VARista: a free web platform for streamlined whole-genome variant analysis across T2T, hg38, and hg19

With the increasing importance of genomic data in understanding genetic diseases, there is an essential need for efficient and user-friendly tools that simplify variant analysis. Although multiple tools exist, many present barriers such as steep learning curves, limited reference genome compatibility, or costs. We developed VARista, a free web-based tool, to address these challenges and provide a streamlined solution for researchers, particularly those focusing on rare monogenic diseases. VARista offers a user-centric interface that eliminates much of the technical complexity typically associated with variant analysis. The tool directly supports VCF files generated using reference genomes hg19, hg38, and the emerging T2T, with seamless remapping capabilities between them. Features such as gene summaries and links, tissue and cell-specific gene expression data for both adults and fetuses, as well as automated PCR design and integration with tools such as SpliceAI and AlphaMissense, enable users to focus on the biology and the case itself. As we demonstrate, VARista proved effective in narrowing down potential disease-causing variants, prioritizing them effectively, and providing meaningful biological context, facilitating rapid decision-making. VARista stands out as a freely available and comprehensive tool that consolidates various aspects of variant analysis into a single platform that embraces the forefront of genomic advancements. Its design inherently supports a shift in focus from technicalities to critical thinking, thereby promoting better-informed decisions in genetic disease research. Given its unique capabilities and user-centric design, VARista has the potential to become an essential asset for the genomic research community. https://VARista.link.

Compound Heterozygosity for Late-Onset Cardiomyopathy-Causative ALPK3 Coding Variant and Novel Intronic Variant Cause Infantile Hypertrophic Cardiomyopathy

Hypertrophic and dilated cardiomyopathy (HCM, DCM) are leading causes of cardiovascular morbidity and mortality in children. The pseudokinase alpha-protein kinase 3 (ALPK3) plays an essential role in sarcomere organization and cardiomyocyte differentiation. ALPK3 coding mutations are causative of recessively inherited pediatric-onset DCM and HCM with variable expression of facial dysmorphism and skeletal abnormalities and implicated in dominantly inherited adult-onset cardiomyopathy. We now report two variants in ALPK3-a coding variant and a novel intronic variant affecting splicing. We demonstrate that compound heterozygosity for both variants is highly suggestive to be causative of infantile-onset HCM with webbed neck, and heterozygosity for the coding variant presents with adult-onset HCM. Our data validate partial penetrance of heterozygous loss-of-function ALPK3 mutations in late-onset hypertrophic cardiomyopathy and expand the genotypic spectrum of autosomal recessive ALPK3-related cardiac disease with Noonan-like features.

Partial penetrance and phenotypic variability of aplasia of lacrimal and salivary glands caused by a novel FGF10 donor splice-site mutation

Thirteen affected individuals of six generations of a single kindred presented with epiphora evident from infancy. Physical exam and Schirmer test revealed variable expression of tear deficiency, congenital punctal atresia, and dry mouth with multiple caries, without concomitant abnormalities of the ears or digits, commensurate with a diagnosis of aplasia of the lacrimal and salivary glands (ALSG). Reconstruction of the upper lacrimal drainage system was performed in some of the affected individuals. Genetic analysis, testing six affected individuals and three non-affected family members, identified a single novel heterozygous splice-site variant, c.429 + 1, G > T in fibroblast growth factor 10 (FGF10) (NM_004465.1), segregating throughout the family as expected for dominant heredity. RT-PCR assays of HEK-293 cells transfected with wild type or mutant FGF10 demonstrated that the variant causes skipping of Exon 2. Notably, individuals sharing the same variant exhibited phenotypic variability, with unilateral or bilateral epiphora, as well as variable expression of dry mouth and caries. Moreover, one of the variant carriers had no ALSG-related clinical findings, demonstrating incomplete penetrance. While coding mutations in FGF10 are known to cause malformations in the nasolacrimal system, this is the second FGF10 splice-site variant and the first donor-site variant reported to cause ALSG. Thus, our study of a unique large kindred with multiple affected individuals heterozygous for the same FGF10 variant highlights intronic splice-site mutations and phenotypic variability/partial penetrance in ALSG.

