Molecular Traits Research Articles

Estimation of genetic polymorphism in quince (Cydonia oblonga Mill.) genotypes using morphological traits and molecular (DNA barcoding) characterizations

Quince (Cydonia oblonga) is a medicinal plant and a member of family Rosaceae. It is native plant of Asia Minor and Europe. It is used in production of jam and jellies and also as a remedy of several ailments. The present study was conducted to evaluate the genetic polymorphism based on morphological and molecular traits. Different varieties of Quince were collected from different ecological zones of Khyber Pakhtunkhwa Pakistan and a total of 26 different morphological traits were recorded among studied genotypes. Based on qualitative morphological trait study, the variety collected from Tindodag was unique one with highest fruit weight (328.82 g). The lowest fruit weight (68.38 g) was recorded for Talash genotype. The Charbagh and Tindodag genotypes showed highest seed length (10.6 mm) while genotypes of Chitral was recorded as lowest (8.4 mm). Statistically, significant level of variation was noted with coefficient of variance ranged from 2.23% to 30.38%. Based on correlation analysis, fruit length had strongly correlation with fruit weight (r = 0.89**), Average Fruit width was found significant with fruit weight (r = 0.90**). Similarly, the Core Width was found strongly significant with Core Length (r = 0.95**). ANOVA analysis indicated 10 quantitative characters to be highly significant, 2 significant and 1 insignificant. Principal component analysis was also computed for the 13 quantitative traits with Eigen value of 0.48 and a total variance of 97.78%. The first principal component shows total variation of 52.52%. In PC2 the total variation was 80.15%, PC3 94.06% while in PC4 it was 97.78%. The NCBI BLAST results shows that all the genotypes have similar origin except Tindodag genotype, which shows differences in its origin. Accession number for all other genotypes is MN216014.1, while accession number of Tindodag genotype is KF861967.1. Based on this study, it can be concluded that Tindodag genotype is unique out of the studied localities. NCBI BLAST have provided further support for the drawn conclusion.

Identification of Molecular Subtypes and Prognostic Traits Based on Chromosomal Instability Phenotype-Related Genes in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits significant molecular heterogeneity; however, previous studies have not fully explored its classification into distinct molecular subtypes. Here, we identified LUAD-significant chromosomal instability (CIN) phenotype genes (n = 24) using a TCGA-LUAD cohort (n = 592) and evaluated their ability to predict pathologic grade. Unsupervised clustering and principal component analysis revealed that LUAD patients could be classified into CIN phenotype-related subtypes (GroupLow, GroupModerate, and GroupHigh), each exhibiting distinct transcriptomic patterns. Notably, the GroupHigh showed significantly poor overall survival [OS; hazard ratio (HR) = 1.43, p-value < 10−3] and disease-free survival (DFS; HR = 1.27, p-value < 10−3). Univariate and multivariate analysis confirmed that its expression status was an independent prognostic predictor (p-value < 10−3, HR = 2.18, 95% C.I = 1.26–3.76) of the clinical outcomes, outperforming pathologic grade (p-value < 10−3, HR = 1.2, 95% C.I = 1.08–1.33). Moreover, analysis of surfactant metabolism-related genes revealed higher expression in the GroupLow, which was associated with a favorable prognosis. By integrating multiple independent cohorts (n = 779), we validated these findings and confirmed that CIN phenotype gene status serves as a critical prognostic marker in LUAD. Furthermore, genomic profiling showed that the GroupHigh exhibited frequent mutations in key genes such as KEAP1, LYST, SETD2, and TP53, with oncogenes in this group preferentially showing copy number gains. Our study highlights the significance of CIN phenotype gene status as a predictor of LUAD prognosis and its association with transcriptomic and genomic alterations, paving the way for further clinical validation and potential therapeutic interventions.

The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity

Abstract The NHGRI-EBI GWAS Catalog serves as a vital resource for the genetic research community, providing access to the most comprehensive database of human GWAS results. Currently, it contains close to 7 000 publications for >15 000 traits, from which more than 625 000 lead associations have been curated. Additionally, 85 000 full genome-wide summary statistics datasets—containing association data for all variants in the analysis—are available for downstream analyses such as meta-analysis, fine-mapping, Mendelian randomisation or development of polygenic risk scores. As a centralised repository for GWAS results, the GWAS Catalog sets and implements standards for data submission and harmonisation, and encourages the use of consistent descriptors for traits, samples and methodologies. We share processes and vocabulary with the PGS Catalog, improving interoperability for a growing user group. Here, we describe the latest changes in data content, improvements in our user interface, and the implementation of the GWAS-SSF standard format for summary statistics. We address the challenges of handling the rapid increase in large-scale molecular quantitative trait GWAS and the need for sensitivity in the use of population and cohort descriptors while maintaining data interoperability and reusability.

