Human ALPI deficiency causes inflammatory bowel disease and highlights a key mechanism of gut homeostasis

Herein, we report the first identification of biallelic-inherited mutations in ALPI as a Mendelian cause of inflammatory bowel disease in two unrelated patients. ALPI encodes for intestinal phosphatase alkaline, a brush border metalloenzyme that hydrolyses phosphate from the lipid A moiety of lipopolysaccharides and thereby drastically reduces Toll-like receptor 4 agonist activity. Prediction tools and structural modelling indicate that all mutations affect critical residues or inter-subunit interactions, and heterologous expression in HEK293T cells demonstrated that all ALPI mutations were loss of function. ALPI mutations impaired either stability or catalytic activity of ALPI and rendered it unable to detoxify lipopolysaccharide-dependent signalling. Furthermore, ALPI expression was reduced in patients’ biopsies, and ALPI activity was undetectable in ALPI-deficient patient\u27s stool. Our findings highlight the crucial role of ALPI in regulating host–microbiota interactions and restraining host inflammatory responses. These results indicate that ALPI mutations should be included in screening for monogenic causes of inflammatory bowel diseases and lay the groundwork for ALPI-based treatments in intestinal inflammatory disorders

Duplication of the IL2RA locus causes excessive IL-2 signaling and may predispose to very early onset colitis

Single genetic mutations predispose to very early onset inflammatory bowel disease (VEO-IBD). Here, we identify a de novo duplication of the 10p15.1 chromosomal region, including the IL2RA locus, in a 2-year-old girl with treatment-resistant pancolitis that was brought into remission by colectomy. Strikingly, after colectomy while the patient was in clinical remission and without medication, the peripheral blood CD4:CD8 ratio was constitutively high and CD25 expression was increased on circulating effector memory, Foxp3(+), and Foxp3(neg) CD4(+) T cells compared to healthy controls. This high CD25 expression increased IL-2 signaling, potentiating CD4(+) T-cell-derived IFN gamma secretion after T-cell receptor (TCR) stimulation. Restoring CD25 expression using the JAK1/3-inhibitor tofacitinib controlled TCR-induced IFN gamma secretion in vitro. As diseased colonic tissue, but not the unaffected duodenum, contained mainly CD4(+) T cells with a prominent IFN gamma-signature, we hypothesize that local microbial stimulation may have initiated colonic disease. Overall, we identify that duplication of the IL2RA locus can associate with VEO-IBD and suggest that increased IL-2 signaling predisposes to colonic intestinal inflammation.Transplantation and immunomodulatio

Bi-allelic variants in IPO8 cause a connective tissue disorder associated with cardiovascular defects, skeletal abnormalities, and immune dysregulation.

Dysregulated transforming growth factor TGF-β signaling underlies the pathogenesis of genetic disorders affecting the connective tissue such as Loeys-Dietz syndrome. Here, we report 12 individuals with bi-allelic loss-of-function variants in IPO8 who presented with a syndromic association characterized by cardio-vascular anomalies, joint hyperlaxity, and various degree of dysmorphic features and developmental delay as well as immune dysregulation; the individuals were from nine unrelated families. Importin 8 belongs to the karyopherin family of nuclear transport receptors and was previously shown to mediate TGF-β-dependent SMADs trafficking to the nucleus in vitro. The important in vivo role of IPO8 in pSMAD nuclear translocation was demonstrated by CRISPR/Cas9-mediated inactivation in zebrafish. Consistent with IPO8's role in BMP/TGF-β signaling, ipo8-/- zebrafish presented mild to severe dorso-ventral patterning defects during early embryonic development. Moreover, ipo8-/- zebrafish displayed severe cardiovascular and skeletal defects that mirrored the human phenotype. Our work thus provides evidence that IPO8 plays a critical and non-redundant role in TGF-β signaling during development and reinforces the existing link between TGF-β signaling and connective tissue defects

