Exome sequencing reveals neurodevelopmental genes in simplex consanguineous Iranian families with syndromic autism.

BACKGROUND AND OBJECTIVE: Autosomal recessive genetic disorders pose significant health challenges in regions where consanguineous marriages are prevalent. The utilization of exome sequencing as a frequently employed methodology has enabled a clear delineation of diagnostic efficacy and mode of inheritance within multiplex consanguineous families. However, these aspects remain less elucidated within simplex families. METHODS: In this study involving 12 unrelated simplex Iranian families presenting syndromic autism, we conducted singleton exome sequencing. The identified genetic variants were validated using Sanger sequencing, and for the missense variants in FOXG1 and DMD, 3D protein structure modeling was carried out to substantiate their pathogenicity. To examine the expression patterns of the candidate genes in the fetal brain, adult brain, and muscle, RT-qPCR was employed. RESULTS: In four families, we detected an autosomal dominant gene (FOXG1), an autosomal recessive gene (CHKB), and two X-linked autism genes (IQSEC2 and DMD), indicating diverse inheritance patterns. In the remaining eight families, we were unable to identify any disease-associated genes. As a result, our variant detection rate stood at 33.3% (4/12), surpassing rates reported in similar studies of smaller cohorts. Among the four newly identified coding variants, three are de novo (heterozygous variant p.Trp546Ter in IQSEC2, heterozygous variant p.Ala188Glu in FOXG1, and hemizygous variant p.Leu211Met in DMD), while the homozygous variant p.Glu128Ter in CHKB was inherited from both healthy heterozygous parents. 3D protein structure modeling was carried out for the missense variants in FOXG1 and DMD, which predicted steric hindrance and spatial inhibition, respectively, supporting the pathogenicity of these human mutants. Additionally, the nonsense variant in CHKB is anticipated to influence its dimerization - crucial for choline kinase function - and the nonsense variant in IQSEC2 is predicted to eliminate three functional domains. Consequently, these distinct variants found in four unrelated individuals with autism are likely indicative of loss-of-function mutations. CONCLUSIONS: In our two syndromic autism families, we discovered variants in two muscular dystrophy genes, DMD and CHKB. Given that DMD and CHKB are recognized for their participation in the non-cognitive manifestations of muscular dystrophy, it indicates that some genes transcend the boundary of apparently unrelated clinical categories, thereby establishing a novel connection between ASD and muscular dystrophy. Our findings also shed light on the complex inheritance patterns observed in Iranian consanguineous simplex families and emphasize the connection between autism spectrum disorder and muscular dystrophy. This underscores a likely genetic convergence between neurodevelopmental and neuromuscular disorders.

COPII cage assembly factor Sec13 integrates information flow regulating endomembrane function in response to human variation.

How information flow is coordinated for managing transit of 1/3 of the genome through endomembrane pathways by the coat complex II (COPII) system in response to human variation remains an enigma. By examining the interactome of the COPII cage-assembly component Sec13, we show that it is simultaneously associated with multiple protein complexes that facilitate different features of a continuous program of chromatin organization, transcription, translation, trafficking, and degradation steps that are differentially sensitive to Sec13 levels. For the trafficking step, and unlike other COPII components, reduction of Sec13 expression decreased the ubiquitination and degradation of wild-type (WT) and F508del variant cargo protein cystic fibrosis transmembrane conductance regulator (CFTR) leading to a striking increase in fold stability suggesting that the events differentiating export from degradation are critically dependent on COPII cage assembly at the ER Golgi intermediate compartment (ERGIC) associated recycling and degradation step linked to COPI exchange. Given Sec13's multiple roles in protein complex assemblies that change in response to its expression, we suggest that Sec13 serves as an unanticipated master regulator coordinating information flow from the genome to the proteome to facilitate spatial covariant features initiating and maintaining design and function of membrane architecture in response to human variation.

Autosomal recessive non-syndromic hearing loss genes in Pakistan during the previous three decades.

Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.

Identification of two novel autism genes, TRPC4 and SCFD2, in Qatar simplex families through exome sequencing.

This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2, were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1, CLCN3, and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research.

Brassinosteroids as promoters of seedling growth and antioxidant activity under heavy metal zinc stress in mung bean (Vigna radiata L.).

