Osteosarcoma is the most prevalent cancer-related bone disease diagnosed in the pediatric age group. The rapid development of metastatic lesions and resistance to chemotherapy remain major mechanisms responsible for the failure of treatments and poor outcome. We established that the expression level of Cysteine-rich protein 61 (CYR61/CCN1) correlates to tumor neo-vascularization and dissemination in preclinical and clinical osteosarcoma samples. The aim of this study was to investigate the CYR61-related mechanisms leading to the acquisition of metastatic capacity by osteosarcoma cells. Transcriptomic data issued from RNA-seq were subjected to pathways and gene set enrichment analyses. Murine and human cell lines with overexpressed or downregulated C-terminal Binding protein 2 (CtBP2) were established by lentiviral transduction. Cell metabolic activity was assessed by Seahorse XF Analyzer; cell replication rate by BrdU incorporation assay; stemness by clonogenicity assay and RT-qPCR detection of markers; cell migration by wound healing assay and Boyden chambers system; cell invasion using Matrigel coated Boyden chambers or fluorescence microscopy of Matrigel embedded 3D spheroids. FFPE samples derived from syngeneic tumor cells grafts into BALB/c mice were analyzed by IHC. The protein interactome was predicted in silico using the STRING database. GSEA revealed that CYR61 modulate the transcription process. The in vitro expression level of CtBP2 and Cyr61 correlated positively in a panel of osteosarcoma cell lines. In silico analysis of protein–protein interaction network revealed a link with stemness markers. Variations in CtBP2 expression levels influenced stemness markers expression levels, cell clonogenicity, cell migration, Matrix Metalloproteinase activity and cell invasion. Surprisingly, while induction of CtBP2 expression under CYR61 correlated with the metastatic dissemination process in vivo, it occurred only at the invasive front of tumors. Hypoxic conditions in central tumor region interfered with CtBP2 induction of expression. Our findings identify for the first time that CtBP2 acts as a required critical inducing factor in the CYR61-related metastatic progression of osteosarcoma, by favoring cell migration and invasiveness. Moreover, we demonstrate that while CtBP2 is a downstream transcriptional target of CYR61 signaling cascade, it occurs only under non-hypoxic conditions. The present study suggests that CtBP2 may represent a potential pivotal target for therapeutic management of metastases spreading in osteosarcoma.

BackgroundTicks, hematophagous Acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes, which includes the main vectors of Lyme disease.ResultsHere, we present the genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus, and I. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes-most strikingly for fatty acid elongases and sulfotransferases.ConclusionsThe integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA.

Primary familial brain calcification (PFBC) is characterized by calcium deposition in the brain, causing progressive movement disorders, psychiatric symptoms, and cognitive decline. PFBC is a heterogeneous disorder currently linked to variants in six different genes, but most patients remain genetically undiagnosed. Here, we identify biallelic NAA60 variants in ten individuals from seven families with autosomal recessive PFBC. The NAA60 variants lead to loss-of-function with lack of protein N-terminal (Nt)-acetylation activity. We show that the phosphate importer SLC20A2 is a substrate of NAA60 in vitro. In cells, loss of NAA60 caused reduced surface levels of SLC20A2 and a reduction in extracellular phosphate uptake. This study establishes NAA60 as a causal gene for PFBC, provides a possible biochemical explanation of its disease-causing mechanisms and underscores NAA60-mediated Nt-acetylation of transmembrane proteins as a fundamental process for healthy neurobiological functioning.

Hidradenitis suppurativa (HS) is a chronic skin disease characterized by painful, recurrent abscesses, nodules, and scarring, primarily in skin folds. The exact causes of HS are multifactorial, involving genetic, hormonal, and environmental factors. It is associated with systemic diseases such as metabolic syndrome and inflammatory bowel disease. Genetic studies have identified mutations in the γ-secretase complex that affect Notch signaling pathways critical for skin cell regulation. Despite its high heritability, most reported HS cases do not follow a simple genetic pattern. In this article, we performed whole-exome sequencing (WES) on a cohort of 100 individuals with HS, and we provide a comprehensive review of the variants known to be described or associated with HS. 91 variants were associated with the γ-secretase complex, and 78 variants were associated with other genes involved in the Notch pathway, keratinization, or immune response. Through this new genetic analysis, we have added ten new variants to the existing catalogs. All variants are available in a .vcf file and are provided as a resource for future studies.

