Factors Influencing Mortality in Children with Central Nervous System Tumors: A Cohort Study on Clinical Characteristics and Genetic Markers.

Multidrug resistance (MDR) commonly leads to cancer treatment failure because cancer cells often expel chemotherapeutic drugs using ATP-binding cassette (ABC) transporters, which reduce drug levels within the cells. This study investigated the clinical characteristics and single nucleotide variant (SNV) in ABCB1, ABCC1, ABCC2, ABCC4, and ABCG2, and their association with mortality in pediatric patients with central nervous system tumors (CNST). Using TaqMan probes, a real-time polymerase chain reaction genotyped 15 SNPs in 111 samples. Patients were followed up until death or the last follow-up day using the Cox proportional hazards model. An association was found between the rs1045642 (ABCB1) in the recessive model (HR = 2.433, 95% CI 1.098-5.392, p = 0.029), and the ICE scheme in the codominant model (HR = 9.810, 95% CI 2.74-35.06, p ≤ 0.001), dominant model (HR = 6.807, 95% CI 2.87-16.103, p ≤ 0.001), and recessive model (HR = 6.903, 95% CI 2.915-16.544, p = 0.038) significantly increased mortality in this cohort of patients. An association was also observed between the variant rs3114020 (ABCG2) and mortality in the codominant model (HR = 5.35, 95% CI 1.83-15.39, p = 0.002) and the dominant model (HR = 4.421, 95% CI 1.747-11.185, p = 0.002). A significant association between the ICE treatment schedule and increased mortality risk in the codominant model (HR = 6.351, 95% CI 1.831-22.02, p = 0.004, HR = 9.571, 95% CI 2.856-32.07, p ≤ 0.001), dominant model (HR = 6.592, 95% CI 2.669-16.280, p ≤ 0.001), and recessive model (HR = 5.798, 95% CI 2.411-13.940, p ≤ 0.001). The genetic variants rs3114020 in the ABCG2 gene and rs1045642 in the ABCB1 gene and the ICE chemotherapy schedule were associated with an increased mortality risk in this cohort of pediatric patients with CNST.

[Polymorphisms of OPRM1, OPRK1, DCC genes and non-suicidal self-injuries in adults]. / Polimorfizmy genov OPRM1, OPRK1 i DCC i nesuitsidal'nye samopovrezhdeniya u vzroslykh.

OBJECTIVE: To investigate the associations of OPRM1 gene rs179971, OPRK1 gene rs6473797 and DCC gene rs8084280 polymorphisms with non-suicidal self-injury (NSSI) characteristics and motivations in adults. MATERIAL AND METHODS: A pilot sample included 28 adult patients with history of NSSI (89.3% (n=25) women, median age (Q1-Q3) - 23 (21.25-25) years). Most patients (78.6%, n=20) had a diagnosis of bipolar disorder. NSSI characteristics and motivations were assessed using the Inventory of Statements about Self-Injury (ISAS) scale. The Childhood Trauma Questionnaire (CTQ) was used to control for childhood trauma - one of the most important environmental factors associated with NSSI. The Baratt Impulsivity Scale (BIS) and the Buss-Perry Aggression Questionnaire (BPAQ) were also used to assess impulsivity and aggression, respectively. RT-PCR was used for genotyping, a genetic effect was assessed using the dominant model. Mann-Whitney U-test, Pearson χ2-test and multiple linear regression were used for statistical analysis. RESULTS: Carriers of the minor G allele of OPRM1 gene rs1779971 had a higher level of aggression assessed by BPAQ (p=0.02). The minor C allele of OPRK1 gene rs6473797 was associated with an increase of the subjective importance of «Affect regulation¼ (B=2.23; CI 95% [0.39-4.06]; p=0.022) and «Anti-dissociation¼ (B=3.31; CI 95% [0.18-6.44]; p=0.039) motivations, whereas the minor T allele of DCC gene rs8084280, on the contrary, was associated with a decrease of the importance of «Affect regulation¼ (B=-1.74; CI 95% [-3.30 - -0.18]; p=0.032). Moreover, this effect was found after adjusting for diagnosis, sex, age, and the presence of childhood trauma. CONCLUSIONS: To our knowledge, this is the first study on the association of genetic markers with NSSI motivations. The results of this pilot study demonstrate that OPRK1 and DCC gene polymorphisms can determine differences in motivations for self-harm, however, these results require confirmation in large samples.

A Genome-Wide Association Study Reveals Two Genetic Markers for Chondromalacia.

