SnapShot: Splicing Alterations in Cancer.

RNA splicing, the spliceosome-catalyzed process by which pre-messenger RNA (pre-mRNA) is processed to mature mRNA, is altered in a number of ways in cancer. Tumor-specific splicing alterations are created by mutations that disrupt splicing-regulatory elements within genes and impair splicing recognition or by altering the RNA-binding preferences of individual splicing factors. This SnapShot summarizes our current understanding of splicing-factor alterations in cancers. To view this SnapShot, open or download the PDF.

Recurrent SRSF2 mutations in MDS affect both splicing and NMD.

Oncogenic mutations in the RNA splicing factors SRSF2, SF3B1, and U2AF1 are the most frequent class of mutations in myelodysplastic syndromes and are also common in clonal hematopoiesis, acute myeloid leukemia, chronic lymphocytic leukemia, and a variety of solid tumors. They cause genome-wide splicing alterations that affect important regulators of hematopoiesis. Several mRNA isoforms promoted by the various splicing factor mutants comprise a premature termination codon (PTC) and are therefore potential targets of nonsense-mediated mRNA decay (NMD). In light of the mechanistic relationship between splicing and NMD, we sought evidence for a specific role of mutant SRSF2 in NMD. We show that SRSF2 Pro95 hot spot mutations elicit enhanced mRNA decay, which is dependent on sequence-specific RNA binding and splicing. SRSF2 mutants enhance the deposition of exon junction complexes (EJCs) downstream from the PTC through RNA-mediated molecular interactions. This architecture then favors the association of key NMD factors to elicit mRNA decay. Gene-specific blocking of EJC deposition by antisense oligonucleotides circumvents aberrant NMD promoted by mutant SRSF2, restoring the expression of PTC-containing transcript. Our study uncovered critical effects of SRSF2 mutants in hematologic malignancies, reflecting the regulation at multiple levels of RNA metabolism, from splicing to decay.

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.

RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence motifs in their target transcripts, but precisely defining their binding specificity remains challenging. Crosslinking and immunoprecipitation (CLIP) allows for mapping of the exact protein-RNA crosslink sites, which frequently reside at specific positions in RBP motifs at single-nucleotide resolution. Here, we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the discovered motifs by genome-wide analysis of allelic binding sites. Our analyses revealed that the prototypical SR protein SRSF1 recognizes clusters of GGA half-sites in addition to its canonical GGAGGA motif. Therefore, SRSF1 regulates splicing of a much larger repertoire of transcripts than previously appreciated, including HNRNPD and HNRNPDL, which are involved in multivalent protein assemblies and phase separation.

Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis.

Transcription and pre-mRNA splicing are key steps in the control of gene expression and mutations in genes regulating each of these processes are common in leukaemia1,2. Despite the frequent overlap of mutations affecting epigenetic regulation and splicing in leukaemia, how these processes influence one another to promote leukaemogenesis is not understood and, to our knowledge, there is no functional evidence that mutations in RNA splicing factors initiate leukaemia. Here, through analyses of transcriptomes from 982 patients with acute myeloid leukaemia, we identified frequent overlap of mutations in IDH2 and SRSF2 that together promote leukaemogenesis through coordinated effects on the epigenome and RNA splicing. Whereas mutations in either IDH2 or SRSF2 imparted distinct splicing changes, co-expression of mutant IDH2 altered the splicing effects of mutant SRSF2 and resulted in more profound splicing changes than either mutation alone. Consistent with this, co-expression of mutant IDH2 and SRSF2 resulted in lethal myelodysplasia with proliferative features in vivo and enhanced self-renewal in a manner not observed with either mutation alone. IDH2 and SRSF2 double-mutant cells exhibited aberrant splicing and reduced expression of INTS3, a member of the integrator complex3, concordant with increased stalling of RNA polymerase II (RNAPII). Aberrant INTS3 splicing contributed to leukaemogenesis in concert with mutant IDH2 and was dependent on mutant SRSF2 binding to cis elements in INTS3 mRNA and increased DNA methylation of INTS3. These data identify a pathogenic crosstalk between altered epigenetic state and splicing in a subset of leukaemias, provide functional evidence that mutations in splicing factors drive myeloid malignancy development, and identify spliceosomal changes as a mediator of IDH2-mutant leukaemogenesis.

Isolated Ni Atoms Enable Near-Unity CH4 Selectivity for Photothermal CO2 Hydrogenation.