Molecular identification of Fusarium species in commercial vanilla and crop wild relatives in Colombia

AbstractVanilla is an economically important crop for low‐lying humid tropical regions, but cultivated plants face serious phytosanitary problems. Fusarium wilt is a devastating disease affecting vanilla crops, caused by the fungal pathogens Fusarium oxysporum f. sp. vanillae (Fov) and F. oxysporum f. sp. radicis‐vanillae (Forv), part of the F. oxysporum species complex (FOSC). We characterized 29 fungal isolates from a vanilla crop and crop wild relatives (CWR) using molecular (EF1‐α and ITS‐rRNA loci) and morphological traits. Fusarium was the predominant genus, followed by Colletotrichum and Clonostachys. Four Fusarium species were identified: F. oxysporum (37.9%), Fusarium solani (20.7%), Fusarium pseudocircinatum (13.8%) and Fusarium concentricum (10.3%). The latter three species were isolated only from CWR and may represent latent pathogens. Fov was isolated from both the crop and CWR, while a Forv‐affiliated isolate was also found in a vanilla crop, marking the first report in the neotropical region. The EF1‐α locus provided greater genotype resolution, as well as having reference sequences for Forv. However, the fungal barcode ITS locus is widely applied. We recommend the continued use of both loci for Fusarium diagnosis in vanilla to facilitate early detection and the development of effective integrated crop management strategies.

ANGI-03. GLIOMA STEM CELLS INDUCE VASECTASIA – A NON-ANGIOGENIC BRAIN TUMOUR NEOVASCULARIZATION PROCESS DRIVEN BY INTERCELLULAR EGFR TRANSFER THROUGH EXTRACELLULAR VESICLES

Abstract Tumour neovascularization in glioblastoma (GBM) is abundant, abnormal and poorly understood, and it likely involves multiple co-existing mechnanisms with distinct modes of regulation. Since glioma stem cells (GSCs) engage in bidirectional interactions with the vasculature we dissected the resulting vascular responses elicited by either proneural (PN), or mesenchymal (MES) GSC subtypes established from patients isolates and able to drive progression of orthotopic intracranial xenografts in mice. We report here that while PN-GSCs elicited mostly angiogenesis-type vascular capillary growth processes, their MES-GSC counterparts elicited non-angiogenic growth of enlarged vessels (vasectesia), paradoxically associated with reduced blood vessel density. Vasectasia was dependent on the expression of oncogenic EGFR/EGFRvIII by MES-GSCs, and on the related kinase/signalling activity, as EGFR/EGFRvIII gene disruption and Dacomitinib treatment suppressed formation of large blood vessels in vivo and resulted in a preponderance of a small calliber (angiogenic) vasculature throughout xenografts. Notably, the analysis of spatial transcriptomes and single cell RNA sequencing revealed distinct molecular traits of endothelial cells asociated with vasectasia and angiogesis, the former enriched in Birc5, but depleted for angiogenic tip cell markers (Vegfr2, Apln). Mechnaistically, vasectasia was linked to the intercellular transfer of EGFR from MES-GSCs to endothelial cells resulting in ectopic activation of EGFR signalling in the endothelial cell bacground, both in vitro and in a model of in vivo blood vessel recruitment into implanted matrigel pellets. Simultaneous pharmacological blockade of both, angiogenesis (anti-VEGR2) and vasectasia (Dacomitinib) lead to a marked increase in survival of mice with aggressive GBM lesions initiated by MES-GSCs. We suggest that, vasectasia driven by intercellular transfer of oncogenic EGFR may represent a new, subtype-specific mechanism of GBM neovascularization, and a plausible target for agents aiming to modify vascular tumour microenvironment.

Ionomic and proteomic changes highlight the effect of silicon supply on the nodules functioning of Trifolium incarnatum L.

