of intestinal epithelial cells and normobiosis of the gut microbiota are essential components to prevent intestinal diseases such as inflammatory bowel diseases (IBD) and colorectal cancer (CRC). Inflammasomes are critical immune regulators that are involved in all of these processes. They are multiprotein complexes able to assemble upon interaction with a noxious stimulus that will subsequently lead to caspase-1 activation. Activated caspase-1 will orchestrate the maturation and release of proinflammatory cytokines IL-1β and IL-18, and induce pyroptosis, an inflammatory form of cell death. Both cytokine release and pyroptosis are initiated after detection of molecular patterns by a distinct inflammasome sensor protein. Absent in melanoma 2 (AIM2) is such an inflammasome sensor that specifically responds to the presence of double stranded DNA (dsDNA) in the cytoplasm, leading to the recruitment and activation of caspase-1. Recent studies revealed additional roles of AIM2 in controlling epithelial cell proliferation, tight junction expression and the microbiome. Therefore, AIM2 plays a significant role in maintaining intestinal homeostasis. This review focuses on the multifunctional role of AIM2 in intestinal homeostasis by regulating intestinal immunity and preventing colorectal cancer development.

ObjectiveLymphocyte recruitment to the inflamed gut is increased in UC. Inhibition of this cell trafficking by vedolizumab (VDZ) was successful in inducing and maintaining remission and in induction of endoscopic mucosal healing. There are no data on histological healing with VDZ. We studied histological changes following VDZ therapy and compared gene expression in patients with UC before and after therapy.DesignForty-one patients with UC from GEMINI I and LTS were studied before and at three time points (weeks 6/12/52) following VDZ therapy. Colonic biopsies were scored using the Geboes index and correlated with Mayo endoscopic subscore. Gene expression was analysed using Affymetrix gene arrays.ResultsFifty-five per cent of patients achieving endoscopic healing (= Mayo endoscopic subscore 0–1) with VDZ at the studied time points also had histological healing (= Geboes grade 0–1). In most healers, some residual histological changes (eg, disturbed architecture and increased mononuclear cell infiltrate) were still observed, although this was less at week 52. VDZ restored expression of many inflammatory genes in patients with endoscopic healing only at week 52 and not before. In VDZ healers, the expression of many genes remained dysregulated at weeks 6/12/52 compared with controls.ConclusionsVDZ induces histological healing in >50% of patients with endoscopic healing, with maximal effect at week 52. VDZ also restored, although incompletely, the colonic expression of many immune-related genes in patients with UC achieving endoscopic healing at week 52. However, persistent histological and gene dysregulations did remain even in healers, suggesting that maintenance therapy will be necessary to control the intestinal inflammation.Trial registration numbers:NCT00783718 and NCT00790933; post-results.

Ample evidence exists that Anti-tumor necrosis factor (TNF) concentrations during induction determine short and long-term outcome in inflammatory bowel disease (IBD). We investigated if a variable number of tandem repeats (VNTR) polymorphism in the neonatal Fc-receptor (FcRn), responsible for extending half-life of IgG, influences anti-TNF concentrations in patients with IBD.Retrospective single-center study, including a cohort of 395 infliximab (IFX) naive IBD patients treated with IFX 5 mg/kg on weeks 0, 2, and 6 and a second cohort of 139 adalimumab naive patients, treated with adalimumab 160-80-40 mg on weeks 0, 2, and 4. Area under the serum anti-TNF concentration-time curve (AUC), from week 2 and 6 for IFX and week 2 and 4 for adalimumab, was used to identify factors influencing these drug concentrations.The VNTR2/VNTR3 genotype was associated with a 14% lower IFX AUC compared with patients homozygous for VNTR3/VNTR3 (P=0.03), although this effect became apparent only when immunogenicity (26% lower concentrations, P=9 × 10The VNTR2/3 genotype in the FcRn gene is associated with lower IFX but also lower adalimumab drug exposure during induction in patients with IBD. Previously identified pharmacokinetic modifying factors were confirmed. Identifying risk factors in patients is important as higher induction doses may be needed to ensure optimal disease outcome.

