Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders.

BACKGROUND: Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression. METHODS: We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance. RESULTS: We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs. CONCLUSION: Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.

High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders.

Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.

Delayed TME Surgery in a Watch-and-Wait Strategy After Neoadjuvant Chemoradiotherapy for Rectal Cancer: An Analysis of Hospital Costs and Surgical and Oncological Outcomes.

BACKGROUND: A watch-and-wait strategy for patients with rectal cancer with a clinical complete response after neoadjuvant chemoradiotherapy is a valuable alternative for rectal resection. However, there are patients who will have residual tumor or regrowth during watch and wait. OBJECTIVE: The aim of this study was to investigate safety and costs for patients who underwent delayed surgery after neoadjuvant chemoradiotherapy. DESIGN: This is a retrospective cohort study with prospectively collected data. SETTINGS: The study was conducted at a large teaching hospital. PATIENTS: Between January 2015 and May 2020, 622 new rectal cancer patients were seen, of whom 200 received neoadjuvant chemoradiotherapy. Ninety-four patients were included, 65 of whom underwent immediate surgery and 29 of whom required delayed surgery after an initial watch-and-wait approach. MAIN OUTCOME MEASURES: Outcome measures included 30-day postoperative morbidity rate, hospital costs. 2-year overall and disease-free survival. RESULTS: There was no difference in length of stay (9 vs 8; p = 0.83), readmissions (27.6% vs 10.0%; p = 0.10), surgical re-interventions (15.0% vs 3.4%; p = 0.16), or stoma-free rate (52.6% vs 31.0%; p = 0.09) between immediate and delayed surgery groups. Hospital costs were similar in the delayed group (€11,913 vs €13,769; p = 0.89). Two-year overall survival (93% vs 100%; p = 0.23) and disease-free survival (78% vs 81%; p = 0.47) rates were comparable. LIMITATIONS: Limitations included small sample size, follow-up time and retrospective design. CONCLUSION: Delayed surgery for regrowth in a watch-and-wait program or for persistent residual disease after a repeated assessment is not associated with an increased risk of postoperative morbidity or a significant rise in costs compared to immediate total mesorectal excision. There also appears to be no evident compromise in oncological outcome. Repeated response assessment in patients with a near complete clinical response after neoadjuvant chemoradiotherapy is a useful approach to identify more patients who can benefit from a watch-and-wait strategy. See Video Abstract at http://links.lww.com/DCR/B836 . CIRUGA DE TME RETRASADA EN UNA ESTRATEGIA DE WATCH AND WAIT DESPUS DE LA QUIMIORRADIOTERAPIA NEOADYUVANTE PARA CNCER DE RECTO UN ANLISIS DE COSTOS HOSPITALARIOS, Y DE RESULTADOS QUIRRGICOS Y ONCOLGICOS: ANTECEDENTES: Una estrategia de Watch and Wait para pacientes con cáncer de recto con una respuesta clínica completa después de quimiorradioterapia neoadyuvante es una alternativa valiosa en vez de resección rectal. Sin embargo, hay pacientes que tendrán tumor residual o un recrecimiento durante el Watch and Wait .OBJETIVO: El objetivo fue investigar la seguridad y los costos para los pacientes que se sometieron a una cirugía diferida después de la quimiorradioterapia neoadyuvante.DISEÑO: Este es un estudio de cohorte retrospectivo con datos recolectados prospectivamente.AJUSTE: El estudio se llevó a cabo en un gran hospital universitario.PACIENTES: Entre enero de 2015 y mayo de 2020, se atendieron 622 nuevos pacientes con cáncer de recto, de los cuales 200 recibieron quimiorradioterapia neoadyuvante. Se incluyeron 94 pacientes, de los cuales 65 se sometieron a cirugía inmediata y 29 pacientes requirieron cirugía diferida después de un enfoque inicial de observación y espera.PRINCIPALES MEDIDAS DE RESULTADO: se incluyeron la tasa de morbilidad posoperatoria a 30 días, los costos hospitalarios y las sobrevidas general y libre de enfermedad a dos años.RESULTADOS: No hubo diferencia en la duración de la estancia (9 vs 8, p = 0,83), reingresos (27,6% vs 10,0%, p = 0,10), reintervenciones quirúrgicas (15,0% vs 3,4%, p = 0,16) y tasa libre de estoma (52,6% vs 31,0%, p = 0,09) entre los grupos de cirugía inmediata y tardía. Los costos hospitalarios fueron similares en el grupo retrasado (11913 € frente a 13769 €, p = 0,89). Las tasas de sobrevida general a dos años (93% frente a 100%, p = 0,23) y sobrevida libre de enfermedad (78% frente a 81%, p = 0,47) fueron comparables.LIMITACIONES: Tamaño de muestra pequeño, tiempo de seguimiento y diseño retrospectivo.CONCLUSIÓN: La cirugía tardía para el recrecimiento en un programa de Watch and Wait o para la enfermedad residual persistente después de una evaluación repetida no se asocia con un riesgo mayor de morbilidad posoperatoria ni con un aumento significativo en los costos, en comparación con la escisión total de mesorrecto inmediata. Tampoco parece haber un compromiso evidente en el resultado oncológico. La evaluación repetida de la respuesta en pacientes con una respuesta clínica casi completa después de la quimiorradioterapia neoadyuvante es un enfoque útil para identificar más pacientes que pueden beneficiarse de una estrategia de Watch and Wait . Consulte Video Resumen en http://links.lww.com/DCR/B836 . (Traducción-Dr. Juan Carlos Reyes ).

Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul.

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole-genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our data set, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders, and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia, and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.

Global Overview of Response Rates in Patient and Health Care Professional Surveys in Surgery: A Systematic Review.

OBJECTIVE: Identify key demographic factors and modes of follow-up in surgical survey response. SUMMARY BACKGROUND DATA: Surveys are widely used in surgery to assess patient and procedural outcomes, but response rates vary widely which compromises study quality. Currently there is no consensus as to what the average response rate is and which factors are associated with higher response rates. METHODS: The National Library of Medicine (MEDLINE/PubMed) was systematically searched from Januray 1, 2007 until February 1, 2020 using the following strategy: (((questionnaire) OR survey) AND "response rate") AND (surgery OR surgical). Original survey studies from surgical(-related) fields reporting on response rate were included. Through one-way analysis of variance we present mean response rate per survey mode over time, number of additional contacts, country of origin, and type of interviewee. RESULTS: The average response is 70% over 811 studies in patients and 53% over 1746 doctor surveys. In-person surveys yield an average 76% response rate, followed by postal (65%) and online (46% web-based vs 51% email) surveys. Patients respond significantly more often than doctors to surveys by mail (P < 0.001), email (P = 0.003), web-based surveys (P < 0.001) and mixed mode surveys (P = 0.006). Additional contacts significantly improve response rate in email (P = 0.26) and web-based (P = 0.041) surveys in doctors. A wide variation in response rates was identified between countries. CONCLUSIONS: Every survey is unique, but the main commonality between studies is response rate. Response rates appear to be highly dependent on type of survey, follow-up, geography, and interviewee type.

Prognostic importance of lymph node count and ratio in rectal cancer after neoadjuvant chemoradiotherapy: Results from a cross-sectional study.

BACKGROUND: The aim of this study was to determine the prognostic value of lymph node count (LNC) and lymph node ratio (LNR) in rectal cancer after neoadjuvant chemoradiotherapy (CRT). METHODS: Patients who underwent neoadjuvant CRT and total mesorectal excision (TME) for Stage I-III rectal cancer were selected from a cross-sectional study including 71 Dutch centres. Primary outcome parameters were disease-free survival (DFS) and overall survival (OS). Prognostic significance of LNC and LNR (cut-off values 0.15, 0.20, 0.30) was tested for different (sub)groups. RESULTS: From 2095 registered patients, 458 were included, of which 240 patients with LNC < 12 and 218 patients with LNC ≥ 12. LNC was not significantly associated with DFS (p = 0.35) and OS (p = 0.59). In univariable analysis, LNR was significantly associated with DFS and OS in the whole cohort and LNC subgroups, but not in multivariable analysis. CONCLUSIONS: LNC was not associated with long-term oncological outcome in rectal cancer patients treated with CRT, nor was LNR when corrected for N-stage. However, LNR might be used to identify subgroups of node-positive patients with a favourable outcome.