Photothermal hydrogenation of carbon dioxide (CO2) into value-added products is an ideal solution for addressing the energy crisis and mitigating CO2 emissions. However, achieving high product selectivity remains challenging due to the simultaneous occurrence of numerous competing intermediate reactions during CO2 hydrogenation. We present a novel approach featuring isolated single-atom nickel (Ni) anchored onto indium oxide (In2O3) nanocrystals, serving as an effective photothermal catalyst for CO2 hydrogenation into methane (CH4) with a remarkable near-unity (∼99%) selectivity. Experiments and theoretical simulations have confirmed that isolated Ni sites on the In2O3 surface can effectively stabilize the intermediate products of the CO2 hydrogenation reaction and reduce the transition state energy barrier, thereby changing the reaction path to achieve ultrahigh selective methanation. This study provides comprehensive insights into the design of single-atom catalysts for the highly selective photothermal catalytic hydrogenation of CO2 to methane.

A nested case-control study of untargeted plasma metabolomics and lung cancer among never-smoking women within the prospective Shanghai Women's Health Study.

The etiology of lung cancer in never-smokers remains elusive, despite 15% of lung cancer cases in men and 53% in women worldwide being unrelated to smoking. Here, we aimed to enhance our understanding of lung cancer pathogenesis among never-smokers using untargeted metabolomics. This nested case-control study included 395 never-smoking women who developed lung cancer and 395 matched never-smoking cancer-free women from the prospective Shanghai Women's Health Study with 15,353 metabolic features quantified in pre-diagnostic plasma using liquid chromatography high-resolution mass spectrometry. Recognizing that metabolites often correlate and seldom act independently in biological processes, we utilized a weighted correlation network analysis to agnostically construct 28 network modules of correlated metabolites. Using conditional logistic regression models, we assessed the associations for both metabolic network modules and individual metabolic features with lung cancer, accounting for multiple testing using a false discovery rate (FDR) < 0.20. We identified a network module of 121 features inversely associated with all lung cancer (p = .001, FDR = 0.028) and lung adenocarcinoma (p = .002, FDR = 0.056), where lyso-glycerophospholipids played a key role driving these associations. Another module of 440 features was inversely associated with lung adenocarcinoma (p = .014, FDR = 0.196). Individual metabolites within these network modules were enriched in biological pathways linked to oxidative stress, and energy metabolism. These pathways have been implicated in previous metabolomics studies involving populations exposed to known lung cancer risk factors such as traffic-related air pollution and polycyclic aromatic hydrocarbons. Our results suggest that untargeted plasma metabolomics could provide novel insights into the etiology and risk factors of lung cancer among never-smokers.

Age at lung cancer diagnosis in females versus males who never smoke by race and ethnicity.

BACKGROUND: We characterized age at diagnosis and estimated sex differences for lung cancer and its histological subtypes among individuals who never smoke. METHODS: We analyzed the distribution of age at lung cancer diagnosis in 33,793 individuals across 8 cohort studies and two national registries from East Asia, the United States (US) and the United Kingdom (UK). Student's t-tests were used to assess the study population differences (Δ years) in age at diagnosis comparing females and males who never smoke across subgroups defined by race/ethnicity, geographic location, and histological subtypes. RESULTS: We found that among Chinese individuals diagnosed with lung cancer who never smoke, females were diagnosed with lung cancer younger than males in the Taiwan Cancer Registry (n = 29,832) (Δ years = -2.2 (95% confidence interval (CI):-2.5, -1.9), in Shanghai (n = 1049) (Δ years = -1.6 (95% CI:-2.9, -0.3), and in Sutter Health and Kaiser Permanente Hawai'i in the US (n = 82) (Δ years = -11.3 (95% CI: -17.7, -4.9). While there was a suggestion of similar patterns in African American and non-Hispanic White individuals. the estimated differences were not consistent across studies and were not statistically significant. CONCLUSIONS: We found evidence of sex differences for age at lung cancer diagnosis among individuals who never smoke.

Phenotypic and genetically predicted leucocyte telomere length and lung cancer risk in the prospective UK Biobank.

We investigated phenotypic leucocyte telomere length (LTL), genetically predicted LTL (gTL), and lung cancer risk among 371 890 participants, including 2829 incident cases, from the UK Biobank. Using multivariable Cox regression, we found dose-response relationships between longer phenotypic LTL (p-trendcontinuous=2.6×10-5), longer gTL predicted using a polygenic score with 130 genetic instruments (p-trendcontinuous=4.2×10-10), and overall lung cancer risk, particularly for adenocarcinoma. The associations were prominent among never smokers. Mendelian Randomization analyses supported causal associations between longer telomere length and lung cancer (HRper 1 SD gTL=1.87, 95% CI: 1.49 to 2.36, p=4.0×10-7), particularly adenocarcinoma (HRper 1 SD gTL=2.45, 95%CI: 1.69 to 3.57, p=6.5×10-6).