IntroductionNumerous studies have reported the beneficial effects of silicon (Si) in alleviating biotic or abiotic stresses in many plant species. However, the role of Si in Fabaceae facing environmental stress is poorly documented. The aim of this study is to investigate the effect of Si on physiological traits and nodulation efficiency in Trifolium incarnatum L.MethodsSi was supplied (1.7 mM in the form of Na2SiO3) plants inoculated with Rhizobium leguminosarum bv trifolii and plant physiological traits and nodule ionomic and molecular traits were monitored over 25 days.ResultsSi supply promoted shoot biomass, the quantity of both Si and N in roots and shoots, and the number, biomass and density of nodules and their nitrogenase abundance which contribute to better dinitrogen (N2) fixation. Ionomic analysis of nodules revealed that Si supply increased the amount of several macroelements (potassium, phosphorus and sulfur) and microelements (copper, zinc and molybdenum) known to improve nodulation efficiency and N2 fixation. Finally, comparative proteomic analysis (+Si versus -Si) of nodules highlighted that Si modulated the proteome of both symbionts with 989 and 212 differentially accumulated proteins (DAPs) in the infected host root cells and their symbiont bacteria, respectively.DiscussionAmong the DAPs, the roles of those involved in nodulation and N2 fixation are discussed. For the first time, this study provides new insights into the effects of Si on both nodular partners and paves the way for a better understanding of the impact of Si on improving nodule function, and more specifically, on the nodules’ N2-fixing capacity.

Morphological, Biochemical and Molecular Characterization of Plant Growth Promoting Rhizobacteria with Synergistic Effect against Fusarium oxysporum

Currently, plant growth-promoting rhizosphere bacteria (PGPR) are heavily exploited as microbial inoculants in agricultural production among which Pseudomonas sp. and Bacillus sp. are widely used in plant growth promotion and disease control as excellent inoculum strains. Plant growth-promoting rhizobacteria has the potential to be used in agriculture to promote plant growth and health through various mechanisms. Therefore, identifying novel strains tailored to specific agricultural requirements continues to be a key area of research. In the present research work, the strains of PGPR isolated from soybean rhizosphere at Department of Plant Pathology and characterized at morphological, biochemical and molecular level. These strains are now used in ‘Biomix’ formulation a microbial consortium product developed at the Department of Plant Pathology VNMKV, Parbhani to benefit the farmers. Studying the molecular, biochemical, and morphological traits of these microbial strains which are now involved in VNMKV produced ‘Biomix formulation is crucial to maintain its consistency, purity and optimize its formulation. Molecular characterization and phylogenetic analysis will ensure accurate identification and classification of the isolates, enhancing the biofertilizer's effectiveness in agriculture. All three isolates have been identified as per Bergey’s Manual for the determination of bacteriology. All isolates tested positive for starch hydrolysis, citrate utilization, catalase activity, indole production, gelatine hydrolysis, and tetrazolium reduction. Additionally, the 16S rDNA gene sequences of the various potential isolates were validated as P. fluorescens VNMKV1, P. putida VNMKV1, and B. subtilis VNMKV1. The potential of these novel strains of plant growth-promoting rhizobacteria as biocontrol agents was explored by screening against soil-borne pathogenic fungi highlighting their potential to be used as bioinoculant agents.

Proximal and classic epithelioid sarcomas are distinct molecular entities defined by MYC/GATA3 and SOX17/endothelial markers, respectively

Epithelioid sarcoma (ES) is a rare tumor hallmarked by the loss of INI1/SMARCB1 expression. Apart from this alteration, little is known about the biology of ES. Despite recent advances in treatment, the prognosis of ES remains unsatisfactory. To elucidate the molecular underpinnings of ES, and to identify diagnostic biomarkers and potential therapeutic vulnerabilities, we performed an integrated omics profiling (RNA sequencing and methylation array) of 24 primary, untreated ESs. Transcriptome and methylome analysis identified two distinct molecular clusters that essentially corresponded to the morphologic variants of ES, classic ES (C-ES) and the more aggressive proximal ES (P-ES). The P-ES group was characterized by hyperactivation of GATA3 and MYC pathways, with extensive epigenetic rewiring associated with EZH2 overexpression. Both DNA methylation and gene expression analysis indicated a striking similarity with the “MYC subgroup” of ATRT, another SMARCB1-deficient tumor, implying a shared molecular background and potential therapeutic vulnerabilities. Conversely, the C-ES group exhibited an endothelial-like molecular profile, with expression of vascular genes and elevated pro-angiogenic SOX17 signaling. Immunohistochemistry validated the overexpression of the chromatin regulators GATA3 (9/12 vs. 0/16) and EZH2 (7/7 vs. 2/6) in P-ESs, and of the vascular factors SOX17 (8/8 vs. 1/10) and N-cadherin (5/9 vs 0/10) in C-ESs. Therefore, these molecules emerge as potential diagnostic tools to fill the gap represented by the lack of ES subtype-specific biomarkers. In summary, our study shows that P-ES and C-ES represent distinct molecular entities defined by MYC/GATA3 and SOX17/endothelial molecular traits, respectively. Besides providing insights into the biology of ES, our study pinpoints subtype-specific biomarkers and potential therapeutic vulnerabilities.