The escalation of harmful pollutants, including heavy metals, due to industrialization and urbanization has become a global concern. To mitigate the negative impacts of heavy metal stress on germination and early plant development, growth regulators have been employed. This study aimed to evaluate the response of mung bean (Vigna radiata L.) to zinc stress in the presence of brassinosteroids, focusing on seedling growth and antioxidant potential. Mung bean seedlings were treated with three concentrations of 24-epibrassinolide (EBL) (0.1, 0.2, and 0.4 PPM) with or without zinc. Results demonstrated that the application of brassinosteroids, combined with zinc stress, significantly enhanced germination percentage (about 47.06, 63.64, and 120%), speed of germination (about 39.13, 50, and 100%), seedling growth (about 38% in case of treatment combined 0.4 PPM 24-EBL and 1.5 mM ZnSO4) and seedling vigor index (204% in case of treatment combined 0.4 PPM 24-EBL and 1.5 mM ZnSO4) compared to zinc-treated seedlings alone after 24 h. The activities of antioxidative enzymes (catalase, ascorbate peroxidase, polyphenol oxidase, and peroxidase) and total soluble protein content decreased, while lipid peroxidation and proline content exhibited a significant increase (p ≤ 0.05) when compared to the control. However, the negative effects induced by heavy metal stress on these parameters were significantly mitigated by EBL application. Notably, the most effective concentration of EBL in overcoming zinc stress was found to be 0.4 PPM. These findings underscore the potential of exogenously applied brassinosteroids as a valuable tool in phytoremediation projects by ameliorating heavy metal stress.

Multinuclear Zinc-Magnesium Hydroxide Carboxylates: A Predesigned Model System for Copolymerization of CO2 with Epoxides.

Among numerous catalysts in the ring-opening copolymerization of epoxides with carbon dioxide (CO2), zinc dicarboxylate complexes are the most common type, and in the family of metal-based homogeneous catalysts, zinc and magnesium complexes have attracted widespread attention. We report on the synthesis and structural characterization of a zinc-magnesium benzoate framework templated by the central hydroxide anion with µ3-κ2:κ2:κ2 coordination mode, [ZnMg2(µ3-OH)(O2CPh)5]n (n = 1 or 2). The resulting heterometallic system forms stable Lewis acid-base adducts with tetrahydrofuran (THF) and cyclohexene oxide (CHO), which crystallize as the hexanuclear zinc-magnesium hydroxide carboxylate cluster [ZnMg2(µ3-OH)(O2CPh)5(L)2]2 (L = THF or CHO). Their X-ray crystal structure analysis revealed that the Zn center prefers 4-fold coordination and the Mg centers demonstrated the ability to accommodate higher coordination numbers, and as a result, the heterocyclic molecules are exclusively bonded to 6-fold Mg atoms. The heteronuclear carboxylate aggregates appeared active in the copolymerization reaction at elevated temperatures to produce an alternating poly(cyclohexene carbonate).

Atrial Fibrillation and Perioperative Inflammation (FIBRILLAMMED Study): A Retrospective Analysis of the Predictive Role of Preoperative Albumin-Adjusted Platelet-Leukocytic Indices in OPCABG.

Objective: New-onset atrial fibrillation (NOAF), an important postoperative complication, has pertinent inflammatory links. Motivated by the encouraging literature on the prognostic role of hypoalbuminemia, leukocytic indices [LIs: neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR)], systemic inflammation response index (SIRI=NLR×monocyte) and platelet-leukocytic indices [PLIs: platelet-to-lymphocyte ratio (PLR)], systemic immune inflammation index (SII=NLR×platelet), aggregate index of systemic inflammation (AISI=NLR×platelet×monocyte), we sought to investigate the NOAF-predictive value of preoperative albumin-adjusted indices (aa-LIs and aa-PLIs) in an off-pump coronary artery bypass grafting (OPCABG) setting. Methods: Of 899 patients, 151 patients (16.79%) developed the primary outcome i.e. NOAF that was analyzed further retrospectively for its predictors instead of the highlighted text perioperative data of 899 patients undergoing elective OPCABG, were retrospectively analyzed. The study participants were categorized into non-NOAF and NOAF groups (defined as new-onset atrial arrhythmia with irregular RR interval with indistinct P wave in the first week postoperatively). Results: One hundred and fifty-one patients (16.79%) developed NOAF. On univariate analysis: age, smoker status, The European System for Cardiac Operative Risk Evaluation (EuroSCORE) II, systemic hypertension, diabetes mellitus, prior congestive heart failure (CHF), and a higher preoperative NLR, PLR, SII, and albumin were significant predictors of NOAF. While age, CHF, and EuroSCORE II retained predictive significance in multivariate analysis, LI-PLIs and albumin did not emerge as independent NOAF predictors. Notably, aa-NLR, aa-PLR, and aa-SII independently predicted NOAF on the computation of model-estimates in the regression analysis (Odds ratio; 95% confidence interval: 31.05;15.75-70.61, 1.04;1.02-1.05, 1.12;1.10-1.14, respectively, P < 0.001). aa-NLR ≥1.32, aa-PLR ≥52.64, and aa-SII ≥344.38 predicted NOAF with the respective AUC;sensitivity;specificity of 0.66;63.6%;73.3%, 0.63;66.2%;59.0%, and 0.65;58.3%;78.2%. Preoperative aa-NLR, aa-PLR and aa-SII also positively correlated with CHA2DS2-VASc score (R=0.40, 0.45 and 0.42; P < 0.001). Conclusion: The independent NOAF predictive value of aa-NLR, aa-PLR, and aa-SII reiterates the inflammatory relationship of the arrhythmic complication following OPCABG.