Epigenome-wide association study of lung cancer among never smokers in two prospective cohorts in Shanghai, China.

BACKGROUND: The aetiology of lung cancer among individuals who never smoked remains elusive, despite 15% of lung cancer cases in men and 53% in women worldwide being unrelated to smoking. Epigenetic alterations, particularly DNA methylation (DNAm) changes, have emerged as potential drivers. Yet, few prospective epigenome-wide association studies (EWAS), primarily focusing on peripheral blood DNAm with limited representation of never smokers, have been conducted. METHODS: We conducted a nested case-control study of 80 never-smoking incident lung cancer cases and 83 never-smoking controls within the Shanghai Women's Health Study and Shanghai Men's Health Study. DNAm was measured in prediagnostic oral rinse samples using Illumina MethylationEPIC array. Initially, we conducted an EWAS to identify differentially methylated positions (DMPs) associated with lung cancer in the discovery sample of 101 subjects. The top 50 DMPs were further evaluated in a replication sample of 62 subjects, and results were pooled using fixed-effect meta-analysis. RESULTS: Our study identified three DMPs significantly associated with lung cancer at the epigenome-wide significance level of p<8.22×10-8. These DMPs were identified as cg09198866 (MYH9; TXN2), cg01411366 (SLC9A10) and cg12787323. Furthermore, examination of the top 1000 DMPs indicated significant enrichment in epithelial regulatory regions and their involvement in small GTPase-mediated signal transduction pathways. Additionally, GrimAge acceleration was identified as a risk factor for lung cancer (OR=1.19 per year; 95% CI 1.06 to 1.34). CONCLUSIONS: While replication in a larger sample size is necessary, our findings suggest that DNAm patterns in prediagnostic oral rinse samples could provide novel insights into the underlying mechanisms of lung cancer in never smokers.

Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or ß-Sheet Conformations on Time of SIVmac251 Acquisition.

The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vaccinated macaque that was protected from multiple simian immunodeficiency virus (SIV) challenges, both target an overlapping, conformationally dynamic epitope in SIV envelope variable region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a ß-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIVmac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIVmac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation. IMPORTANCE Studies suggest that the protection against SIV/simian-human immunodeficiency virus (SHIV) acquisition afforded by the SIV/HIV V1 deletion-containing envelope immunogens, delivered by the DNA/ALVAC vaccine platform, requires multiple innate and adaptive host responses. Anti-inflammatory macrophages and tolerogenic dendritic cells (DC-10), together with CD14+ efferocytes, are consistently found to correlate with a vaccine-induced decrease in the risk of SIV/SHIV acquisition. Similarly, V2-specific antibody responses mediating ADCC, Th1 and Th2 cells expressing no or low levels of CCR5, and envelope-specific NKp44+ cells producing interleukin 17 (IL-17) also are reproducible correlates of decreased risk of virus acquisition. We focused on the function and the antiviral potential of two monoclonal antibodies (NCI05 and NCI09) isolated from vaccinated animals that differ in antiviral function in vitro and recognize V2 in a linear (NCI09) or coil/helical (NCI05) conformation. We demonstrate that NCI05, but not NCI09, delays SIVmac251 acquisition, highlighting the complexity of antibody responses to V2.

Quartet Fiduccia-Mattheyses revisited for larger phylogenetic studies.

MOTIVATION: With the recent breakthroughs in sequencing technology, phylogeny estimation at a larger scale has become a huge opportunity. For accurate estimation of large-scale phylogeny, substantial endeavor is being devoted in introducing new algorithms or upgrading current approaches. In this work, we endeavor to improve the Quartet Fiduccia and Mattheyses (QFM) algorithm to resolve phylogenetic trees of better quality with better running time. QFM was already being appreciated by researchers for its good tree quality, but fell short in larger phylogenomic studies due to its excessively slow running time. RESULTS: We have re-designed QFM so that it can amalgamate millions of quartets over thousands of taxa into a species tree with a great level of accuracy within a short amount of time. Named "QFM Fast and Improved (QFM-FI)", our version is 20 000× faster than the previous version and 400× faster than the widely used variant of QFM implemented in PAUP* on larger datasets. We have also provided a theoretical analysis of the running time and memory requirements of QFM-FI. We have conducted a comparative study of QFM-FI with other state-of-the-art phylogeny reconstruction methods, such as QFM, QMC, wQMC, wQFM, and ASTRAL, on simulated as well as real biological datasets. Our results show that QFM-FI improves on the running time and tree quality of QFM and produces trees that are comparable with state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: QFM-FI is open source and available at https://github.com/sharmin-mim/qfm_java.

ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data.

MOTIVATION: Spatial domain identification is a very important problem in the field of spatial transcriptomics. The state-of-the-art solutions to this problem focus on unsupervised methods, as there is lack of data for a supervised learning formulation. The results obtained from these methods highlight significant opportunities for improvement. RESULTS: In this article, we propose a potential avenue for enhancement through the development of a semi-supervised convolutional neural network based approach. Named "ScribbleDom", our method leverages human expert's input as a form of semi-supervision, thereby seamlessly combines the cognitive abilities of human experts with the computational power of machines. ScribbleDom incorporates a loss function that integrates two crucial components: similarity in gene expression profiles and adherence to the valuable input of a human annotator through scribbles on histology images, providing prior knowledge about spot labels. The spatial continuity of the tissue domains is taken into account by extracting information on the spot microenvironment through convolution filters of varying sizes, in the form of "Inception" blocks. By leveraging this semi-supervised approach, ScribbleDom significantly improves the quality of spatial domains, yielding superior results both quantitatively and qualitatively. Our experiments on several benchmark datasets demonstrate the clear edge of ScribbleDom over state-of-the-art methods-between 1.82% to 169.38% improvements in adjusted Rand index for 9 of the 12 human dorsolateral prefrontal cortex samples, and 15.54% improvement in the melanoma cancer dataset. Notably, when the expert input is absent, ScribbleDom can still operate, in a fully unsupervised manner like the state-of-the-art methods, and produces results that remain competitive. AVAILABILITY AND IMPLEMENTATION: Source code is available at Github (https://github.com/1alnoman/ScribbleDom) and Zenodo (https://zenodo.org/badge/latestdoi/681572669).

Functional and biochemical characterisation of remote homologues of type IV pili proteins PilN and PilO in Helicobacter pylori.

Helicobacter pylori encodes homologues of PilM, PilN and PilO from bacteria with Type IV pili, where these proteins form a pilus alignment complex. Inactivation of pilO changes H. pylori motility in semi-solid media, suggesting a link to the chemosensory pathways or flagellar motor. Here, we showed that mutation of the pilO or pilN gene in H. pylori strain SS1 reduced the mean linear swimming speed in liquid media, implicating PilO and PilN in the function, or regulation of, the flagellar motor. We also demonstrated that the soluble variants of H. pylori PilN and PilO share common biochemical properties with their Type IV pili counterparts which suggests their adapted function in the bacterial flagellar motor may be similar to that in the Type IV pili.

A prospective study of smoking-related white blood cell DNA methylation markers and risk of bladder cancer.

Bladder cancer, a common neoplasm, is primarily caused by tobacco smoking. Epigenetic alterations including DNA methylation have the potential to be used as prospective markers of increased risk, particularly in at-risk populations such as smokers. We aimed to investigate the potential of smoking-related white blood cell (WBC) methylation markers to contribute to an increase in bladder cancer risk prediction over classical questionnaire-based smoking metrics (i.e., duration, intensity, packyears) in a nested case-control study within the prospective prostate, lung, colorectal, and ovarian (PLCO) Cancer Screening Trial and the alpha-tocopherol, beta-carotene cancer (ATBC) Prevention Study (789 cases; 849 controls). We identified 200 differentially methylated sites associated with smoking status and 28 significantly associated (after correction for multiple testing) with bladder cancer risk among 2670 previously reported smoking-related cytosine-phosphate-guanines sites (CpGs). Similar patterns were observed across cohorts. Receiver operating characteristic (ROC) analyses indicated that cg05575921 (AHHR), the strongest smoking-related association we identified for bladder cancer risk, alone yielded similar predictive performance (AUC: 0.60) than classical smoking metrics (AUC: 0.59-0.62). Best prediction was achieved by including the first principal component (PC1) from the 200 smoking-related CpGs alongside smoking metrics (AUC: 0.63-0.65). Further, PC1 remained significantly associated with elevated bladder cancer risk after adjusting for smoking metrics. These findings suggest DNA methylation profiles reflect aspects of tobacco smoke exposure in addition to those captured by smoking duration, intensity and packyears, and/or individual susceptibility relevant to bladder cancer etiology, warranting further investigation.