First report of leaf spot disease caused by Fusarium asiaticum on Lonicera caerulea L. in Heilongjiang Province, China.

Heilongjiang is the largest province with the small, cultivated fruit plant, blue honeysuckle (Lonicera caerulea L.), in China (Sun et al. 2024). Between September 2022 and September 2023, a leaf spot disease was observed on about 10 percent of blue honeysuckles of the 'Lanjingling' cultivar grown in a 6.66-ha field in Mudanjiang (129.38°E, 44.59°N), Heilongjiang Province, China. The typical symptoms include a few small brown sunken leaf spots (approximately 2 mm) in the fruiting stage that gradually expand into larger brown sunken lesions (approximately 10 mm) in the senescence stage (Fig. S1). Small 3-4-mm segments of infected tissue from 100 randomly selected leaf samples with typical symptoms were surface sterilized with 75% ethanol and 5% sodium hypochlorite, rinsed in sterile distilled water, and transferred to 9-cm Petri dishes containing potato dextrose agar (PDA) after drying. Finally, 10 isolated fungi were obtained through single-spore culture on PDA, and their conidia displayed a morphology consistent with Fusarium spp. (Zheng et al. 2023), and no other fungi were isolated. The fungal colonies on PDA were pink to dark red with fluffy aerial mycelium and pigmentation (Fig. S2). Microconidia were not observed, and the macroconidia of fungi had 2 to 6 septa, which were slender, sickle-shaped to nearly curved, with an average size of 38.83 (21.30 to 55.20) × 3.87 (2.70 to 6.60) μm (n = 50) on carnation leaf agar (Fig. S3). Genomic DNA was extracted from the representative isolate LD-245 for molecular verification, and PCR amplification was performed with ITS1/ITS4 (White et al. 1990), RPB2-5F2/RPB2-7CR (Liu et al. 1999), and EFl/EF2 (O'Donnell et al. 1998) primers. Sequences of LD-245 ITS (OR565903), RPB2 (OR584061), and TEF (PP965657) revealed 99 to 100% (494/494, 722/726, and 654/654) of identity with Fusarium asiaticum (MT322117, MH582121, and MT330257). Phylogenetic tree was constructed based on the concatenated sequences of ITS, RPB2, and TEF genes, and LD-245 was clustered with F. asiaticum (Fig. S4, Table S1). Therefore, based on the morphological characteristics and molecular phylogeny, LD-245 was identified as F. asiaticum. Six two-year-old healthy plants of the 'Lanjingling' cultivar were selected for a pathogenicity test. Three plants were inoculated with LD-245 conidial suspension (1 × 106 spores/ml) or with sterile water as an experimental control. All plants were cultured in a greenhouse (28℃, 75% relative humidity, 12 h light and dark cycle), and each experiment was replicated three times. Typical leaf spot symptoms were observed on inoculated leaves after 10 days (Fig. S5), whereas no symptoms were detected on water-treated leaves. The pathogens re-isolated from infected leaves displayed the same morphological and molecular traits as the initial isolate, and were again identified as F. asiaticum, confirming Koch's postulate. F. asiaticum was previously reported on giant elephant's ear (Alocasia macrorrhizos) (Zheng et al. 2023), causing leaf spot disease in China. This study is the first report of blue honeysuckle leaf spot disease caused by F. asiaticum in China. China has the largest blue honeysuckle cultivation area globally, and the production of blue honeysuckle with horticultural value is important for growers (Sun et al. 2024). Therefore, we hope researchers can develop efficient measures to manage emerging plant diseases in the future.