UNC45A deficiency causes microvillus inclusion disease–like phenotype by impairing myosin VB–dependent apical trafficking

International audienceVariants in the UNC45A cochaperone have been recently associated with a syndrome combining diarrhea, cholestasis, deafness, and bone fragility. Yet the mechanism underlying intestinal failure in UNC45A deficiency remains unclear. Here, biallelic variants in UNC45A were identified by next-generation sequencing in 6 patients with congenital diarrhea. Corroborating in silico prediction, variants either abolished UNC45A expression or altered protein conformation. Myosin VB was identified by mass spectrometry as client of the UNC45A chaperone and was found misfolded in UNC45A(KO) Caco-2 cells. In keeping with impaired myosin VB function, UNC45A(KO) Caco-2 cells showed abnormal epithelial morphogenesis that was restored by full-length UNC45A, but not by mutant alleles. Patients and UNC45A(KO) 3D organoids displayed altered luminal development and microvillus inclusions, while 2D cultures revealed Rab11 and apical transporter mislocalization as well as sparse and disorganized microvilli. All those features resembled the subcellular abnormalities observed in duodenal biopsies from patients with microvillus inclusion disease. Finally, microvillus inclusions and shortened microvilli were evidenced in enterocytes from unc45a-deficient zebrafish. Taken together, our results provide evidence that UNC45A plays an essential role in epithelial morphogenesis through its cochaperone function of myosin VB and that UNC45A loss causes a variant of microvillus inclusion disease

Inherited p40^{phox} deficiency differs from classic chronic granulomatous disease

Biallelic loss-of-function (LOF) mutations of the NCF4 gene, encoding the p40^{phox} subunit of the phagocyte NADPH oxidase, have been described in only 1 patient. We report on 24 p40^{phox}-deficient patients from 12 additional families in 8 countries. These patients display 8 different in-frame or out-of-frame mutations of NCF4 that are homozygous in 11 of the families and compound heterozygous in another. When overexpressed in NB4 neutrophil-like cells and EBV-transformed B cells in vitro, the mutant alleles were found to be LOF, with the exception of the p.R58C and c.120_134del alleles, which were hypomorphic. Particle-induced NADPH oxidase activity was severely impaired in the patients’ neutrophils, whereas PMA-induced dihydrorhodamine-1,2,3 (DHR) oxidation, which is widely used as a diagnostic test for chronic granulomatous disease (CGD), was normal or mildly impaired in the patients. Moreover, the NADPH oxidase activity of EBV-transformed B cells was also severely impaired, whereas that of mononuclear phagocytes was normal. Finally, the killing of Candida albicans and Aspergillus fumigatus hyphae by neutrophils was conserved in these patients, unlike in patients with CGD. The patients suffer from hyperinflammation and peripheral infections, but they do not have any of the invasive bacterial or fungal infections seen in CGD. Inherited p40^{phox} deficiency underlies a distinctive condition, resembling a mild, atypical form of CGD

Inherited p40phox deficiency differs from classic chronic granulomatous disease

Biallelic loss-of-function (LOF) mutations of the NCF4 gene, encoding the p40phox subunit of the phagocyte NADPH oxidase, have been described in only 1 patient. We report on 24 p40phox-deficient patients from 12 additional families in 8 countries. These patients display 8 different in-frame or out-of-frame mutations of NCF4 that are homozygous in 11 of the families and compound heterozygous in another. When overexpressed in NB4 neutrophil-like cells and EBV-transformed B cells in vitro, the mutant alleles were found to be LOF, with the exception of the p.R58C and c.120_134del alleles, which were hypomorphic. Particle-induced NADPH oxidase activity was severely impaired in the patients' neutrophils, whereas PMA-induced dihydrorhodamine-1,2,3 (DHR) oxidation, which is widely used as a diagnostic test for chronic granulomatous disease (CGD), was normal or mildly impaired in the patients. Moreover, the NADPH oxidase activity of EBV-transformed B cells was also severely impaired, whereas that of mononuclear phagocytes was normal. Finally, the killing of Candida albicans and Aspergillus fumigatus hyphae by neutrophils was conserved in these patients, unlike in patients with CGD. The patients suffer from hyperinflammation and peripheral infections, but they do not have any of the invasive bacterial or fungal infections seen in CGD. Inherited p40phox deficiency underlies a distinctive condition, resembling a mild, atypical form of CGD.info:eu-repo/semantics/publishedVersio