Customised Implant for Temporomandibular Joint: New Technique to Design and Stress Analysis to Balance the Loading at Both Ends.

The temporomandibular joint (TMJ) is a critical joint for the opening and closing of the mouth. The generation of customised TMJs according to individuals' dental anatomy is needed. Currently, the implants available on the market lack consideration of the patient's dental anatomy. This leads to the creation of an imbalance in the reaction forces on both ends of the TMJ. This requires a slight structural change in the design parameters to give a solution. The purpose of this study is to propose a new design that includes the geometry and materials for a TMJ implant. Stress analysis was carried out on the TMJ to balance the reaction forces at both TMJ ends. A static analysis was performed using ANSYS Workbench, to compare the results of two customised designs of TMJ implants, in order to better balance the reaction forces at both ends. The model in the study showed that the reaction forces for both the patient-specific TMJ implants were nearly balanced. The reaction forces were better balanced, and almost equivalent to the intact conditions. The stresses in the mandible were more uniformly distributed in the customised design of the TMJ implant. The two types of design showed that the custom design took up less space in the patient's region of surgery, making it a better option compared to a stock TMJ implant. The custom implant would allow faster patient rehabilitation, as the reaction forces would be close to those in intact conditions.

Deletion of TRPC6, an Autism Risk Gene, Induces Hyperexcitability in Cortical Neurons Derived from Human Pluripotent Stem Cells.

Autism spectrum disorder (ASD) is a complex and heterogeneous neurodevelopmental disorder linked to numerous rare, inherited, and arising de novo genetic variants. ASD often co-occurs with attention-deficit hyperactivity disorder and epilepsy, which are associated with hyperexcitability of neurons. However, the physiological and molecular mechanisms underlying hyperexcitability in ASD remain poorly understood. Transient receptor potential canonical-6 (TRPC6) is a Ca2+-permeable cation channel that regulates store-operated calcium entry (SOCE) and is a candidate risk gene for ASD. Using human pluripotent stem cell (hPSC)-derived cortical neurons, single-cell calcium imaging, and electrophysiological recording, we show that TRPC6 knockout (KO) reduces SOCE signaling and leads to hyperexcitability of neurons by increasing action potential frequency and network burst frequency. Our data provide evidence that reduction of SOCE by TRPC6 KO results in neuronal hyperexcitability, which we hypothesize is an important contributor to the cellular pathophysiology underlying hyperactivity in some ASD.

A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome.

In a patient diagnosed with both Kallmann syndrome (KS) and intellectual disability (ID), who carried an apparently balanced translocation t(7;12)(q22;q24)dn, array comparative genomic hybridization (aCGH) disclosed a cryptic heterozygous 4.7 Mb deletion del(12)(p11.21p11.23), unrelated to the translocation breakpoint. This novel discovery prompted us to consider the possibility that the combination of KS and neurological disorder in this patient could be attributed to gene(s) within this specific deletion at 12p11.21-12p11.23, rather than disrupted or dysregulated genes at the translocation breakpoints. To further support this hypothesis, we expanded our study by screening five candidate genes at both breakpoints of the chromosomal translocation in a cohort of 48 KS patients. However, no mutations were found, thus reinforcing our supposition. In order to delve deeper into the characterization of the 12p11.21-12p11.23 region, we enlisted six additional patients with small copy number variations (CNVs) and analyzed eight individuals carrying small CNVs in this region from the DECIPHER database. Our investigation utilized a combination of complementary approaches. Firstly, we conducted a comprehensive phenotypic-genotypic comparison of reported CNV cases. Additionally, we reviewed knockout animal models that exhibit phenotypic similarities to human conditions. Moreover, we analyzed reported variants in candidate genes and explored their association with corresponding phenotypes. Lastly, we examined the interacting genes associated with these phenotypes to gain further insights. As a result, we identified a dozen candidate genes: TSPAN11 as a potential KS candidate gene, TM7SF3, STK38L, ARNTL2, ERGIC2, TMTC1, DENND5B, and ETFBKMT as candidate genes for the neurodevelopmental disorder, and INTS13, REP15, PPFIBP1, and FAR2 as candidate genes for KS with ID. Notably, the high-level expression pattern of these genes in relevant human tissues further supported their candidacy. Based on our findings, we propose that dosage alterations of these candidate genes may contribute to sexual and/or cognitive impairments observed in patients with KS and/or ID. However, the confirmation of their causal roles necessitates further identification of point mutations in these candidate genes through next-generation sequencing.