Ecological Momentary Assessment: A Field Evaluation of Subjective Ratings of Speech in Noise.

PURPOSE: As hearing rehabilitation research evolves to include both retrospective and momentary assessment outcome measures, it is important to understand how in-the-moment contextual factors influence subjective ratings. We aimed to determine, over a 4-week period of participants responding to ecological momentary assessments (EMAs) in their own environments, whether: (1) participants will complete surveys in speech-in-noise listening situations; (2) ratings of speech in noise change in a predictable manner as the acoustic conditions change; and (3) EMAs provide patient insights beyond those provided from retrospective ratings. DESIGN: Fourteen adults aged 26 to 86 years with at least 6 months of hearing aid experience were recruited for an 8-week crossover field trial (4 weeks wearing hearing aids with no EMA; 4 weeks wearing hearing aids with EMA). Participants were fitted with hearing aids and provided with a streamer and a smartphone with an app that analyzed the acoustic signal from the hearing aids and alerted the participant to respond to a survey when predetermined acoustic conditions were detected. Participants were prompted to complete brief surveys up to 9 times/day that contained establishing questions, quality ratings, and items assessing perceived benefit, residual activity limitation, and satisfaction. Participants also completed retrospective questionnaires at intake and after each 4-week field trial. RESULTS: Participants completed an average of 4.4 surveys per day. The quality ratings changed as the acoustics changed: Ratings of intelligibility were lower for 10 dB signal-to-noise ratio (SNR) than 20 dB SNR (p = 0.006); ratings of noisiness were higher for 10 dB SNR than 20 dB SNR (p = 0.001) and higher for 65 dB SPL than 50 dB SPL (p < 0.001); ratings of effort were higher for 65 dB SPL than 50 dB SPL (p = 0.004); ratings of loudness were higher for 65 dB SPL than 50 dB SPL (p = 0.001). Descriptive analysis of satisfaction, benefit, and residual activity limitation responses showed that the momentary surveys provided more detail about individual variability across acoustic conditions than the retrospective questions. CONCLUSIONS: Participants completed more than 99% of the triggered surveys, demonstrating high compliance. Because the quality ratings generally changed in the hypothesized direction, it is concluded that the participants provided valid responses. The greater variability in responses with EMA than retrospective questionnaires demonstrates its potential utility as a clinical tool for exploring hearing aid outcomes in real-world environments.

Surveys in Surgical Education: A Systematic Review and Reporting Guideline.

OBJECTIVES: Survey studies are a commonly used method for data collection in surgical education research. Nevertheless, studies investigating survey design and response rates in surgical education research are lacking. The aim of this study was to gain an insight into survey response rates among surgical residents and medical students, and provide an initial reporting guideline for future survey studies in this field. DESIGN: PubMed (MEDLINE) was systematically searched for survey studies in surgical education from January 2007 until February 2020, according to the PRISMA statements checklist. Study selection was conducted by 2 authors, independently. Surveys directed at surgical residents and/or medical students were included if data on response rates was available. Studies reporting solely from nonsurgical fields of medicine, paramedicine, or nursing were excluded. Subgroup analyses were performed, comparing response rates for varying modes of survey, per country, and for the 10 journals with the most identified surveys. RESULTS: From the 5,693 records screened for a larger surgical survey database, a total of 312 surveys were included; 173 studies focused on surgical residents and 139 on medical students. The mean (SD) response rate was 55.7% (24.7%) for surgical residents and 69.0% (20.8%) for medical students. The number of published surveys increased yearly, mostly driven by an increase in surgical resident surveys. Although most surveys were Web-based (n = 166, 53.2%), this survey mode resulted in the lowest response rates (mean 52.6%). The highest response rates, with a mean of 79.8% (13.1%), were seen in in-person surveys (n = 89, 28.5%). Wide variations in response rates were seen between different countries and journals. CONCLUSIONS: Web-based surveys are gaining popularity for medical research in general and for surgical education specifically; however, this mode results in lower response rates than those of in-person surveys. The response rate of in-person surveys is especially high when focusing on medical students. To improve reporting of survey studies, we present the first step towards a reporting guideline.

Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders.

Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in ~260 genes. Albeit that many genes are implicated in IRD, for 30-50% of the cases, the gene defect is unknown. These cases may be explained by novel gene defects, by overlooked structural variants, by variants in intronic, promoter or more distant regulatory regions, and represent synonymous variants of known genes contributing to the dysfunction of the respective proteins. Patients with one subgroup of IRD, namely incomplete congenital stationary night blindness (icCSNB), show a very specific phenotype. The major cause of this condition is the presence of a hemizygous pathogenic variant in CACNA1F. A comprehensive study applying direct Sanger sequencing of the gene-coding regions, exome and genome sequencing applied to a large cohort of patients with a clinical diagnosis of icCSNB revealed indeed that seven of the 189 CACNA1F-related cases have intronic and synonymous disease-causing variants leading to missplicing as validated by minigene approaches. These findings highlight that gene-locus sequencing may be a very efficient method in detecting disease-causing variants in clinically well-characterized patients with a diagnosis of IRD, like icCSNB.

Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing.

Pathogenic variants in BRCA1 and BRCA2 only explain the underlying genetic cause of about 10% of hereditary breast and ovarian cancer families. Because of cost-effectiveness, multigene panel testing is often performed even if the clinical utility of testing most of the genes remains questionable. The purpose of our study was to assess the contribution of rare, deleterious-predicted variants in DNA repair genes in familial breast cancer (BC) in a well-characterized and homogeneous population. We analyzed 113 DNA repair genes selected from either an exome sequencing or a candidate gene approach in the GENESIS study, which includes familial BC cases with no BRCA1 or BRCA2 mutation and having a sister with BC (N = 1,207), and general population controls (N = 1,199). Sequencing data were filtered for rare loss-of-function variants (LoF) and likely deleterious missense variants (MV). We confirmed associations between LoF and MV in PALB2, ATM and CHEK2 and BC occurrence. We also identified for the first time associations between FANCI, MAST1, POLH and RTEL1 and BC susceptibility. Unlike other associated genes, carriers of an ATM LoF had a significantly higher risk of developing BC than carriers of an ATM MV (ORLoF = 17.4 vs. ORMV = 1.6; p Het = 0.002). Hence, our approach allowed us to specify BC relative risks associated with deleterious-predicted variants in PALB2, ATM and CHEK2 and to add MAST1, POLH, RTEL1 and FANCI to the list of DNA repair genes possibly involved in BC susceptibility. We also highlight that different types of variants within the same gene can lead to different risk estimates.

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.

Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants. Results: We present a framework for defining cancer clones using most reliable variants of high depth of coverage and assigning functional mutations to the detected clones. The key element of our framework is QuantumClone, a method for variant clustering into clones based on VAFs, genotypes of corresponding regions and information about tumor purity. We validated QuantumClone and our framework on simulated data. We then applied our framework to whole genome sequencing data for 19 neuroblastoma trios each including constitutional, diagnosis and relapse samples. We confirmed an enrichment of damaging variants within such pathways as MAPK (mitogen-activated protein kinases), neuritogenesis, epithelial-mesenchymal transition, cell survival and DNA repair. Most pathways had more damaging variants in the expanding clones compared to shrinking ones, which can be explained by the increased total number of variants between these two populations. Functional mutational rate varied for ancestral clones and clones shrinking or expanding upon treatment, suggesting changes in clone selection mechanisms at different time points of tumor evolution. Availability and implementation: Source code and binaries of the QuantumClone R package are freely available for download at https://CRAN.R-project.org/package=QuantumClone. Contact: gudrun.schleiermacher@curie.fr or valentina.boeva@inserm.fr. Supplementary information: Supplementary data are available at Bioinformatics online.

