Profiling genetically driven alternative splicing across the Indonesian archipelago.

One of the regulatory mechanisms influencing the functional capacity of genes is alternative splicing (AS). Previous studies exploring the splicing landscape of human tissues have shown that AS has contributed to human biology, especially in disease progression and the immune response. Nonetheless, this phenomenon remains poorly characterized across human populations, and it is unclear how genetic and environmental variation contribute to AS. Here, we examine a set of 115 Indonesian samples from three traditional island populations spanning the genetic ancestry cline that characterizes Island Southeast Asia. We conduct a global AS analysis between islands to ascertain the degree of functionally significant AS events and their consequences. Using an event-based statistical model, we detected over 1,500 significant differential AS events across all comparisons. Additionally, we identify over 6,000 genetic variants associated with changes in splicing (splicing quantitative trait loci [sQTLs]), some of which are driven by Papuan-like genetic ancestry, and only show partial overlap with other publicly available sQTL datasets derived from other populations. Computational predictions of RNA binding activity reveal that a fraction of these sQTLs directly modulate the binding propensity of proteins involved in the splicing regulation of immune genes. Overall, these results contribute toward elucidating the role of genetic variation in shaping gene regulation in one of the most diverse regions in the world.

Multicentric Longitudinal Prospective Study in a European Cohort of MYO7A Patients: Disease Course and Implications for Gene Therapy.

Purpose: We investigated the natural history of retinal dystrophy owing to variants in the MYO7A gene. Methods: Fifty-three patients (mean age, 33.6 ± 16.7 years) with Usher syndrome owing to biallelic, mostly pathogenic, variants in MYO7A underwent baseline and two annual follow-up visits. Best-corrected visual acuity (BCVA), semiautomatic kinetic visual field, full-field electroretinogram, color fundus imaging, microperimetry, spectral-domain optical coherence tomography, and fundus autofluorescence were assessed. Results: At baseline, all patients presented with decreased BCVA (66.4 ± 17.9 Early Treatment Diabetic Retinopathy score and 59.5 ± 21.7 Early Treatment Diabetic Retinopathy score, in the better- and worse-seeing eyes, respectively), restricted semiautomatic kinetic visual field (III4e area, 3365.8 ± 4142.1°2; 4176.4 ± 4400.3°2) and decreased macular sensitivity (9.7 ± 9.9 dB; 9.0 ± 10.2 dB). Spectral-domain optical coherence tomography revealed reduced central macular thickness (259.6 ± 63.0 µm; 250.7 ± 63.3 µm) and narrowed ellipsoid zone band width (2807.5 ± 2374.6 µm; 2615.5 ± 2370.4 µm). Longitudinal analyses (50 patients) showed a significant decrease of BCVA in better-seeing eyes, whereas no changes were observed in worse-seeing eyes for any parameter. BCVA, semiautomatic kinetic visual field (III4e and V4e) and macular sensitivity were related significantly to age at baseline. Hyperautofluorescent foveal patch (16 eyes [31.4%]) and abnormal central hypoautofluorescence (9 eyes [17.6%]) were significantly associated with worse morphological and functional read-outs compared with the hyperautofluorescent ring pattern (22 eyes [43.1%]). Conclusions: Our European multicentric study offers the first prospective longitudinal analysis in one of the largest cohorts of MYO7A patients described to date, confirming the slow disease progression. More important, this study emphasizes the key role of fundus autofluorescence patterns in retinal impairment staging and advocates its adoption as an objective biomarker in patient selection for future gene therapy clinical trials.

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata).

Marsupials exhibit distinctive modes of reproduction and early development that set them apart from their eutherian counterparts and render them invaluable for comparative studies. However, marsupial genomic resources still lag far behind those of eutherian mammals. We present a series of novel genomic resources for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that, due to its ease of husbandry and ex-utero development, is emerging as a laboratory model. We constructed a highly representative multi-tissue de novo transcriptome assembly of dunnart RNA-seq reads spanning 12 tissues. The transcriptome includes 2,093,982 assembled transcripts and has a mammalian transcriptome BUSCO completeness score of 93.3%, the highest amongst currently published marsupial transcriptomes. This global transcriptome, along with ab initio predictions, supported annotation of the existing dunnart genome, revealing 21,622 protein-coding genes. Altogether, these resources will enable wider use of the dunnart as a model marsupial and deepen our understanding of mammalian genome evolution.

Defining and Reducing Variant Classification Disparities.