Button-Hole Disco-Osteotomy Drainage-A Novel Approach for High-Risk Patients with Cervical Abscess.

Spinal epidural abscess (SEA) is a very serious infection of the central nervous system (CNS). It is of very low incidence with a peak age in the geriatric age group. Immunocompromised patients are more susceptible to SEA. It can present with significant neurological deficits, which can be permanent if not identified and treated promptly. In this case report, a 75-year-old immunocompromised patient presented with progressive spastic quadriparesis and septicemia. He was diagnosed with a case of cervical spinal epidural abscess with underlying cord compression. Anterior retropharyngeal approach and button-hole disco-osteotomy of C5-C6 was performed and the cervical SEA was drained, followed by antibiotic saline irrigation (cranially and caudally) was done, total duration of surgery was 70 min. At the time of discharge (7th postoperative day), the patient improved neurologically and sepsis had resolved.

Currarino Syndrome Presenting in Adulthood: A Rare Case.

Currarino syndrome or Currarino triad is a complex condition consisting of congenital anomalies. The triad consists of anterior sacral mass (meningocele, teratoma or dermoid/epidermoid cyst), sacral bone defect (hypoplasia, agenesis ), anorectal malformation/congenital anorectal stenosis. This condition is named after Dr Guido Currarino, an Italian-American paediatric radiologist, who first described it in 1975. This needs a multidisciplinary treatment approach. We describe a case of successfully managed young adult with Currarino syndrome. The latest artificial intelligence tool, Chat Generative Pre-Trained Transformer (ChatGPT), helped to write this case report.

A microdeletion del(12)(p11.21p11.23) with a cryptic unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome.

In an apparently balanced translocation t(7;12)(q22;q24)dn exhibiting both Kallmann syndrome (KS) and intellectual disability (ID), we detected a cryptic heterozygous 4.7 Mb del(12)(p11.21p11.23) unrelated to the translocation breakpoint. This new finding raised the possibility that KS combined with neurological disorder in this patient could be caused by gene(s) within this deletion at 12p11.21-12p11.23 instead of disrupted or dysregulated genes at the genomic breakpoints. Screening of five candidate genes at both breakpoints in 48 KS patients we recruited found no mutation, corroborating our supposition. To substantiate this hypothesis further, we recruited six additional subjects with small CNVs and analyzed eight individuals carrying small CNVs in this region from DECIPHER to dissect 12p11.21-12p11.23. We used multiple complementary approaches including a phenotypic-genotypic comparison of reported cases, a review of knockout animal models recapitulating the human phenotypes, and analyses of reported variants in the interacting genes with corresponding phenotypes. The results identified one potential KS candidate gene ( TSPAN11 ), seven candidate genes for the neurodevelopmental disorder ( TM7SF3 , STK38L , ARNTL2 , ERGIC2 , TMTC1 , DENND5B , and ETFBKMT ), and four candidate genes for KS with ID ( INTS13 , REP15 , PPFIBP1 , and FAR2 ). The high-level expression pattern in the relevant human tissues further suggested the candidacy of these genes. We propose that the dosage alterations of the candidate genes may contribute to sexual and/or cognitive impairment in patients with KS and/or ID. Further identification of point mutations through next generation sequencing will be necessary to confirm their causal roles.

The Crystallization of Disordered Materials under Shock Is Governed by Their Network Topology.

When the shock load is applied, materials experience incredibly high temperature and pressure conditions on picosecond timescales, usually accompanied by remarkable physical or chemical phenomena. Understanding the underlying physics that governs the kinetics of shocked materials is of great importance for both physics and materials science. Here, combining experiment and large-scale molecular dynamics simulation, the ultrafast nanoscale crystal nucleation process in shocked soda-lime silicate glass is investigated. By adopting topological constraints theory, this study finds that the propensity of nucleation is governed by the connectivity of the atomic network. The densification of local networks, which appears once the crystal starts to grow, results in the underconstrained shell around the crystal and prevents further crystallization. These results shed light on the nanoscale crystallization mechanism of shocked materials from the viewpoint of topological constraint theory.