Lunar Age-Dependent Oscillations in Expression of the Genes for Kisspeptin, GnIH, and Their Receptors in the Grass Puffer during the Spawning Season.

Grass puffer is a semilunar-synchronized spawner: spawning occurs on beaches only for several days of spring tide around new moon (lunar age 0) and full moon (lunar age 15) every 2 weeks from spring to early summer. To investigate the role of kisspeptin and gonadotropin-inhibitory hormone (GnIH) in the semilunar-synchronized spawning, lunar age-dependent expression of the genes encoding kisspeptin (kiss2), kisspeptin receptor (kissr2), GnIH (gnih), GnIH receptor (gnihr), gonadotropin-releasing hormone 1 (GnRH1) (gnrh1), and three gonadotropin (GTH) subunits (gpa, fshb, lhb) was examined in the male grass puffer, which was kept in an aquarium under natural light condition in a lunar month during the spawning period. In the brain, both kiss2 and kissr2 showed lunar variations with a peak at lunar age 10, while both gnih and gnihr showed semilunar variations with two peaks at lunar age 0 and 20. On the other hand, gnrh1 showed semilunar variation with two peaks at lunar age 0 and 15. In the pituitary, kiss2, kissr2, gnih, and gnihr showed similar variations to those shown in the brain. The fshb and lhb mRNA levels showed semilunar variations with two peaks at lunar age 0 and 15. The present study shows lunar and semilunar oscillations of kiss2/kissr2 and gnih/gnihr expressions, respectively, with their peaks around spring tide in the brain and pituitary along with the semilunar expressions of gnrh1 and the pituitary GTH subunit genes. These results suggest that the lunar age-dependent expressions of the kisspeptin, GnIH, and their receptor genes may be primarily important in the control of the precisely timed semilunar spawning of the grass puffer.

Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry.

Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.

Food insecurity, environment, institutional quality, and health outcomes: evidence from South Asia.

BACKGROUND: Food insecurity and environmental degradation pose significant threats to health outcomes in South Asia, necessitating effective policy interventions. Therefore, this study aims to examine the impact of food insecurity and environmental degradation on health outcome indicators amidst global inflationary shocks and institutional quality arrangements. Additionally, it aims to explore the intricate moderating role of institutional quality on the relationship between food insecurity, endogenous variables, and external shocks. METHOD: In alignment with the study's objectives, a set of panel data spanning from 2000 to 2021 is compiled for South Asia. The study introduces a novel variable representing inflationary shock, crafted through the integration of inflation datapoints and the application of the generalized autoregressive conditional heteroskedasticity model. Additionally, a distinctive aggregate institutional quality index is formulated, drawing from six key measures of the Worldwide Governance indicators. To scrutinize the effects of food insecurity, environmental degradation, and other explanatory variables, the study employs the two-step system generalized method of moment technique, offering a robust analytical approach to uncover complex relationships and dynamics in the region. RESULTS: The results indicate that the prevalence of undernourishment, inequality in per capita calorie intake, and CO2 emissions significantly reduce life expectancy and increase mortality rates. Additionally, it shows that per capita kilocalorie supply, per capita GDP, per capita health expenditures, and urbanization are statistically significant for increasing life expectancy and decreasing mortality rates. The findings reveal that inflationary shocks severely affect food insecurity and environmental factors, exerting further pressure on contemporary life expectancy and mortality rates. In rebuttal, the institutional quality index is found to have significant effects on increasing and decreasing life expectancy and mortality rates, respectively. Furthermore, the institutional quality index is effective in moderating the nexus between food insecurity, environmental degradation, and health outcomes while also neutralizing the negative impact of inflationary shocks on the subject. CONCLUSION: The results verify triple health constraints such as food insecurity, environmental factors, and economic vulnerability to global shocks, which impose severe effects on life expectancy and mortality rates. Furthermore, poor institutional quality is identified as a hindrance to health outcomes in South Asia. The findings suggest specific policy implications that are explicitly discussed.

Role of women empowerment on mental health problems and care-seeking behavior among married women in Nepal: secondary analysis of nationally representative data.