Monitoring the presence of RNA from emerging pathogenic viruses, such as SARS-CoV-2, in wastewater (WW) samples requires suitable methods to ensure an effective response. Genome sequencing of WW is one of the crucial methods, but it requires high-quality RNA in sufficient quantities, especially for monitoring emerging variants. Consequently, methods for viral concentration and RNA extraction from WW samples have to be optimized before sequencing. The purpose of this study was to achieve high coverage (> 90 %) and sequencing objective was to determine the range of SARS-CoV-2 RNA concentrations that allow high-quality sequencing, and the optimal sample volume for analysis. Ultrafiltration (UF) methods were used to concentrate viral particles from large influent samples (up to 500 mL). An RNA extraction protocol using silica beads, neutral phenolchloroform treatment, and a PCR inhibitor removal kit was chosen for its effectiveness in extracting RNA and eliminating PCR inhibitors, as well as its adaptability for use with large influent samples. Recovery rates ranged enough for UF concentration, as they showed high quality sequencing analyses with between 5 x 10(4) GC/L and 6 x 10(3) GC/L. Below 6 x 10(3) GC/L, high-quality sequencing was also achieved for similar to 40 % of the samples using 500 mL of WW. Sequencing analysis for variant detection was performed on 200 mL WW samples with coverage (66 %-100 %). The use of UF methods in combination with a suitable RNA extraction protocol appear promising for sequencing enveloped viruses in WW in a context of viral emergence.

The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes of 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale population structure across Brittany and the downstream Loire basin and increased population differentiation between the northern and southern sides of the river Loire, associated with higher proportions of steppe vs. Neolithic-related ancestry. We also found increased allele sharing between individuals from Western Brittany and those associated with the Bell Beaker complex. Our results emphasise the need for investigating local populations to better understand the distribution of rare (putatively deleterious) variants across space and the importance of common genetic legacy in understanding the sharing of disease-related alleles between Brittany and people from western Britain and Ireland. Here, the authors look at present day and medieval genome samples from Northern France to piece together demographic history and population structure across Brittany and the Loire basin.