Hyperinsulinism/hyperammonemia syndrome caused by biallelic SLC25A36 mutation

Hyperinsulinism/hyperammonemia (HI/HA) syndrome has been known to be caused by dominant gain-of-function mutations in GLUD1, encoding the mitochondrial enzyme glutamate dehydrogenase. Pathogenic GLUD1 mutations enhance enzymatic activity by reducing its sensitivity to allosteric inhibition by GTP. Two recent independent studies showed that a similar HI/HA phenotype can be caused by biallelic mutations in SLC25A36, encoding pyrimidine nucleotide carrier 2 (PNC2), a mitochondrial nucleotide carrier that transports pyrimidine and guanine nucleotides across the inner mitochondrial membrane: one study reported a single case caused by a homozygous truncating mutation in SLC25A36 resulting in lack of expression of SLC25A36 in patients' fibroblasts. A second study described two siblings with a splice site mutation in SLC25A36, causing reduction of mitochondrial GTP content, putatively leading to hyperactivation of glutamate dehydrogenase. In an independent study, through combined linkage analysis and exome sequencing, we demonstrate in four individuals of two Bedouin Israeli related families the same disease-causing SLC25A36 (NM_018155.3) c.284 + 3A > T homozygous splice-site mutation found in the two siblings. We demonstrate that the mutation, while causing skipping of exon 3, does not abrogate expression of mRNA and protein of the mutant SLC25A36 in patients' blood and fibroblasts. Affected individuals had hyperinsulinism, hyperammonemia, borderline low birth weight, tonic-clonic seizures commencing around 6 months of age, yet normal intellect and no significant other morbidities. Chronic constipation, hypothyroidism, and developmental delay previously described in a single patient were not found. We thus verify that biallelic SLC25A36 mutations indeed cause HI/HA syndrome and clearly delineate the disease phenotype.

Laser tissue soldering of the gastrointestinal tract: A systematic review LTS of the gastrointestinal tract

Background

Laser Tissue Soldering (LTS) is a promising tissue bonding technique in which a solder is applied between the tissues and then irradiated by laser, causing it to solidify and form links with the tissue.

Methods

A comprehensive systematic review summarizing the state of research of LTS in the gastrointestinal tract.

Results

Most studies were conducted on large animal tissues, using liquid proteinaceous solder, and irradiated by a continuous wave laser at 808 nm. LTS can provide better sealing and burst pressure than conventional methods. The application of LTS on top of or in addition to sutures showed an impressive increase in burst pressures. LTS may decrease the inflammatory and foreign body reaction caused by sutures.

Conclusions

LTS has strong potential to be applied in a clinical setting in leak prevention and in closure of gastrointestinal structures as an adjunct or additional anastomotic technology, decreasing leak rates, morbidity, and mortality.

PSMC1 variant causes a novel neurological syndrome

Proteasome 26S, the eukaryotic proteasome, serves as the machinery for cellular protein degradation. It is composed of the 20S core particle and one or two 19S regulatory particles, composed of a base and a lid. To date, several human diseases have been associated with mutations within the 26S proteasome subunits; only one of them affects a base subunit. We now delineate an autosomal recessive syndrome of failure to thrive, severe developmental delay and intellectual disability, spastic tetraplegia with central hypotonia, chorea, hearing loss, micropenis and undescended testes, as well as mild elevation of liver enzymes. None of the affected individuals achieved verbal communication or ambulation. Ventriculomegaly was evident on MRI. Homozygosity mapping combined with exome sequencing revealed a disease‐associated p.I328T PSMC1 variant. Protein modeling demonstrated that the PSMC1 variant is located at the highly conserved putative ATP binding and hydrolysis domain, and is suggested to interrupt a hydrophobic core within the protein. Fruit flies in which we silenced the Drosophila ortholog Rpt2 specifically in the eye exhibited an apparent phenotype that was highly rescued by the human wild‐type PSMC1, yet only partly by the mutant PSMC1, proving the functional effect of the p.I328T disease‐causing variant.

[SURGICAL PALLIATION FOR PANCREATIC CANCER]

INTRODUCTION

Pancreatic cancer (PC) is the 11th most common malignancy worldwide, however, entailing a mortality in excess of 90% within 5 years from diagnosis, it is the 4th most fatal malignant disease. PC is commonly diagnosed at an advanced stage, in which curative resection is no longer possible. Even patients who present with potentially curable disease will have upward of 30% recurrence of their disease within the first year. Thus, palliative therapy has paramount importance in patient management. The purpose of palliative care in these patients is to relieve symptoms and improve quality of life. This article reviews the current state of invasive palliation techniques for advanced PC, which are commonly directed towards three main symptoms: gastric/duodenal obstruction, obstructive jaundice, and epigastric pain. We describe the pros and cons of the different techniques, along with current front-line technology advancements. Endoscopic stenting is highly efficient in patients with gastric/duodenal obstruction or obstructive jaundice, with a generally low complication rate, short hospitalization and sustained quality of life. Bypass surgery should be considered in patients with a long-anticipated life expectancy, following higher rates of long-term stent failure, or when endoscopic stent procedure is not possible or has failed. When treating abdominal pain, celiac plexus neurolysis is considered as the first-line treatment. Pancreatic cancer is a complex and commonly lethal disease strongly affecting patient quality of life. It is important to consider the specific patient's personal characteristics and disease status when planning their palliative care.