Background: Multiplexed Assays of Variant Effects (MAVEs) can test all possible single variants in a gene of interest. The resulting saturation-style data may help resolve variant classification disparities between populations, especially for variants of uncertain significance (VUS). Methods: We analyzed clinical significance classifications in 213,663 individuals of European-like genetic ancestry versus 206,975 individuals of non-European-like genetic ancestry from All of Us and the Genome Aggregation Database. Then, we incorporated clinically calibrated MAVE data into the Clinical Genome Resource's Variant Curation Expert Panel rules to automate VUS reclassification for BRCA1, TP53, and PTEN . Results: Using two orthogonal statistical approaches, we show a higher prevalence ( p ≤5.95e-06) of VUS in individuals of non-European-like genetic ancestry across all medical specialties assessed in all three databases. Further, in the non-European-like genetic ancestry group, higher rates of Benign or Likely Benign and variants with no clinical designation ( p ≤2.5e-05) were found across many medical specialties, whereas Pathogenic or Likely Pathogenic assignments were higher in individuals of European-like genetic ancestry ( p ≤2.5e-05). Using MAVE data, we reclassified VUS in individuals of non-European-like genetic ancestry at a significantly higher rate in comparison to reclassified VUS from European-like genetic ancestry ( p =9.1e-03) effectively compensating for the VUS disparity. Further, essential code analysis showed equitable impact of MAVE evidence codes but inequitable impact of allele frequency ( p =7.47e-06) and computational predictor ( p =6.92e-05) evidence codes for individuals of non-European-like genetic ancestry. Conclusions: Generation of saturation-style MAVE data should be a priority to reduce VUS disparities and produce equitable training data for future computational predictors.

PRPH2-Related Retinal Dystrophies: Mutational Spectrum in 103 Families from a Spanish Cohort.

PRPH2, one of the most frequently inherited retinal dystrophy (IRD)-causing genes, implies a high phenotypic variability. This study aims to analyze the PRPH2 mutational spectrum in one of the largest cohorts worldwide, and to describe novel pathogenic variants and genotype-phenotype correlations. A study of 220 patients from 103 families recruited from a database of 5000 families. A molecular diagnosis was performed using classical molecular approaches and next-generation sequencing. Common haplotypes were ascertained by analyzing single-nucleotide polymorphisms. We identified 56 variants, including 11 novel variants. Most of them were missense variants (64%) and were located in the D2-loop protein domain (77%). The most frequently occurring variants were p.Gly167Ser, p.Gly208Asp and p.Pro221_Cys222del. Haplotype analysis revealed a shared region in families carrying p.Leu41Pro or p.Pro221_Cys222del. Patients with retinitis pigmentosa presented an earlier disease onset. We describe the largest cohort of IRD families associated with PRPH2 from a single center. Most variants were located in the D2-loop domain, highlighting its importance in interacting with other proteins. Our work suggests a likely founder effect for the variants p.Leu41Pro and p.Pro221_Cys222del in our Spanish cohort. Phenotypes with a primary rod alteration presented more severe affectation. Finally, the high phenotypic variability in PRPH2 hinders the possibility of drawing genotype-phenotype correlations.

The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes.

BACKGROUND: Although the p.C759F (c.2276G>T, p.Cys759Phe) variant in the USH2A gene has been identified in association with retinal degeneration by several authors, its pathogenicity has been questioned once by the publication of two unaffected homozygotes from a single family. OBJECTIVES: The objective of the study was to ascertain the role of p.C759F in hereditary retinal disease. METHODS: We examined 87 research articles reporting on patients carrying this variant and then used this information as primary data for a series of meta-analytical tests. RESULTS: Independent statistical analyses showed that p.C759F (i) is highly enriched in patients with respect to healthy individuals, (ii) represents a clear-cut recessive allele causing disease when it is in trans with other mutations, (iii) is pathogenic in homozygotes. CONCLUSIONS: Our results confirm that p.C759F is a bona fide mutation, leading to retinal blindness according to a recessive pattern of inheritance.

Increasing diversity of functional genetics studies to advance biological discovery and human health.

In this perspective we discuss the current lack of genetic and environmental diversity in functional genomics datasets. There is a well-described Eurocentric bias in genetic and functional genomic research that has a clear impact on the benefit this research can bring to underrepresented populations. Current research focused on genetic variant-to-function experiments aims to identify molecular QTLs, but the lack of data from genetically diverse individuals has limited analyses to mostly populations of European ancestry. Although some efforts have been established to increase diversity in functional genomic studies, much remains to be done to consistently generate data for underrepresented populations from now on. We discuss the major barriers for this continuity and suggest actionable insights, aiming to empower research and researchers from underserved populations.

TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa.

Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.

Are the Blueberries We Buy Good Quality? Comparative Study of Berries Purchased from Different Outlets.

Blueberries (Vaccinium corymbosum L.) are becoming increasingly popular for their nutritional and health benefits, and their economic value is therefore increasing. The loss of quality that can occur due to softening and fungal attack is an important consideration when marketing blueberries. Despite the added value of blueberries, no studies have been carried out on how the fruit arrives at the outlets just before purchase by the consumer in terms of firmness, physico-chemical parameters, phenolic compounds, and fungal growth. The aim of this work has been, therefore, to investigate possible differences in quality parameters between blueberries purchased from ten different outlets, regardless of the supplier. The results showed that all the samples were of acceptable quality, although they all had a low maturity index at the point of sale. None of the samples studied showed clear signs of fungal decay at the time of purchase, although we were able to grow and identify some pathogen specimens after cultivation. In terms of total phenolic and anthocyanin content, as well as antioxidant activity, all the samples showed low values, possibly due to their postharvest storage, but they were within the expected range for this fruit. On the other hand, differences in the measured parameters were observed between samples of the same cultivar while no differences were found between conventionally and organically grown blueberries. This suggests that preharvest (such as edaphoclimatic conditions, agricultural practices, and cultivars) and postharvest factors (such as treatments used, storage, and transport temperatures) could influence the berry quality when they reach the consumer.

Comprehensive Genotyping and Phenotyping Analysis of GUCY2D-Associated Rod- and Cone-Dominated Dystrophies.

PURPOSE: To describe the genetic and clinical spectrum of GUCY2D-associated retinopathies and to accurately establish their prevalence in a large cohort of patients. DESIGN: Retrospective case series. METHODS: Institutional study of 47 patients from 27 unrelated families with retinal dystrophies carrying disease-causing GUCY2D variants from the Fundación Jiménez Díaz hospital dataset of 8000 patients. Patients underwent ophthalmological examination and molecular testing by Sanger or exome sequencing approaches. Statistical and principal component analyses were performed to determine genotype-phenotype correlations. RESULTS: Four clinically different associated phenotypes were identified: 66.7% of families with cone/cone-rod dystrophy, 22.2% with Leber congenital amaurosis, 7.4% with early-onset retinitis pigmentosa, and 3.7% with congenital night blindness. Twenty-three disease-causing GUCY2D variants were identified, including 6 novel variants. Biallelic variants accounted for 28% of patients, whereas most carried dominant alleles associated with cone/cone-rod dystrophy. The disease onset had statistically significant differences according to the functional variant effect. Patients carrying GUCY2D variants were projected into 3 subgroups by allelic combination, disease onset, and presence of nystagmus or night blindness. In contrast to patients with the most severe phenotype of Leber congenital amaurosis, 7 patients with biallelic GUCY2D had a later and milder rod form with night blindness in infancy as the first symptom. CONCLUSIONS: This study represents the largest GUCY2D cohort in which 4 distinctly different phenotypes were identified, including rare intermediate presentations of rod-dominated retinopathies. We established that GUCY2D is linked to about 1% of approximately 3000 molecularly characterized families of our cohort. All of these findings are critical for defining cohorts for inclusion in future clinical trials.

Pediatric Palliative Care at Home: A Prospective Study on Subcutaneous Drug Administration.

CONTEXT: The subcutaneous route is a useful alternative for drug administration in palliative care. Although there is scientific evidence on its use in adult patients, the literature in pediatric palliative care is almost nonexistent. OBJECTIVES: To describe the experience of a pediatric palliative care unit (PPCU) with in-home subcutaneous drug administration symptom control. METHODS: Prospective observational study of patients receiving home-based subcutaneous treatment administered as part of a PPCU treatment regimen over 16 months. Analysis includes demographic and clinical variables and treatment received. RESULTS: Fifty-four different subcutaneous lines were inserted in the 15 patients included, mainly in the thigh (85.2%). The median time of needle in situ was 5.5 days (range: 1-36 days). A single drug was administered in 55.7% of treatments. The most frequently used drugs were morphine chloride (82%) and midazolam (55.7%). Continuous subcutaneous infusion was the predominant administration route (96.7%), with infusion rates oscillating between 0.1 mL/h and 1.5 mL/h. A statistically significant relationship was found between the maximum infusion rate and induration onset. Of the 54 lines placed, 29 (53.7%) had an associated complication requiring line removal. The primary cause for removal was insertion-site induration (46.3%). Subcutaneous lines were mainly used to manage pain, dyspnea, and epileptic seizures. CONCLUSION: In the pediatric palliative care patients studied, the subcutaneous route is most frequently used for administering morphine and midazolam in continuous infusion. The main complication was induration, especially with longer dwell times or higher infusion rates. However, further studies are required to optimize management and prevent complications.