SummaryBackground The long-term efficacy of infliximab in patients with Crohn's disease is suboptimal. Aim To study prognostic factors for real-life long-term effcacy of infliximab in Crohn's disease. Methods All consecutive Crohn's disease patients treated with infliximab at a tertiary centre were retrospectively analysed. Only patients who received scheduled infliximab maintenance treatment were considered. Patient- and disease-related factors were used to identify independent predictors of infliximab failure-free survival using Cox proportional hazards regression. Results Of 1031 patients with Crohn's disease, 261 were eligible for inclusion. Median time on infliximab was 2.4 [IQR 1.4–4.7] years, and 65 (24.9%) patients experienced infliximab failure. Estimated 5-year infliximab failure-free survival was 65.9% (95% CI 58.3–73.5). Multivariate Cox regression identified disease duration ≥1 year (HR 2.5 (95% CI 1.2–5.2), P = 0.02), L1 disease location [HR 2.0 (1.1–3.5), P = 0.02], prior anti-TNF use [HR 2.3 (1.1–4.8), P = 0.03], haemoglobin

A. Palotie on työryhmän Int IBD Genetics Consortium jäsen. One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.

[Arijs, Ingrid] Hasselt Univ, Fac Med & Life Sci, Campus Diepenbeek,Agoralaan Gebouw D, B-3590 Diepenbeek, Hasselt, Belgium. [Arijs, Ingrid] Jessa Hosp, Hasselt, Belgium. [Arijs, Ingrid] Katholieke Univ Leuven, Translat Res Gastrointestinal Disorders TARGID, Dept Clin & Expt Med, Leuven, Belgium. [Cleynen, Isabelle] Katholieke Univ Leuven, Dept Human Genet, Lab Complex Genet, Leuven, Belgium.

Inflammatory bowel disease is a heterogeneous disorder in terms of severity of inflammation, disease progression, and response to treatment. This implicates difficulties for clinical management of the disease. Tools for a precision medicine approach with optimized diagnosis and disease management and cost-effective treatment strategies and less adverse events are indeed eagerly awaited. Molecular profiling could help in this regard. To date, however, molecular profiling of disease progression and treatment responses has lingered behind in the management of inflammatory bowel disease. Still, thanks to technological advances and optimized study designs, predicting phenotypes of inflammatory bowel disease by molecular profiling using different types of omics has been rapidly evolving. In this chapter, we summarize the current status of prediction of disease progression, response to therapy, and adverse events in inflammatory bowel disease to highlight the recent progress made in molecular profiling.

Background Several large genome wide association studies have identified an increasing number of IBD risk loci with currently more than 240 established loci and generated robust data on disease association. However, knowledge remains limited on distinctive associations to specific clinical characteristics. The Swiss IBD Cohort Study (SIBDCS) represents a large prospective cohort study with clinically and phenotypically sound data collection since 2006 including genotyping. In this study, we aimed to determine individual associations of known risk loci with clinical features of patients in the SIBDCS, as well as their combined effect on clinical outcomes. Methods Based on 158 analysed SNPs, we investigated the numerical distribution of risk alleles and determined an individual SNP risk score (defined as percentage of risk alleles; i.e. number of risk alleles divided by twice the number of given SNPs multiplied with 100). We then performed linear regression modelling to investigate, whether relevant clinical disease characteristics associate with this SNP risk score. Further, for each given clinical outcome, a model was run with all SNPs as potential predictors, and the number of significant associations per SNP counted. Results In a total of 2304 genotyped patients, we observed a median number of risk alleles of 167, 168 and 167 for IBD overall, CD and UC/IC, respectively with a narrow inter quartile range [11 (q25 = 162, q75 = 173) for IBD and CD; 12 (q25 = 161, q75 = 173) for UC/IC]. A higher SNP risk score was significantly associated with any complications (defined as a composite of any or more of colorectal cancer, colon dysplasia, intestinal lymphoma, osteopenia/-porosis, anaemia, deep venous thrombosis, pulmonary embolism, nephro- or cholelithiasis, malabsorption syndrome, massive haemorrhage, perforation/peritonitis, pouchitis), stenosis in CD patients; pancolitis, conversion to CD, female sex in UC patients; higher clinical disease activity in both CD & UC. Regarding individual SNPs, we identified substantial differences in terms of the frequency of associations to disease-related outcomes with up to 11 for rs4899554 in CD and 7 for rs9557195 in UC, respectively. Conclusion In our large population of IBD patients there is high per patient frequency of hetero- and homozygous SNP risk alleles. The association of higher SNP risk score with several disease-related outcomes indicates a potential interplay of per patient given SNP risk alleles.