A syndrome of severe intellectual disability, hypotonia, failure to thrive, dysmorphism, and thinning of corpus callosum maps to chromosome 7q21.13-q21.3

Six individuals of consanguineous Bedouin kindred presented at infancy with an autosomal recessive syndrome of severe global developmental delay, positive pyramidal signs, unique dysmorphism, skeletal abnormalities, and severe failure to thrive with normal birth weights. Patients had a profound intellectual disability and cognitive impairment with almost no acquired developmental milestones by 12 months. Early‐onset axial hypotonia evolved with progressive muscle weakness, reduced muscle tone, and hyporeflexia. Craniofacial dysmorphism consisted of a triangular face with a prominent forehead and midface hypoplasia. Magnetic resonance imaging (MRI) demonstrated thinning of the corpus callosum and paucity of white matter. Genome‐wide linkage analysis identified a single ~4 Mbp disease‐associated locus on chromosome 7q21.13‐q21.3 (LOD score>5). Whole‐exome and genome sequencing identified no nonsynonymous pathogenic biallelic variants in any of the genes within this locus. Following the exclusion of partially resembling syndromes, we now describe a novel autosomal recessive syndrome mapped to a ~4Mbp locus on chromosome 7.

0128 Mild Upper Airway Obstruction Leads to Increased Energy Intake and Growth Retardation that Persists After the Obstruction Removal

Introduction

Whereas pediatric obstructive sleep apnea may cause insufficient body weight gain and growth retardation, in some studies, metabolic syndrome and obesity were observed. Interestingly, treatment by adenotonsillectomy can lead to accelerated weight gain by an unclear mechanism. Here, we explored the effects of moderate upper airway obstruction (AO) and mild AO (mAO) and its removal (OR) on ventilation, resting energy expenditure (REE), food intake and growth during the diurnal cycle, from weaning to adulthood.

Methods

The trachea of 22-day-old rats was surgically narrowed to generate AO, mAO, and OR was performed after two weeks on mAO animals. Minute ventilation was recorded by whole body plethysmography and diurnal food intake, and REE was explored with metabolic cages 12 weeks post surgery.

Results

Following tracheal narrowing, inspiratory swings in esophageal pressure increased by 177% (p<0.01) and 36% (p<0.01) in AO and mAO rats, respectively, and was similar to the controls in the OR group. REE (Kcal/h/kg) was 3.7±0.1, 5.7±0.12 (p<0.01), 4.1±0.08 (p<0.01), and 3.6±0.15 in the control, AO, mAO, and OR groups, respectively. Increased EE in the AO and mAO groups was associated with up-regulation of ventilation by 133% and 56%, respectively (p<0.01). In all groups, energy intake (EE) was higher during a 12 h active period compared to a sleep period (p<0.01). EE during the lights on of AO and mAO animals increased by 136 % and 126%, respectively, and was similar to the control in the OR group. Active period EE increased by 19% in both obstructed groups (p<0.01). Active period EE was 16.7 % higher in the OR group despite the normalization of ventilation and tracheal diameter to the control value. Increased REE was associated with hindrance of bone elongation (p<0.01), and OR partially improved growth.

Conclusion

The need to maintain respiratory homeostasis during upper airway obstruction was associated with a persistent increase in energy intake. Surgical intervention may not be sufficient to correct the energy intake elevation, and endocrine regulation of feeding and growth may have greater impacts post intervention.

Support

This study was supported by the Israel Science Foundation grant no. 164/2018

Grape Berry Acclimation to Excessive Solar Irradiance Leads to Repartitioning between Major Flavonoid Groups

Warm viticulture regions are associated with inferior wines, resulting from the interaction between microclimate and fruit biochemistry. Solar irradiance triggers biosynthetic processes in the fruit and dominates its thermal balance. Therefore, deciphering its impact on fruit metabolism is pivotal to develop strategies for fruit protection and ameliorate its quality traits. Here, we modified light quality and intensity in the fruit-zone and integrated micrometeorology with grape and wine metabolomics, allowing a complete assessment, from field to bottle. We analyzed the dynamics of fruit's adaptation to altered conditions during ripening and constructed temporal-based metabolic networks. Micrometeorological modifications shifted the balance between the major flavonoids, associating increased solar exposure with lower levels of anthocyanins and flavan-3-ols, and higher flavonols. Differences were fixed from 2 weeks postveraison until harvest, suggesting a controlled acclimation response rather than external modulation. Differences in grape composition manifested in the wine and resulted in higher color intensity and improved wine hue under partial shading.