Leptodactylus sertanejo Giaretta & Costa, 2007, a junior synonym of Leptodactylus jolyi Sazima & Bokermann, 1978 (Amphibia, Anura, Leptodactylidae)

The genus Leptodactylus currently comprises 84 species of predominantly Neotropical lowland frogs. The L. fuscus group is the most species-rich in the genus, including the nominal species L. jolyi and L. sertanejo. In a published comprehensive study, involving a total evidence analysis of molecular and non-molecular traits, the grouping of L. jolyi and L. sertanejo was very poorly supported, denoting indifferentiation, and indicated that both species cannot be reliably distinguished from each other morphologically. We analysed the overall morphology and color pattern of the specimens attributed to L. jolyi and L. sertanejo and verified that they are closely similar or even identical. The Comparative Anatomy Index did not present dissimilarities for any morphometric variable. Submitting the values to the Principal Component Analysis, we confirmed the morphometric similarity for all variables. To evaluate the discrepancy degree, the values obtained were submitted to the adherence test of the χ2 and we found that no significant morphometric differences did exist. The advertisement calls of 17 specimens attributed to L. jolyi and L. sertanejo are composed of a single harmonic note constituted by one to four pulses. There are no bioacoustic dissimilarities among the specimens analyzed. The multivariate canonical analysis did not discriminate differences among the specimens. Consequently, considering the poor molecular differentiation and based on the analysis of morphological and meristic characters and on advertisement calls, the synonymization of Leptodactylus sertanejo with L. jolyi is proposed.

Comparative and Phylogenetic Analysis of Anthurium andraeanum Hybridization Based on Molecular and Morphological Traits

Hybridization is considered an important mode of species evolution, but the genetic evolutionary process of Anthurium andraeanum hybridization is still poorly characterized. In order to provide the molecular and morphological basis for phylogenetic analysis in A. andraeanum hybridization, we analyzed the morphological, nuclear genomic, and chloroplast genomic data of five A. andraeanum cultivars and explored the correlations between different traits and nuclear and chloroplast genome characteristics. A. andraeanum hybrid 1 is an A. andraeanum ‘Baron’ (♀) × A. andraeanum ‘Spice’ (♂) cross, and A. andraeanum hybrid 2 is an A. andraeanum ‘Cheers’ (♀) × A. andraeanum hybrid 1 (♂) cross. The A. andraeanum hybrids reflected their parents’ heterozygous features in their morphologies, nuclear genomes, and chloroplast genomes. The morphological traits in the F1 generation were widely separated, showing continuous variation. Based on cluster analysis, the five A. andraeanum cultivars could be divided into two groups. The ISSR analysis results were highly correlated with the spathe color. Among the five A. andraeanum cultivars, the composition and structure features of chloroplast genomes were completely the same or highly similar, respectively. Phylogenetic analysis based on complete chloroplast genome data showed that the genetic stability of the chloroplast is high in A. andraeanum, manifested as uniparental maternal inheritance, where the chloroplast genome composition and structural features of hybrids are highly similar to those of the maternal parent.

Prevalence and Characterization of Plant-Parasitic Nematodes Existing in RD41 Rice Fields in Pathum Thani Province, Thailand, with Emphasis on Hirschmanniella mucronata and Meloidogyne graminicola

Plant parasitic nematodes (PPNs) are one of the most destructive pests affecting rice growth worldwide. In this study, populations of PPNs associated with RD41 rice fields in Pathum Thani Province, Thailand, were surveyed and the dominant PPNs found in the fields were identified using a combination of morphological and molecular traits. A total of 105 soil or root samples were taken from 21 paddy fields in 7 districts of Pathum Thani, and nematode extraction was processed in a laboratory. In all sampled rice fields, 6 nematode genera, namely Hirschmanniella sp., Meloidogyne sp., Pratylenchus sp., Tylenchorhynchus sp., Helicotylenchus sp., and Tylenchus sp., were extracted. Of these 6 nematode genera, Hirschmanniella sp. was the most prevalent in both soil and root samples (66.7 - 100 % occurrence observed), followed by Meloidogyne sp., which was found in only 4 districts of the province (0.2 to 8.7 % occurrence observed). The species of these predominant PPNs were morphologically and molecularly characterized. The identification results remained consistent across morphological features and molecular techniques, confirming the presence of Hirschmanniella mucronata and Meloidogyne graminicola in the studied rice fields. The results of this study provide useful baseline data of the occurrence of PPNs in Thailand's rice fields. The incidence of some PPNs found in this study is likely to become a significant factor limiting rice production yields if they are not better managed. HIGHLIGHTS Plant-parasitic nematode (PPN) populations in RD41 rice fields located in Pathum Thani province, Thailand were examined Six PPN genera were extracted from soil and root samples The predominant PPNs were characterized using morphological and molecular traits The main PPNs were identified as mucronata and M. graminicola This study provides useful baseline data of PPNs found in Thailand's rice fields GRAPHICAL ABSTRACT

A new leaf spot caused by Alternaria alternata on Atractylodes lancea in Jiangsu, China.