OBJECTIVE: It is unknown why some athletes develop chondromalacia and others do not, even when accounting for similar workloads between individuals. Genetic differences between individuals may be a contributing factor. The purpose of this work was to screen the entire genome for genetic markers associated with chondromalacia. DESIGN: Genome-wide association (GWA) analyses were performed utilizing data from the Kaiser Permanente Research Board (KPRB) and the UK Biobank. Chondromalacia cases were identified based on electronic health records from KPRB and UK Biobank. GWA analyses from both cohorts were tested for chondromalacia using a logistic regression model adjusting for sex, height, weight, age of enrollment, and race/ethnicity using allele counts for single-nucleotide polymorphisms (SNPs). The data from the 2 GWA studies (KPRB and UK Biobank) were combined in a meta-analysis. RESULTS: There were a total of 3,872 combined cases of chondromalacia from the KPRB and the UK Biobank cohorts. Genome-wide significant associations with chondromalacia were found for rs144449054 in the ARHGAP15 gene (OR = 3.70 [2.32-5.90]; P = 1.4 × 10-8) and rs188900564 in the MAGEC2 (OR = 2.07 [1.61-2.65]; P = 3.7 × 10-9). CONCLUSIONS: Genetic markers in ARHGAP15 and MAGEC2 appear to be associated with chondromalacia and are potential risk factors that deserve further validation regarding molecular mechanisms.

Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India.

Commercial interest in the culinary herb, Eryngium foetidum L., has increased worldwide due to its typical pungency, similar to coriander or cilantro, with immense pharmaceutical components. The molecular delimitation and taxonomic classification of this lesser-known medicinal plant are restricted to conventional phenotyping and DNA-based marker evaluation, which hinders accurate identification, genetic conservation, and safe utilization. This study focused on species discrimination using DNA sequencing with chloroplast-plastid genes (matK, Kim matK, and rbcL) and the nuclear ITS2 gene in two Eryngium genotypes collected from the east coast region of India. The results revealed that matK discriminated between two genotypes, however, Kim matK, rbcL, and ITS2 identified these genotypes as E. foetidum. The ribosomal nuclear ITS2 region exhibited significant inter- and intra-specific divergence, depicted in the DNA barcodes and the secondary structures derived based on the minimum free energy. Although the efficiency of matK genes is better in species discrimination, ITS2 demonstrated polyphyletic phylogeny, and could be used as a reliable marker for genetic divergence studies understanding the mechanisms of RNA molecules. The results of this study provide insights into the scientific basis of species identification, genetic conservation, and safe utilization of this important medicinal plant species.

Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer.

Circulating tumour DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer genotyping and longitudinal disease monitoring1. However, owing to past emphasis on targeted and low-resolution profiling approaches, our understanding of the distinct populations that comprise bulk ctDNA is incomplete2-12. Here we perform deep whole-genome sequencing of serial plasma and synchronous metastases in patients with aggressive prostate cancer. We comprehensively assess all classes of genomic alterations and show that ctDNA contains multiple dominant populations, the evolutionary histories of which frequently indicate whole-genome doubling and shifts in mutational processes. Although tissue and ctDNA showed concordant clonally expanded cancer driver alterations, most individual metastases contributed only a minor share of total ctDNA. By comparing serial ctDNA before and after clinical progression on potent inhibitors of the androgen receptor (AR) pathway, we reveal population restructuring converging solely on AR augmentation as the dominant genomic driver of acquired treatment resistance. Finally, we leverage nucleosome footprints in ctDNA to infer mRNA expression in synchronously biopsied metastases, including treatment-induced changes in AR transcription factor signalling activity. Our results provide insights into cancer biology and show that liquid biopsy can be used as a tool for comprehensive multi-omic discovery.

Circulating Cell Free DNA and DNA Integrity Index as Discriminating Tools between Breast Cancer and Benign Breast Disease.

OBJECTIVES: Early diagnosis of cancer remains a great challenge in the field of laboratory medicine. We investigated the ability of ccf DNA and DNA integrity index (DNA II) in differentiating benign from malignant breast diseases. METHODS: Serum samples were collected from 50 patients with benign breast disease (BBD) and 50 newly diagnosed breast cancer (BC) patients, in addition to 50 control women. VEGF was measured by ELISA, while Real-time q-PCR was used to measure ccf DNA concentrations and to assess the concentrations of ALU repeats, both short fragments (115 bp) and long fragments (247 bp), then DNA II was calculated (all were done before and after radical mastectomy). RESULTS: BC group showed significantly higher ccf DNA concentrations and DNA II compared to BBD and control groups, meanwhile, no statistically significant differences were found between BBD and control groups. Ccf DNA concentrations decreased significantly after surgery (P <0.001). Good AUC was found for ccf DNA (AUC=0.860), fair AUC was found for DNA II (AUC=0.727), while VEGF AUC failed to discriminate between BBD and BC cases. CONCLUSION: ccf DNA and DNA II could be used as excellent molecular biomarkers for early diagnosis of BC and for monitoring the efficiency of therapy in such patients. Utilizing these molecular markers would improve both the healthcare and economic burden of malignancy.