B3GAT3-related disorder with craniosynostosis and bone fragility due to a unique mutation.

PurposeBased on prenatal suspicion of the combination of radioulnar or radiohumeral synostosis and a peculiar shape of the skull suggestive of craniosynostosis, we report on six patients from four unrelated consanguineous families in whom Antley-Bixler syndrome was suspected during the prenatal period without mutation in genes known to be associated with the syndrome.MethodsMolecular diagnosis involved whole-exome and gene-panel sequencing. RESULTS: All sequenced patients showed a unique homozygous mutation of c.667G>A, p.Gly223Ser (NM_012200) in the beta-1,3-glucuronyltransferase 3 (B3GAT3) gene known to be involved in linkeropathy syndrome. Linkeropathies correspond to a recently identified group of heterogeneous genetic syndromes along a spectrum of skeletal and connective tissue disorders. These patients featured mainly craniosynostosis, midface hypoplasia, bilateral radioulnar synostosis, multiple neonatal fractures, dislocated joints, joint contracture, long fingers, foot deformity, and cardiovascular abnormalities. All died before 1 year of age.ConclusionWe identified a novel B3GAT3-related disorder with craniosynostosis and bone fragility, due to a unique homozygous mutation in B3GAT3. This syndrome should be considered in the prenatal period in light of the severe outcome and as an alternative diagnosis to Antley-Bixler or Shprintzen-Goldberg syndrome.

Expanding the clinical spectrum of recessive truncating mutations of KLHL7 to a Bohring-Opitz-like phenotype.

BACKGROUND: Bohring-Opitz syndrome (BOS) is a rare genetic disorder characterised by a recognisable craniofacial appearance and a typical 'BOS' posture. BOS is caused by sporadic mutations ofASXL1. However, several typical patients with BOS have no molecular diagnosis, suggesting clinical and genetic heterogeneity. OBJECTIVES: To expand the phenotypical spectrum of autosomal recessive variants of KLHL7, reported as causing Crisponi syndrome/cold-induced sweating syndrome type 1 (CS/CISS1)-like syndrome. METHODS: We performed whole-exome sequencing in two families with a suspected recessive mode of inheritance. We used the Matchmaker Exchange initiative to identify additional patients. RESULTS: Here, we report six patients with microcephaly, facial dysmorphism, including exophthalmos, nevus flammeus of the glabella and joint contractures with a suspected BOS posture in five out of six patients. We identified autosomal recessive truncating mutations in the KLHL7 gene. KLHL7 encodes a BTB-kelch protein implicated in the cell cycle and in protein degradation by the ubiquitin-proteasome pathway. Recently, biallelic mutations in the KLHL7 gene were reported in four families and associated with CS/CISS1, characterised by clinical features overlapping with our patients. CONCLUSION: We have expanded the clinical spectrum of KLHL7 autosomal recessive variants by describing a syndrome with features overlapping CS/CISS1 and BOS.

Haploinsufficiency of Dmxl2, encoding a synaptic protein, causes infertility associated with a loss of GnRH neurons in mouse.