Seeing humans through an evolutionary lens.

A collection of mammalian genomes provides insights into human biology and evolution.

Hypogammaglobulinemia after front-line immunochemotherapy in patients with follicular lymphoma.

INTRODUCTION: Hypogammaglobulinemia after front-line immunochemotherapy for follicular lymphoma is a poorly studied adverse event that could be related to the appearance of severe and/or recurrent non-neutropenic infections which could affect the quality of life of the patients, even motivating a need of long-term replacement therapy with human immunoglobulins. METHODS: Observational, retrospective study aiming to estimate the incidence of hypogammaglobulinemia, as well as its severity and clinical consequences, and to explore possible predictive factors for its development. Specific immunoglobulin deficiencies were also studied. RESULTS: 76.5% of patients had hypogammaglobulinemia during or after front-line treatment, mostly grade 1-2; with 38.8% patients who developed clinically relevant infections and 20% patients requiring human immunoglobulins replacement therapy. A high-risk FLIPI score was identified as a risk factor for hypogammaglobulinemia (ods ratio: 4.51; 95% confidence interval: 1.29-15.68; p < 0.001) and basal gamma globulin level as a protective factor (odds ratio: 0.92; 95% confidence interval: 0.988-0.996; p = 0.018). Any type of immunochemotherapy regimen was associated with different risks of hypogammaglobulinemia in our study. CONCLUSIONS: Hypogammaglobulinemia appears in a high percentage of patients with follicular lymphoma in a real-world population, identifying a high-risk FLIPI score as a risk factor for its development and basal gamma globulins as a protective factor.

Leveraging massively parallel reporter assays for evolutionary questions.

A long-standing goal of evolutionary biology is to decode how gene regulation contributes to organismal diversity. Doing so is challenging because it is hard to predict function from non-coding sequence and to perform molecular research with non-model taxa. Massively parallel reporter assays (MPRAs) enable the testing of thousands to millions of sequences for regulatory activity simultaneously. Here, we discuss the execution, advantages, and limitations of MPRAs, with a focus on evolutionary questions. We propose solutions for extending MPRAs to rare taxa and those with limited genomic resources, and we underscore MPRA's broad potential for driving genome-scale, functional studies across organisms.

Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks.

Screening for pathogenic variants in the diagnosis of rare genetic diseases can now be performed on all genes thanks to the application of whole exome and genome sequencing (WES, WGS). Yet the repertoire of gene-disease associations is not complete. Several computer-based algorithms and databases integrate distinct gene-gene functional networks to accelerate the discovery of gene-disease associations. We hypothesize that the ability of every type of information to extract relevant insights is disease-dependent. We compiled 33 functional networks classified into 13 knowledge categories (KCs) and observed large variability in their ability to recover genes associated with 91 genetic diseases, as measured using efficiency and exclusivity. We developed GLOWgenes, a network-based algorithm that applies random walk with restart to evaluate KCs' ability to recover genes from a given list associated with a phenotype and modulates the prediction of new candidates accordingly. Comparison with other integration strategies and tools shows that our disease-aware approach can boost the discovery of new gene-disease associations, especially for the less obvious ones. KC contribution also varies if obtained using recently discovered genes. Applied to 15 unsolved WES, GLOWgenes proposed three new genes to be involved in the phenotypes of patients with syndromic inherited retinal dystrophies.

Gestational diabetes prevalence and outcomes in women undergoing assisted reproductive techniques (ART).