Purpose: To assess the likely pathogenic/pathogenic (LP/P) variants rates in Mendelian dementia genes and the moderate-to-strong risk factors rates in patients with Alzheimer disease (AD). Methods: We included 700 patients in a prospective study and performed exome sequencing. A panel of 28 Mendelian and 6 risk-factor genes was interpreted and returned to patients. We built a framework for risk variant interpretation and risk gradation and assessed the detection rates among early-onset AD (EOAD, age of onset (AOO) <= 65 years, n = 608) depending on AOO and pedigree structure and late-onset AD (66 < AOO < 75, n = 92). Results: Twenty-one patients carried a LP/P variant in a Mendelian gene (all with EOAD, 3.4%), 20 of 21 affected APP, PSEN1, or PSEN2. LP/P variant detection rates in EOAD ranged from 1.7% to 11.6% based on AOO and pedigree structure. Risk factors were found in 69.5% of the remaining 679 patients, including 83 (12.2%) being heterozygotes for rare risk variants, in decreasing order of frequency, in TREM2, ABCA7, ATP8B4, SORL1, and ABCA1, including 5 heterozygotes for multiple rare risk variants, suggesting non-monogenic inheritance, even in some autosomal-dominant-like pedigrees. Conclusion: We suggest that genetic screening should be proposed to all EOAD patients and should no longer be prioritized based on pedigree structure. (c) 2024 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Venous thromboembolism (VT) is a frequent (annual incidence of 1 to 2 per 1,000) and potentially life-threatening (case-fatality rate up to 10%) disease. VT is associated with serious short-term and long-term complications including a recurrence rate of approximately 20% within five years. Anticoagulant therapy, the mainstay of VT treatment, drastically reduces the risk of early VT recurrence, but it exposes patients to a substantial risk of bleeding. We analysed the genomic architecture of VT recurrence using data from 6,571 patients across eight cohorts, 1,816 of whom experienced recurrence, with a particular focus on the clinical manifestation of the type of first VT event. Through genome-wide association studies (GWAS), we identified three loci significantly associated (P<5×10-8) with VT recurrence in the general VT population: GPR149/MME, L3MBTL4, and THSD7B. Protein Quantitative Trait Locus and Mendelian Randomization analyses further identified elevated plasma levels of coagulation factor XI and GOLM2 as risk factors for recurrence, while decreased levels of PCSK9 and pro-IL16 were linked to reduced VT recurrence risk. Subgroup analyses revealed 18 loci associated with VT recurrence, with notable differences between pulmonary embolism (PE) and deep vein thrombosis (DVT). For example, the exonic variant SLC4A1 p.Glu40Lys was significantly associated with recurrence in PE patients (Hazard Ratio (HR)=3.23, P=9.7×10-12) but showed no effect in DVT (HR=1.00, P=0.98). These findings emphasize the role of specific genetic loci and protein pathways in influencing VT recurrence and provide valuable insights into potential therapeutic targets. Further research is needed to clarify the biological mechanisms driving these associations.

BACKGROUND:Isolated posterior leaflet mitral valve prolapse (PostMVP), a common form of MVP, often referred as fibroelastic deficiency, is considered a degenerative disease. PostMVP patients are usually asymptomatic and often undiagnosed until chordal rupture. The present study aims to characterize familial PostMVP phenotype and familial recurrence, its genetic background, and the pathophysiological processes involved. METHODS:We prospectively enrolled 284 unrelated MVP probands, of whom 178 (63%) had bi-leaflet MVP and 106 had PostMVP (37%). Familial screening within PostMVP patients allowed the identification of 20 families with inherited forms of PostMVP for whom whole genome sequencing was carried out in probands. Functional in vivo and in vitro investigations were performed in zebrafishand in Hek293T cells. RESULTS:In the 20 families with inherited form of PostMVP, 38.8% of relatives had a MVP/prodromal form, mainly of the posterior leaflet, with transmission consistent with an autosomal dominant mode of inheritance. Compared with control relatives, PostMVP family patients have clear posterior leaflet dystrophy on echocardiography. Patients with PostMVP present a burden of rare genetic variants in ARHGAP24. ARHGAP24 encodes the filamin A binding RhoGTPase-activating protein FilGAP and its silencing in zebrafish leads to atrioventricular regurgitation. In vitro functional studies showed that variants of FilGAP, found in PostMVP families, are loss-of-function variants impairing cellular adhesion and mechano-transduction capacities. CONCLUSIONS:PostMVP should not only be considered an isolated degenerative pathology but as a specific heritable phenotypic trait with genetic and functional pathophysiological origins. The identification of loss-of-function variants in ARHGAP24 further reinforces the pivotal role of mechano-transduction pathways in the pathogenesis of MVP. CLINICAL PERSPECTIVE:Isolated posterior mitral valve prolapse (PostMVP), often called fibro-elastic deficiency MVP, is at least in some patients, a specific inherited phenotypic traitPostMVP has both genetic and functional pathophysiological origins Genetic variants in the ARHGAP24 gene, which encodes for the FilGAP protein, cause progressive Post MVP in familial cases, and impair cell adhesion and mechano-transduction capacities.

Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.