Characterization of the genetic defects causing gonadotropic deficiency has made a major contribution to elucidation of the fundamental role of Kisspeptins and Neurokinin B in puberty onset and reproduction. The absence of puberty may also reveal neurodevelopmental disorders caused by molecular defects in various cellular pathways. Investigations of these neurodevelopmental disorders may provide information about the neuronal processes controlling puberty onset and reproductive capacity. We describe here a new syndrome observed in three brothers, which involves gonadotropic axis deficiency, central hypothyroidism, peripheral demyelinating sensorimotor polyneuropathy, mental retardation, and profound hypoglycemia, progressing to nonautoimmune insulin-dependent diabetes mellitus. High-throughput sequencing revealed a homozygous in-frame deletion of 15 nucleotides in DMXL2 in all three affected patients. This homozygous deletion was associated with lower DMXL2 mRNA levels in the blood lymphocytes of the patients. DMXL2 encodes the synaptic protein rabconnectin-3α, which has been identified as a putative scaffold protein for Rab3-GAP and Rab3-GEP, two regulators of the GTPase Rab3a. We found that rabconnectin-3α was expressed in exocytosis vesicles in gonadotropin-releasing hormone (GnRH) axonal extremities in the median eminence of the hypothalamus. It was also specifically expressed in cells expressing luteinizing hormone (LH) and follicle-stimulating hormone (FSH) within the pituitary. The conditional heterozygous deletion of Dmxl2 from mouse neurons delayed puberty and resulted in very low fertility. This reproductive phenotype was associated with a lower number of GnRH neurons in the hypothalamus of adult mice. Finally, Dmxl2 knockdown in an insulin-secreting cell line showed that rabconnectin-3α controlled the constitutive and glucose-induced secretion of insulin. In conclusion, this study shows that low levels of DMXL2 expression cause a complex neurological phenotype, with abnormal glucose metabolism and gonadotropic axis deficiency due to a loss of GnRH neurons. Our findings identify rabconectin-3α as a key controller of neuronal and endocrine homeostatic processes.

KIF1C mutations in two families with hereditary spastic paraparesis and cerebellar dysfunction.

BACKGROUND: Hereditary spastic paraparesis (HSP) (syn. Hereditary spastic paraplegia, SPG) are a group of genetic disorders characterised by spasticity of the lower limbs due to pyramidal tract dysfunction. Nearly 60 disease loci have been identified, which include mutations in two genes (KIF5A and KIF1A) that encode motor proteins of the kinesin superfamily. Here we report a novel genetic defect in KIF1C of patients with spastic paraparesis and cerebellar dysfunction in two consanguineous families of Palestinian and Moroccan ancestry. METHODS AND RESULTS: We performed autozygosity mapping in a Palestinian and classic linkage analysis in a Moroccan family and found a locus on chromosome 17 that had previously been associated with spastic ataxia type 2 (SPAX2, OMIM %611302). Whole-exome sequencing revealed two homozygous mutations in KIF1C that were absent among controls: a nonsense mutation (c.2191C>T, p.Arg731*) that segregated with the disease phenotype in the Palestinian kindred resulted in the entire absence of KIF1C protein from the patient's fibroblasts, and a missense variant (c.505C>T, p.Arg169Trp) affecting a conserved amino acid of the motor domain that was found in the Moroccan kindred. CONCLUSIONS: Kinesin genes encode a family of cargo/motor proteins and are known to cause HSP if mutated. Here we identified nonsense and missense mutations in a further member of this protein family. The KIF1C mutation is associated with a HSP subtype (SPAX2/SAX2) that combines spastic paraplegia and weakness with cerebellar dysfunction.

SEMA3A, a gene involved in axonal pathfinding, is mutated in patients with Kallmann syndrome.