A circuit for secretion-coupled cellular autonomy in multicellular eukaryotic cells.

Cancers represent complex autonomous systems, displaying self-sufficiency in growth signaling. Autonomous growth is fueled by a cancer cell's ability to "secrete-and-sense" growth factors (GFs): a poorly understood phenomenon. Using an integrated computational and experimental approach, here we dissect the impact of a feedback-coupled GTPase circuit within the secretory pathway that imparts secretion-coupled autonomy. The circuit is assembled when the Ras-superfamily monomeric GTPase Arf1, and the heterotrimeric GTPase Giαßγ and their corresponding GAPs and GEFs are coupled by GIV/Girdin, a protein that is known to fuel aggressive traits in diverse cancers. One forward and two key negative feedback loops within the circuit create closed-loop control, allow the two GTPases to coregulate each other, and convert the expected switch-like behavior of Arf1-dependent secretion into an unexpected dose-response alignment behavior of sensing and secretion. Such behavior translates into cell survival that is self-sustained by stimulus-proportionate secretion. Proteomic studies and protein-protein interaction network analyses pinpoint GFs (e.g., the epidermal GF) as key stimuli for such self-sustenance. Findings highlight how the enhanced coupling of two biological switches in cancer cells is critical for multiscale feedback control to achieve secretion-coupled autonomy of growth factors.

Production of α-Synuclein Fibrillar-Specific scFv from Inclusion Bodies.

Recombinant antibody fragments such as Fab, scFvs, and diabodies against α-syn have become a viable alternative to the conventional full-length antibodies in immunotherapeutic approaches due to their benefits which include smaller size, higher stability, specificity, and affinity. However, the majority of recombinant antibody fragments typically express as inclusion bodies (IBs) in E. coli, which makes their purification incredibly difficult. Here, we describe a method involving a mild solubilizing protocol followed by slow on-column refolding to purify active single-chain variable fragment (scFv-pF) antibody that can recognize the pathogenic α-syn fibrils.

Structural and Biophysical Characterization of Stable Alpha-Synuclein Oligomers.

The aggregation of α-synuclein (α-syn) into neurotoxic oligomers and fibrils is an important pathogenic feature of synucleinopatheis, including Parkinson's disease (PD). A further characteristic of PD is the oxidative stress that results in the formation of aldehydes by lipid peroxidation. It has been reported that the brains of deceased patients with PD contain high levels of protein oligomers that are cross-linked to these aldehydes. Increasing evidence also suggests that prefibrillar oligomeric species are more toxic than the mature amyloid fibrils. However, due to the heterogenous and metastable nature, characterization of the α-syn oligomeric species has been challenging. Here, we generated and characterized distinct α-syn oligomers in vitro in the presence of DA and lipid peroxidation products 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE). HNE and ONE oligomer were stable towards the treatment with SDS, urea, and temperature. The secondary structure analysis revealed that only HNE and ONE oligomers contain ß-sheet content. In the seeding assay, both DA and ONE oligomers significantly accelerated the aggregation. Furthermore, all oligomeric preparations were found to seed the aggregation of α-syn monomers in vitro and found to be cytotoxic when added to SH-SY5Y cells. Finally, both HNE and ONE α-syn oligomers can be used as a calibrator in an α-syn oligomers-specific ELISA.

Communication-efficient algorithms for solving pressure Poisson equation for multiphase flows using parallel computers.

Numerical solution of partial differential equations on parallel computers using domain decomposition usually requires synchronization and communication among the processors. These operations often have a significant overhead in terms of time and energy. In this paper, we propose communication-efficient parallel algorithms for solving partial differential equations that alleviate this overhead. First, we describe an asynchronous algorithm that removes the requirement of synchronization and checks for termination in a distributed fashion while maintaining the provision to restart iterations if necessary. Then, we build on the asynchronous algorithm to propose an event-triggered communication algorithm that communicates the boundary values to neighboring processors only at certain iterations, thereby reducing the number of messages while maintaining similar accuracy of solution. We demonstrate our algorithms on a successive over-relaxation solver for the pressure Poisson equation arising from variable density incompressible multiphase flows in 3-D and show that our algorithms improve time and energy efficiency.