Background Factor V (FV) is a key molecular player in the coagulation cascade. FV plasma levels have been associated with several human diseases, including thrombosis, bleeding, and diabetic complications. So far, 2 genes have been robustly found through genome‐wide association analyses to contribute to the inter‐individual variability of plasma FV levels: structural F5 gene and PLXDC2. Methods and Results The authors used the underestimated Brown‐Forsythe methodology implemented in the QuickTest software to search for non‐additive genetic effects that could contribute to the inter‐individual variability of FV plasma activity. QUICKTEST was applied to 4 independent genome‐wide association studies studies (LURIC [Ludwigshafen RIsk and Cardiovascular Health Study], MARTHA [Marseille Thrombosis Association], MEGA [Multiple Environmental and Genetic Assessment], and RETROVE [Riesgo de Enfermedad Tromboembolica Venosa]) totaling 4505 participants of European ancestry with measured FV plasma levels. Results obtained in the 4 cohorts were meta‐analyzed using a fixed‐effect model. Additional analyses involved exploring haplotype and gene×gene interactions in downstream investigations. A genome‐wide significant signal at the PSKH2 locus on chr8q21.3 with lead variant rs75463553 with no evidence for heterogeneity across cohorts was observed ( P =0.518). Although rs75463553 did not show an association with mean FV levels ( P =0.49), it demonstrated a robust significant ( P =3.38x10 −9 ) association with the variance of FV plasma levels. Further analyses confirmed the reported association of PSKH2 with neutrophil biology and revealed that rs75463553 likely interacts with two loci, GRIN2A and POM121L12 , known for their involvement in smoking biology. Conclusions This comprehensive approach identifies the role of PSKH2 as a novel molecular player in the genetic regulation of FV, shedding light on the contribution of neutrophils to FV biology.

INTRODUCTIONGenetics of cerebral amyloid angiopathy (CAA) remains understudied.METHODSWe assessed variants in Alzheimer's disease (AD) risk factor genes and differential diagnosis genes by performing exome sequencing among 78 patients with early-onset definite or probable CAA, after negative screening for APP mutation or duplication.RESULTSAmong 14 genes involved in non-A beta CAA, or vascular leukoencephalopathies, we detected pathogenic NOTCH3 variants in two patients, who exhibited lobar hematomas at the ages of 58 and 65, leading to a diagnosis redirection toward CADASIL. Of the remaining 76 patients, 23.1% carried at least one apolipoprotein E (APOE) epsilon 2 allele and 43.6% carried at least one APOE epsilon 4 allele, known as CAA risk factors. A total of 15 out of 76 (19.7%) carried either a loss-of-function or a rare predicted damaging missense or known AD risk variant in SORL1, TREM2, ABCA7, ABCA1, and ATP8B4.DISCUSSIONExome sequencing allowed the redirection toward CADASIL in two patients and suggested shared genetic factors between AD and CAA, beyond the APOE gene.Highlights The genetic component of cerebral amyloid angiopathy (CAA) remains understudied. Rare differential diagnoses such as CADASIL should be considered, even in cases of cerebral hemorrhage. Our study suggests shared genetic factors between AD and CAA, beyond the APOE gene. Rare variants in SORL1, TREM2, ABCA7, ABCA1 and ATP8B4 might be susceptibility factors in early-onset CAA.,