Atractylodes lancea is an important Chinese herbal medicine, which is mainly produced in Jiangsu province, China. In June 2022, leaf spots symptom were observed on some A. lancea seedlingsgrowing in a Chinese herbal medicine resource garden of NanjingBotanical Garden, Jiangsu. Approximately 75% of 100 A. lancea seedlings suffered from the disease. Initially, gray to black spots appeared at the tip of the blade, then spread deep into the petiole, finally causing the blade to wither and fall. To isolate the pathogen, five diseased leaves were collected from five different seedlings. Leaf sections (3 to 4 mm) were excised from the margins between healthy and diseased tissues, surface sterilized in 75% alcohol for 30 s, then in 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃in darkness. Pure cultures were obtained by monosporic isolation. Eighteen isolates were obtained, and 77.8% of isolates was identified as Alternaria spp. A representative isolate, CS4-1 was used for further investigation. The colony of CS4-1, growing on PDA was cotton-like and black to brown with gray-white aerial hyphae on their surfaces, and dark gray on the back. The conidia were solitary on conidiophores and were oval to pear-shaped, brown in color, with 1 to 4 transverse septa and 0 to 1 oblique septa, parietal cells extending into the beak, and measured 8.9 to 39.5×6.0 to 13.5 µm (n=35). These characteristics were consistent with the description of Alternaria spp. (Simmons 2007). Six DNA regions, i.e.,internal transcribed spacer (ITS),large subunit ribosomal RNA (LSU), small subunit ribosomal RNA (SSU), anonymous region OPA10-2, Alt a 1 major allergen (Alta1), glyceraldehyde 3-phosphate dehydrogenase (GAPDH)and translation elongation factor 1-alpha (TEF1)with the respective GenBank Accession No. OP836052, OP836054, OP836051, OP851487, OP851488, OP851489, and OP851490, were amplified and sequenced with the primer pairs described by White et al. (1990) and Woudenberg et al. (2015). A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7, and CS4-1 clustered in the A. alternata clade. To test pathogenicity, 12 leaves, on three one-month-old A. lancea seedlings (four leaves from each seedling) were wounded with a sterile needle and inoculated with 20 μL of conidial suspension (1×106 spores/mL) on the left sides of leaves. The right sides of the leaves were inoculated with 20 µL sterile water and used as the control. All inoculated detached leaves and seedlings were covered with clear polyethylene bags to keep moisture and were incubated in a greenhouse at 25℃, 80% relative humidity, and a 12-h light/dark cycle. The experiment was repeated three times. After 4 days, typical gray to black spots were visible on the left sides of all inoculated leaves and the inoculated seedlings, and the right sides remained asymptomatic. Subsequently, the same fungus was reisolated and identified based on morphological and molecular traits. A. alternata has a very wide host range but has never been reported on A. lancea worldwide (nt.ars-grin.gov). Because of the medicinal value of A. lancea, further studies should be directed toward control of this disease.

Natural variation in the chickpea metabolome under drought stress.

Chickpea is the world's fourth largest grown legume crop, which significantly contributes to food security by providing calories and dietary protein globally. However, the increased frequency of drought stress has significantly reduced chickpea production in recent years. Here, we have performed a field experiment with 36 diverse chickpea genotypes to evaluate grain yield, photosynthetic activities and molecular traits related to drought stress. For metabolomics analysis, leaf tissue was collected at three time points representing different pod-filling stages. We identified L-threonic acid, fructose and sugar alcohols involved in chickpea adaptive drought response within the mid-pod-filling stage. A stress susceptibility index for each genotype was calculated to identify tolerance capacity under drought, distributing the 36 genotypes into four categories from best to worst performance. To understand how biochemical mechanisms control different traits for genetic improvement, we performed a differential Jacobian analysis, which unveiled the interplay between various metabolic pathways across three time points, including higher flux towards inositol interconversions, glycolysis for high-performing genotypes, fumarate to malate conversion, and carbon and nitrogen metabolism perturbations. Metabolic GWAS (mGWAS) analysis uncovered gene candidates involved in glycolysis and MEP pathway corroborating with the differential biochemical Jacobian results. Accordingly, this proposed data analysis strategy bridges the gap from pure statistical association to causal biochemical relations by exploiting natural variation. Our study offers new perspectives on the genetic and metabolic understanding of drought tolerance-associated diversity in the chickpea metabolome and led to the identification of metabolic control points that can be also tested in other legume crops.