Infertility affects millions worldwide and use of assisted reproductive techniques (ART) is in high demand. AIMS: To investigate whether women that underwent ART at our hospital had a higher incidence of GDM than women who conceived spontaneously, if the ART subtype affects the GDM rate and to study obstetrical outcomes in women with GDM in both groups. METHODS: This was a retrospective analysis of prospectively collected data of singleton pregnancies attended at Hospital Universitari Dexeus between 2008 and 2019. Age<18 years, pregestational diabetes, metformin prior to pregnancy and multiple pregnancies were excluded. RESULTS: A total of 29,529 patients were included. Pregnancy was achieved by ART in 2596 (8.8%): in vitro fertilisation (IVF/ICSI) 32.8%, frozen embryo transfer (FET) 37.7%, oocyte donor receptors (ODR) 17.2% and insemination 12.2%. The GDM rate was 8.9% (12.7% in ART vs 8.5% in non-ART, p<0.001). The GDM was 11.2% in IVF/ICSI, 17.7% in ODR, 13% in FET and 9.1% in the insemination group (p=0.001). In a multivariable analysis adjusting for age, parity and BMI, ART was not associated with GDM [OR 1.03 (0.90-1.19)], nor was type of ART. Pregnancy outcomes in GDM patients were similar in both groups except for C-section rates (30.0% in ART vs 15.9% in non-ART (p<0.001). CONCLUSIONS: Despite a higher prevalence of GDM in ART pregnancies, ART was not associated with an increased risk of GDM when adjusting for age, parity and BMI. The prognosis of GDM in ART and non-ART was similar except for C-section rates.

Denisovan introgression has shaped the immune system of present-day Papuans.

Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.

Short-Term Gaseous Treatments Improve Rachis Browning in Red and White Table Grapes Stored at Low Temperature: Molecular Mechanisms Underlying Its Beneficial Effect.

Short-term gaseous treatments improve rachis quality during table grape postharvest, but little is known about the mechanisms involved. In this work, we observed that the application of a 3-day CO2 treatment at 0 °C improved rachis browning of Superior Seedless and Red Globe bunches, affecting the non-enzymatic antioxidant system by reducing the total phenolic content, the antioxidant activity and the expression of different stilbene synthase genes. Lipid peroxidation levels revealed lower oxidative stress in CO2-treated rachis of both cultivars linked to the activation of the enzymatic antioxidant system. Furthermore, whereas a positive correlation was denoted between rachis browning and the accumulation of key ABA regulatory genes in Red Globe bunches, this effect was restricted to ACS1, a key synthetic ethylene gene, in Superior Seedless clusters. This work also corroborated the important role of ethylene-responsive factors in the beneficial effect of the gaseous treatment, not only in the berries but also in the rachis. Finally, the application of the gaseous treatment avoided the induction of cell wall-degrading enzyme-related genes in both cultivars, which could favor the maintenance of rachis quality. This work provides new insight into specific responses modulated by the gaseous treatment focused on mitigating rachis browning independently of the cultivar.

Transcriptomic analysis of CO2-treated strawberries (Fragaria vesca) with enhanced resistance to softening and oxidative stress at consumption.

One of the greatest threats to wild strawberries (Fragaria vesca Mara des Bois) after harvest is the highly perishability at ambient temperature. Breeders have successfully met the quality demands of consumers, but the prevention of waste after harvest in fleshy fruits is still pending. Most of the waste is due to the accelerated progress of senescence-like process after harvest linked to a rapid loss of water and firmness at ambient temperature. The storage life of strawberries increases at low temperature, but their quality is limited by the loss of cell structure. The application of high CO2 concentrations increased firmness during cold storage. However, the key genes related to resistance to softening and cell wall disassembly following transference from cold storage at 20°C remain unclear. Therefore, we performed RNA-seq analysis, constructing a weighted gene co-expression network analysis (WGCNA) to identify which molecular determinants play a role in cell wall integrity, using strawberries with contrasting storage conditions, CO2-cold stored (CCS), air-cold stored (ACS), non-cold stored (NCS) kept at ambient temperature, and intact fruit at harvest (AH). The hub genes associated with the cell wall structural architecture of firmer CO2-treated strawberries revealed xyloglucans stabilization attributed mainly to a down-regulation of Csl E1, XTH 15, Exp-like B1 and the maintenance of expression levels of nucleotide sugars transferases such as GMP and FUT as well as improved lamella integrity linked to a down-regulation of RG-lyase, PL-like and PME. The preservation of cell wall elasticity together with the up-regulation of LEA, EXPA4, and MATE, required to maintain cell turgor, is the mechanisms controlled by high CO2. In stressed air-cold stored strawberries, in addition to an acute softening, there is a preferential transcript accumulation of genes involved in lignin and raffinose pathways. Non-cold stored strawberries kept at 20°C after harvest are characterized by an enrichment in genes mainly involved in oxidative stress and up-expression of genes involved in jasmonate biosynthesis. The present results on transcriptomic analysis of CO2-treated strawberries with enhanced resistance to softening and oxidative stress at consumption will help to improve breeding strategies of both wild and cultivated strawberries.