Background: De novo mutations (DNMs) significantly impact health, particularly through developmental disorders. DNMs occur in both paternal and maternal germlines via diverse mechanisms including parental early embryonic mosaicism, which increases recurrence risk for future pregnancies through germline mosaicism. Embryonic mosaicism is divided based on primordial germ cell specification (PGCS): pre-PGCS events may affect both germline and somatic tissues, while post-PGCS events are only found in the germline. The specific contribution of germline mosaicism to DNMs across the genome is not well defined. We aimed at categorizing DNMs and their recurrence risk by detecting a large set of DNMs followed by systematic deep sequencing of parental blood and sperm DNA. Methods: We performed trio-based short-read genome sequencing for initial DNM detection and long-read genome sequencing for phasing, followed by high-depth targeted sequencing of parental blood and paternal sperm to detect germline mosaicism. Results: We detected a total of 428 DNMs (on average 85.6 per trio, n = 5 trios), with an expected paternal bias of 80%. Targeted resequencing of parental blood and sperm (depth > 5000x) unveiled 20/334 parental germline mosaics (2–5 per trio) with variant allele fractions (VAFs) ranging from 0.24–14.7%, including 7 that were detected in paternal sperm exclusively (1–2 per trio). We estimate that individual genomes harbour about 2 paternal and 2 maternal pre-PGCS DNMs and 2 paternal post-PGCS DNMs (detectable in sperm only). Due to paternal bias, maternally phased variants appear 3.4x more likely to be mosaic in blood. By using average VAFs in sperm as a direct indicator, we estimate recurrence risk of genome -wide paternally phased de novo variants to be 0.3%, prior to any sperm sequencing assessment. This estimate is an average between a majority of variants with a null recurrence risk and a handful of variants with a high recurrence risk. Conclusions: Genetic counselling of DNM may not rely anymore on empirical estimates of recurrence risk. Sperm sequencing may be an effective method to reliably specify the recurrence risk of most individual DNMs. Long-read sequencing, allowing the phasing of DNMs, may also become critical in this process.

T cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and complications. Hematopoietic stem cells (HSC) transplantation constitutes a valuable option to restore proper immune function. However, delayed T cell reconstitution is observed compared to other lineages. To overcome this difficulty, we developed a new approach to identify populations with efficient lymphoid reconstitution properties. To this end, we use a DNA barcoding strategy based on the insertion into a cell chromosome of a lentivirus (LV) carrying a non-coding DNA fragment named barcode (BC). These will segregate through cell divisions and be present in cells' progeny. The remarkable characteristic of the method is that different cell types can be tracked simultaneously in the same mouse. Thus, we in vivo barcoded LMPP and CLP progenitors to test their ability to reconstitute the lymphoid lineage. Barcoded progenitors were co-grafted in immuno-compromised mice and their fate analyzed by evaluating the BC composition in transplanted mice. The results highlight the predominant role of LMPP progenitors for lymphoid generation and reveal valuable novel insights to be reconsidered in clinical transplantation assays.

A bstract Semicontinuous data, characterized by an excess of zeros followed by a non-negative and right-skewed distribution, are frequently observed in biomedical research. Different statistical models have been proposed to investigate the association of covariates with such outcome. Motivated by the search of genetic factors associated with Neutrophil Extracellular Traps (NETs), a semicontinuous biomarker involved in thrombosis, we here investigated the impact of the selected model for semicontinuous traits in the context of a Genome Wide Association Study (GWAS). We compared three models that jointly model zero and positive values while allowing the estimation of a single association parameter of covariates with the global mean: Tobit, Negative Binomial and Compound Poisson-Gamma. We assessed the fit of these models to a sample of 657 participants of the FARIVE study measured for NETs plasma levels. For each of these three models, we performed a GWAS on NETs in FARIVE participants and results were compared. A simulation study was also conducted to evaluate the control of the type I error. Compound Poisson-Gamma and Negative Binomial models fitted NETs data observed in FARIVE better than the Tobit model. However, the Negative Binomial model suffered from an inflation of its type I error, attributable to extreme positive values of the NETs and low frequency variants. Conversely, the Compound Poisson-Gamma model was robust to both phenomena. Using the latter model, a GWAS identified a genome wide significant locus on chr21q21.3. The lead variant was rs57502213, a deletion of two nucleotides located ∼40kb upstream the non-coding RNA (miR155HG) hosting the miR-155 that was recently highlighted to have a role in NETs formation. This work indicates that the modeling strategy for a semicontinuous outcome in the framework of GWAS studies is crucial. The choice of the model should take into account the nature of the process generating zero values and the presence of extreme values. Our work also suggests that the Compound Poisson-Gamma model, while still marginally employed, can be a robust modeling strategy for GWAS analysis on a semicontinuous trait.