Systematic evaluation of multifactorial causal associations for Alzheimer's disease and an interactive platform MRAD developed based on Mendelian randomization analysis.

Alzheimer's disease (AD) is a complex degenerative disease of the central nervous system, and elucidating its pathogenesis remains challenging. In this study, we used the inverse-variance weighted (IVW) model as the major analysis method to perform hypothesis-free Mendelian randomization (MR) analysis on the data from MRC IEU OpenGWAS (18,097 exposure traits and 16 AD outcome traits), and conducted sensitivity analysis with six models, to assess the robustness of the IVW results, to identify various classes of risk or protective factors for AD, early-onset AD, and late-onset AD. We generated 400,274 data entries in total, among which the major analysis method of the IVW model consists of 73,129 records with 4840 exposure traits, which fall into 10 categories: Disease, Medical laboratory science, Imaging, Anthropometric, Treatment, Molecular trait, Gut microbiota, Past history, Family history, and Lifestyle trait. More importantly, a freely accessed online platform called MRAD (https://gwasmrad.com/mrad/) has been developed using the Shiny package with MR analysis results. Additionally, novel potential AD therapeutic targets (CD33, TBCA, VPS29, GNAI3, PSME1) are identified, among which CD33 was positively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. TBCA and VPS29 were negatively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. GNAI3 and PSME1 were negatively associated with the main outcome traits of AD, as well as with LOAD, but had no significant causal association with EOAD. The findings of our research advance our understanding of the etiology of AD.

Systematic evaluation of multifactorial causal associations for Alzheimer’s disease and an interactive platform MRAD developed based on Mendelian randomization analysis

Alzheimer’s disease (AD) is a complex degenerative disease of the central nervous system, and elucidating its pathogenesis remains challenging. In this study, we used the inverse-variance weighted (IVW) model as the major analysis method to perform hypothesis-free Mendelian randomization (MR) analysis on the data from MRC IEU OpenGWAS (18,097 exposure traits and 16 AD outcome traits), and conducted sensitivity analysis with six models, to assess the robustness of the IVW results, to identify various classes of risk or protective factors for AD, early-onset AD, and late-onset AD. We generated 400,274 data entries in total, among which the major analysis method of the IVW model consists of 73,129 records with 4840 exposure traits, which fall into 10 categories: Disease, Medical laboratory science, Imaging, Anthropometric, Treatment, Molecular trait, Gut microbiota, Past history, Family history, and Lifestyle trait. More importantly, a freely accessed online platform called MRAD (https://gwasmrad.com/mrad/) has been developed using the Shiny package with MR analysis results. Additionally, novel potential AD therapeutic targets (CD33, TBCA, VPS29, GNAI3, PSME1) are identified, among which CD33 was positively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. TBCA and VPS29 were negatively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. GNAI3 and PSME1 were negatively associated with the main outcome traits of AD, as well as with LOAD, but had no significant causal association with EOAD. The findings of our research advance our understanding of the etiology of AD.

Shank3 mutation impairs glutamate signaling and myelination in ASD mouse model and human iPSC-derived OPCs.

Autism spectrum disorder (ASD) is characterized by social and neurocognitive impairments, with mutations of the SHANK3 gene being prominent in patients with monogenic ASD. Using the InsG3680 mouse model with a Shank3 mutation seen in humans, we revealed an unknown role for Shank3 in postsynaptic oligodendrocyte (OL) features, similar to its role in neurons. This was shown by impaired molecular and physiological glutamatergic traits of InsG3680-derived primary OL cultures. In vivo, InsG3680 mice exhibit significant reductions in the expression of key myelination-related transcripts and proteins, along with deficits in myelin ultrastructure, white matter, axonal conductivity, and motor skills. Last, we observed significant impairments, with clinical relevance, in induced pluripotent stem cell-derived OLs from a patient with the InsG3680 mutation. Together, our study provides insight into Shank3's role in OLs and reveals a mechanism of the crucial connection of myelination to ASD pathology.