Diagnostic yield of next-generation sequencing in very early-onset inflammatory bowel diseases: a multicenter study (vol 12, pg 1104, 2021)

Transplantation and immunomodulatio

Caractérisation des entéropathies monogéniques

Background: Mendelian mutations causing monogenic enteropathies are identified in an increasing number of genes and are responsible for either chronic inflammatory diseases (frequently called VEO-IBD for very early-onset inflammatory bowel diseases) or for congenital diarrheal disorders (CDD). Management of many patients with monogenic enteropathies requires difficult therapeutic decisions and heavy treatments, such as hematopoietic stem cell transplantation for VEO-IBD patients, or total parenteral nutrition and intestinal transplantation for CDD patients. Early molecular diagnosis is crucial to define the most pertinent treatment and increase life expectancy. During my thesis, I introduced in the laboratory big data management tool (e. g. online dedicated database) and applied next-generation sequencing tools (whole exome sequencing (WES) and targeted gene panel sequencing (TGPS)) to a cohort of patients suffering from monogenic enteropathies in order to characterize them phenotypically and genetically. Methods: My thesis was divided in 4 steps. In Step 1, patients (n=216 in January 2016, n=260 in August 2016) recruited through a French research protocol (Immunobiota, 12 centers) and European network (GENIUS, 33 centers) were phenotypically characterized through an online dedicated database. Following precise phenotyping, molecular diagnoses were obtained by Sanger sequencing of candidate genes suggested by functional tests in Step 2. Step 3 was the adaptation of WES for our cohort of patients (59 patients were sequenced in trio and 11 sequenced by themselves or in duo) and lastly, in Step 4, TGSP was designed and applied to our cohort (173 patients without a molecular diagnosis). Findings: The cohort gathered 57 patients including 22 with a molecular diagnosis in January 2012, and 216 patients including 70 with a diagnosis in January 2016, corresponding to a global diagnosis rate of 1/3. Approximately 50 new patients are recruited each year, with blood samples taken from each patient, both parents and siblings. During this period, 11 diagnoses were obtained by a phenotype-based approach, with identification of mutations notably in IL-10R (4 patients) and XIAP (4 patients). Eleven patients obtained a genetic diagnosis by WES including two siblings with a MALT1 deficiency responsible for an IPEX-like syndrome. Because of the increasing number of genes involved in monogenic enteropathies, we developed, in collaboration with Genomics, Bioinformatics and Translational Genetics platforms from the Institut IMAGINE, a custom-made TGPS gathering 68 genes responsible for either VEO-IBD or CDD. The sequencing of all negative patients (n=173) on this panel allowed to identify 28 new diagnoses (among which 8 were made in patients included before 2012). Interpretation: This work lead to the identification of the genetic diagnosis in 1/3 patients. The close investigations of phenotype-genotype correlations highlighted frequent overlaps among monogenic enteropathies. Following completion of this work, we suggest to use TGPS as a first-line genetic test in addition to a precise phenotyping of the patient. Depending on the results, TGPS will either reach an early molecular diagnosis crucial to optimize treatments in a cost-effective manner, or allow to perform further genetic analysis notably by WES.Pas de résum

Loss-of-Function Mutation in PTPN2 Causes Aberrant Activation of JAK Signaling Via STAT and Very Early Onset Intestinal Inflammation

International audienc