Background Inflammatory bowel diseases (IBD) are complex genetic diseases for which 242 susceptibility loci have been identified thus far. For translational or functional follow-up studies it can be of interest to know the genotype of specific variants. For other studies a composite genetic risk score–the polygenic risk score–is of value. There currently is a gap in technology to genotype a few hundred variants in a flexible and cost-effective way. We therefore developed a genotyping assay for the 242 validated IBD susceptibility loci. Methods Using MIPgen v.1.1, we designed molecular inversion probes (MIPs) covering 269 independent variants from the 242 IBD loci. MIP libraries were prepared according to Neveling et al. (Clin Chem. 2017), followed by paired-end sequencing using a MiSeq® System (Illumina). In the pilot studies, 16 IBD patients were genotyped, and results were compared with available immunochip (ichip) data. Genotypes for the covered variants were obtained using an in-house developed pipeline, and performance metrics were assessed (incl. genotyping call rate, percentage off-target reads and concordance with ichip-based genotypes). After optimisation, we genotyped 279 individuals (168 IBD patients and 111 non-IBD controls). We also calculated a weighted IBD polygenic risk score (PRSice 2.0) for these. Results Despite a genotyping call rate of 94.3%, the first pilot run suffered from a high rate of off-target reads (52.5%). After redesigning poorly-performing MIPs, off-target reads dropped to 9.4%, and the genotyping call rate increased to 97.5%. Concordance with genotypes previously obtained from ichip was 99.3%. When applying the optimised design on a larger scale (i.e. on the 279 individuals), we obtained similar performance metrics, with 8.0% off-target reads and a genotyping call rate of 97.3%. Moreover, upscaling resulted in a turnaround time of 2.5 working days/96 samples and a cost of €14/sample. The calculated IBD polygenic risk scores showed higher scores in patients as compared with controls (5.5E−03 vs. 4.0E−03, p = 8.80E−10; R² IBD polygenic risk score = 0.15, p = 1.28E−07), however with a large overlap between both groups. Quartile analysis showed that individuals within the highest quartile had an 8.1-fold (95% CI: 3.7–17.5) increase in risk towards IBD compared with individuals in the first quartile. Conclusion We developed a cost-effective genotyping assay for currently known IBD risk loci, with an integrated bioinformatics pipeline from raw sequencing data to individual genotypes and calculation of a polygenic risk score. Furthermore, this assay enables genotyping of individuals on a large scale while remaining flexible to implement newly identified genetic variants.

Background: The genetic component of Crohn's disease (CD) is well known, with 140 susceptibility loci identified so far. In addition to single nucleotide polymorphisms typically studied in genome-wide scans, copy number variation is responsible for a large proportion of human genetic variation. Methods: We performed a genome-wide search for copy number variants associated with CD using array comparative genomic hybridization. One of the found regions was validated independently through real-time PCR. Serum levels of the found gene were measured in patients and control subjects. Results: We found copy number differences for the C4S and C4L gene variants of complement component C4 in the central major histocompatibility complex region on chromosome 6p21. Specifically, we saw that CD patients tend to have lower C4L and higher C4S copies than control subjects (P = 5.00 x 10(-03) and P = 9.11 x 10(-04)), which was independent of known associated classical HLA I and II alleles (P = 7.68 x 10(-03) and P = 6.29 x 10(-03)). Although C4 serum levels were not different between patients and control subjects, the relationship between C4 copy number and serum level was different for patients and control subjects with higher copy numbers leading to higher serum concentrations in control subjects, compared with CD patients (P < 0.001). Conclusions: C4 is part of the classical activation pathway of the complement system, which is important for (auto)immunity. Low C4L or high C4S copy number, and corresponding effects on C4 serum level, could lead to an exaggerated response against infections, possibly leading to (auto)immune disease.