A compendium of genetic variations associated with promoter usage across 49 human tissues

Promoters play a crucial role in regulating gene transcription. However, our understanding of how genetic variants influence alternative promoter selection is still incomplete. In this study, we implement a framework to identify genetic variants that affect the relative usage of alternative promoters, known as promoter usage quantitative trait loci (puQTLs). By constructing an atlas of human puQTLs across 49 different tissues from 838 individuals, we have identified approximately 76,856 independent loci associated with promoter usage, encompassing 602,009 genetic variants. Our study demonstrates that puQTLs represent a distinct type of molecular quantitative trait loci, effectively uncovering regulatory targets and patterns. Furthermore, puQTLs are regulating in a tissue-specific manner and are enriched with binding sites of epigenetic marks and transcription factors, especially those involved in chromatin architecture formation. Notably, we have also found that puQTLs colocalize with complex traits or diseases and contribute to their heritability. Collectively, our findings underscore the significant role of puQTLs in elucidating the molecular mechanisms underlying tissue development and complex diseases.

Identification of a senescence-related transcriptional signature to uncover molecular subtypes and key genes in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a cancer caused by abnormal cell growth due to faulty signal transduction. Cells secrete tumor suppressor factors in response to potential carcinogenic signals, inducing cellular senescence (CS) as a countermeasure. However, accurately measuring CS levels in different types of tumors is challenging due to tumor heterogeneity and the lack of universal and specific CS markers. Machine learning has revealed unique molecular traits in HCC patients, leading to clinical advantages. More research is needed to understand senescence-related molecular features in these patients. In this study, the gene expression profile features of patients with HCC were analyzed by integrating single-cell RNA sequencing and bulk RNA-seq datasets from HCC samples. The analysis identified the senescence-related pathways exhibiting HCC specificity. Subsequently, genes from these pathways were used to identify senescence-related molecular subtypes in HCC, showing significant variations in biological and clinical attributes. An HCC-specific CS risk model developed in this study revealed substantial associations between the patients' CS scores and prognosis grouping, clinical staging, immune infiltration levels, immunotherapy response, and drug sensitivity levels. Within the constructed model, G6PD was identified as a key gene, potentially serving as a senescence-related target in liver cancer. Molecular biology experiments demonstrated that overexpression of G6PD effectively promotes the proliferative, invasive, and migration capacities of HepG2 and SK-HEP-1 cells. In conclusion, this analysis offers a valuable framework for understanding senescence in HCC and introduces a new biomarker. These findings improve our understanding of senescence in HCC and have potential for future research.

Comprehensive transcriptomic analysis identifies three distinct subtypes of pituitary adenomas: insights into tumor behavior, prognosis, and stem cell characteristics

BackgroundPituitary adenomas (PAs) are the second most common intracranial tumor. While current diagnostic practices rely primarily on histological testing, they often fail to capture the molecular complexities of pituitary adenomas, underscoring the need for a molecular-based classification to refine therapeutic strategies and prognostic assessments. This study aims to provide a molecularly unbiased classification of pituitary adenomas and explore their unique gene expression patterns and clinical features.MethodsWe performed unsupervised hierarchical clustering of the gene expression profiles of 117 PA samples to identify three distinct molecular subtypes. Subsequently, we analyzed the compiled transcriptomic profiles of each individual subtype for pathway enrichment. We also validated the new classification with a validation set containing 158 PAs and 24 pituitary adenoma stem cells (PASCs).ResultsConsensus clustering of transcriptomic data from 117 pituitary adenoma (PA) samples identified three distinct molecular subtypes, each showing unique gene expression patterns and associated biological processes: Group I is enriched in signaling pathways, such as the cAMP signaling pathway and the calcium signaling pathway. Group II is primarily related to metabolic processes, including nitrogen metabolism and arginine biosynthesis in cancer. Group III predominantly shows enrichment in immune responses and potential malignant transformation of the disease, especially through cancer-related pathways such as the JAK–STAT signaling pathway and the PI3K–Akt signaling pathway. The immune profiling revealed distinct patterns for each subtype: Group I had higher dendritic cells and fewer CD8+ T cells, Group II had more monocytes and macrophages, and Group III had elevated levels of T cells. Additionally, there were differences in clinical characteristics and prognosis among the subtypes, with Group III having a worse prognosis, despite the smaller tumor size compared to other groups. Notably, differences in PASCs correlated with the molecular subtypes, with Group III stem cells being enriched in tumorigenesis pathways, PI3K–Akt signaling pathway and Ras signaling pathway.ConclusionOur study introduces a novel molecular classification for pituitary adenomas, independent of traditional histological methods. Each subtype features distinct genetic, molecular, and immunological profiles. We have isolated pituitary adenoma stem-like cells (PASCs), pairing them with tumor tissues for detailed transcriptomic analysis. These PASCs exhibit diverse molecular traits consistent with the new classification.