Kallmann syndrome (KS) associates congenital hypogonadism due to gonadotropin-releasing hormone (GnRH) deficiency and anosmia. The genetics of KS involves various modes of transmission, including oligogenic inheritance. Here, we report that Nrp1(sema/sema) mutant mice that lack a functional semaphorin-binding domain in neuropilin-1, an obligatory coreceptor of semaphorin-3A, have a KS-like phenotype. Pathohistological analysis of these mice indeed showed abnormal development of the peripheral olfactory system and defective embryonic migration of the neuroendocrine GnRH cells to the basal forebrain, which results in increased mortality of newborn mice and reduced fertility in adults. We thus screened 386 KS patients for the presence of mutations in SEMA3A (by Sanger sequencing of all 17 coding exons and flanking splice sites) and identified nonsynonymous mutations in 24 patients, specifically, a frameshifting small deletion (D538fsX31) and seven different missense mutations (R66W, N153S, I400V, V435I, T688A, R730Q, R733H). All the mutations were found in heterozygous state. Seven mutations resulted in impaired secretion of semaphorin-3A by transfected COS-7 cells (D538fsX31, R66W, V435I) or reduced signaling activity of the secreted protein in the GN11 cell line derived from embryonic GnRH cells (N153S, I400V, T688A, R733H), which strongly suggests that these mutations have a pathogenic effect. Notably, mutations in other KS genes had already been identified, in heterozygous state, in five of these patients. Our findings indicate that semaphorin-3A signaling insufficiency contributes to the pathogenesis of KS and further substantiate the oligogenic pattern of inheritance in this developmental disorder.

Eyes on crowding: crowding is preserved when responding by eye and similarly affects identity and position accuracy.

Peripheral vision guides recognition and selection of targets for eye movements. Crowding­a decline in recognition performance that occurs when a potential target is surrounded by other, similar, objects­influences peripheral object recognition. A recent model study suggests that crowding may be due to increased uncertainty about both the identity and the location of peripheral target objects, but very few studies have assessed these properties in tandem. Eye tracking can integrally provide information on both the perceived identity and the position of a target and therefore could become an important approach in crowding studies. However, recent reports suggest that around the moment of saccade preparation crowding may be significantly modified. If these effects were to generalize to regular crowding tasks, it would complicate the interpretation of results obtained with eye tracking and the comparison to results obtained using manual responses. For this reason, we first assessed whether the manner by which participants responded­manually or by eye­affected their performance. We found that neither recognition performance nor response time was affected by the response type. Hence, we conclude that crowding magnitude was preserved when observers responded by eye. In our main experiment, observers made eye movements to the location of a tilted Gabor target while we varied flanker tilt to manipulate target-flanker similarity. The results indicate that this similarly affected the accuracy of peripheral recognition and saccadic target localization. Our results inform about the importance of both location and identity uncertainty in crowding.

Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels.

Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count - both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.

Characterisation of gut microbiota composition in patients with axial spondyloarthritis and its modulation by TNF inhibitor treatment.

OBJECTIVE: To assess whether gut microbiota composition is associated with patient characteristics and may have predictive value on the response to TNF inhibitor (TNFi) treatment in axial spondyloarthritis (AxSpA). METHODS: The study involved 61 patients fulfilling the Assessment of SpondyloArthritis International Society classification criteria for AxSpA. All patients had active disease despite non-steroidal anti-inflammatory drugs intake and were eligible for treatment with a TNFi. At baseline, the mean Ankylosing Spondylitis Disease Activity Score was 2.9±1 and mean C reactive protein (CRP) level 9.7±11.4 mg/L. Bacterial 16S ribosomal RNA gene sequencing was performed on stool samples collected at baseline (month 0 (M0)) and 3 months after TNFi initiation (month 3 (M3)). Alpha and beta diversity metrics were calculated on the relative abundance of core operational taxonomic units (OTUs). RESULTS: The HLA-B27 status affected at least in part the global composition of faecal microbiota at M0 as well as the abundance/prevalence of several anaerobic bacteria in the families Oscillospiraceae, Lachnospiraceae and Bifidobacteriaceae. In contrast, smoking affected the global composition of faecal microbiota at both M0 and M3. The prevalence/abundance of seven bacterial OTUs at M0 was associated with response to TNFi treatment. One of the candidates, present only in non-responders, is the genus Sutterella, and the other six candidates are in the class Clostridia. CONCLUSIONS: Several SpA patients' characteristics modulate the composition of gut microbiota as did TNFi treatment. Moreover, the abundance/prevalence of seven OTUs at baseline may be used as a novel non-invasive index that predicts the response to TNFi with greater accuracy than HLA-B27 status, CRP level and measures of disease activity.

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that-in the case of the interdependent tumor cell morphology and adapted immune response-reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.