PURPOSE: This study investigates the associations between women empowerment and the prevalence of mental health symptoms and care-seeking behavior among ever-married Nepalese women aged 15-49 years. METHODS: We utilized 2022 Nepal Demographic and Health Survey data to measure women empowerment, employing the Survey-Based Women's Empowerment (SWPER) index. The index focuses on the domains of social independence, decision-making, and attitudes towards violence. Symptoms of anxiety and depression were measured using the Generalized Anxiety Disorder-7 scale (GAD-7) and the Patient Health Questionnaire (PHQ-9), respectively. Multiple logistic regression was performed to estimate adjusted odds ratio (aOR) for associations of women empowerment domains and mental health problems and care-seeking behavior. RESULTS: Among 5556 women, the prevalence of symptoms of anxiety and depression was 23.1% and 6.1%, respectively. Among those with any symptoms of anxiety or depression, 18.3% sought care. Compared to women with low level of empowerment in the "social independence" domain, those with high level of empowerment were less likely to suffer from symptoms of anxiety (aOR = 0.68; 95%CI, 0.57-0.82) and depression (aOR = 0.69; 95%CI, 0.50-0.94). However, high empowerment in "decision-making" domain was associated with higher likelihood of anxiety (aOR = 1.67; 95%CI, 1.33-2.10) and depression (aOR = 1.80; 95%CI, 1.26-2.58). There was evidence of positive association between high empowerment in "decision-making" and care-seeking (aOR = 1.28; 95%CI, 0.96-1.71). CONCLUSIONS: This study underscores important roles of women empowerment on mental health symptoms and care-seeking behavior, suggesting the need to integrate empowerment initiatives into strategies to promote mental health among women in Nepal and similar low- and middle-income settings.

Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA.

Intronic splicing enhancers and silencers (ISEs and ISSs) are two groups of splicing-regulatory elements (SREs) that play critical roles in determining splice-site selection, particularly for alternatively spliced introns or exons. SREs are often short motifs; their mutation or dysregulation of their cognate proteins frequently causes aberrant splicing and results in disease. To date, however, knowledge about SRE sequences and how they regulate splicing remains limited. Here, using an SMN2 minigene, we generated a complete pentamer-sequence library that comprises all possible combinations of 5 nucleotides in intron 7, at a fixed site downstream of the 5' splice site. We systematically analyzed the effects of all 1023 mutant pentamers on exon 7 splicing, in comparison to the wild-type minigene, in HEK293 cells. Our data show that the majority of pentamers significantly affect exon 7 splicing: 584 of them are stimulatory and 230 are inhibitory. To identify actual SREs, we utilized a motif set enrichment analysis (MSEA), from which we identified groups of stimulatory and inhibitory SRE motifs. We experimentally validated several strong SREs in SMN1/2 and other minigene settings. Our results provide a valuable resource for understanding how short RNA sequences regulate splicing. Many novel SREs can be explored further to elucidate their mechanism of action.

Barriers to healthcare utilization among married women in Afghanistan: the role of asset ownership and women's autonomy.

Women face multiple socio-economic, cultural, contextual, and perceived barriers in health service utilization. Moreover, poor autonomy and financial constraints act as crucial factors to their healthcare accessibility. Therefore, the objective of the present study is to study the association between health care utilization barriers and women empowerment, including asset ownership among currently married women in Afghanistan. Data of 28,661 currently married women from Afghanistan demographic health survey (2015) was used to carry out this study. Barriers to access healthcare were computed based on problems related to permission, money, distance, and companionship, whereas women empowerment and asset ownership were computed as potential covariates along with other socio-economic risk factors. Bivariate and logistic analysis was carried out to study the association and odds of explanatory variables. Our results confirm the significant and strong association between the barriers to access healthcare and various explanatory variables. Women having any decision-making autonomy are less likely to face any odds [(AOR = 0.56, p < 0.001), CI: 0.51-0.61] among the currently married women than those who don't have any decision-making authority. Similarly, women who justify their beating for some specific reasons face the greater difficulty of accessing health care [(AOR = 1.76, p < 0.001), CI: 1.61-1.93]. In terms of asset ownership, women having any asset ownership (land or household) are less likely to face any barriers in health services utilization given the lower odds [(AOR = 0.91, p < 0.001), CI: 0.90-0.98]. Accessing maternal health is a crucial policy challenge in Afghanistan. A substantial proportion of women face barriers related to approval, money, distance, and companionship while accessing the health services utilization in Afghanistan. Similarly, women empowerment and asset ownership are significantly associated with health service accessibility. This paper therefore suggests for some policy interventions to strengthen the healthcare needs of women and ensure healthcare accessibility by scaling down these potential barriers like poor autonomy, asset ownership and domestic violence.