NanoString in the screening of genetic abnormalities associated with thyroid cancer.

In the setting of cancer pathology, molecular characterization of tumors providing diagnostic and predictive information is acquiring more and more relevance. Moreover, the advent of innovative technologies continuously improves the knowledge of the molecular landscape of tumors and strengthens the links between clinics, tumor pathology and molecular features. In the clinical management of patients with thyroid nodules and thyroid tumors, the aid of molecular testing is encouraged but still not strongly recommended by current guidelines. Also for this reason this field of study is attracting much interest. The nCounter system is a relatively new technology based on a direct hybridization of fluorescent probes to specific nucleic acid targets, followed by digital measurement of signals; the reaction is highly multiplexable and results are robust and reproducible. This review reports and discusses the available data related to the application of this specific technique to thyroid nodules and thyroid tumors samples. The available data indicate that nCounter system represents a solid approach for the research of relevant diagnostic and prognostic biomarkers in thyroid pathology.

Molecular diagnosis in non-small-cell lung cancer: expert opinion on ALK and ROS1 testing.

The effectiveness of targeted therapies with tyrosine kinase inhibitors in non-small-cell lung cancer (NSCLC) depends on the accurate determination of the genomic status of the tumour. For this reason, molecular analyses to detect genetic rearrangements in some genes (ie, ALK, ROS1, RET and NTRK) have become standard in patients with advanced disease. Since immunohistochemistry is easier to implement and interpret, it is normally used as the screening procedure, while fluorescence in situ hybridisation (FISH) is used to confirm the rearrangement and decide on ambiguous immunostainings. Although FISH is considered the most sensitive method for the detection of ALK and ROS1 rearrangements, the interpretation of results requires detailed guidelines. In this review, we discuss the various technologies available to evaluate ALK and ROS1 genomic rearrangements using these techniques. Other techniques such as real-time PCR and next-generation sequencing have been developed recently to evaluate ALK and ROS1 gene rearrangements, but some limitations prevent their full implementation in the clinical setting. Similarly, liquid biopsies have the potential to change the treatment of patients with advanced lung cancer, but further research is required before this technology can be applied in routine clinical practice. We discuss the technical requirements of laboratories in the light of quality assurance programmes. Finally, we review the recent updates made to the guidelines for the determination of molecular biomarkers in patients with NSCLC.

Existence of genetic lineages within Asian genotype of Taenia solium-Genetic characterization based on mitochondrial and ribosomal DNA markers.

Taenia solium cysticercosis is a potentially eradicable neglected zoonotic disease with public health importance. The genetic lineages of T. solium in Asia and Africa/America are distinct and the genetic composition of the parasite was found to influence the clinical symptoms in patients with cysticercosis. In the present study, the Cysticerci collected from pigs of two southern states of India (Karnataka and Andhra Pradesh) were genetically characterized based on mitochondrial (COX 1 and Cyt b) and ribosomal (ITS-1 and TBR) DNA markers. The study confirms the existence of two mitochondrial lineages of the parasite as Asian and African/American. Cytochrome oxidase 1 (COX 1) based analysis revealed the existence of two sub-lineages of the parasite within the Asian lineage based on the polymorphism at 994 position as 994A/G. In India, both the sub-lineages were identified and genetic divergence among different Indian isolates was evident. Further, the sequence analysis of Cytochrome B (Cyt b) revealed the existence of six sub-lineages of T. solium in India as 69T/69G, 97A/97G as well as 264T/264C. The analysis of nucleotide sequence of large subunit ribosomal DNA (TBR) revealed the existence of two sub-lineages in India based on the deletion of a nucleotide at 624th position. The cysts collected in the present study were more closely related to those of China and Indonesia than with other Indian isolates. Further, the sequence analysis did not indicate the presence of Taenia asiatica in the examined pigs and African/American lineages of T. solium. The results of the present study help to better understand the genetic diversity of T. solium in India.

Differential expression of miRNAs involved in biological processes responsible for inflammation and immune response in lichen sclerosus urethral stricture disease.

PURPOSE: To better understand the pathophysiology of lichen sclerosus (LS) urethral stricture disease (USD), we aimed to investigate expression profiles of microRNAs (miRNAs) in tissue samples from men undergoing urethroplasty. METHODS: Urethral stricture tissue was collected from 2005-2020. Histologic features diagnostic of LS were the basis of pathologic evaluation. Foci of areas diagnostic for LS or non-LS strictures were chosen for RNA evaluation. In an initial screening analysis, 13 LS urethral strictures and 13 non-LS strictures were profiled via miRNA RT-qPCR arrays for 752 unique miRNA. A validation analysis of 23 additional samples (9 LS and 14 non-LS) was performed for 15 miRNAs. Statistical analyses were performed using SPSS v25. Gene Ontology (GO) analysis was performed using DIANA-mirPath v. 3.0. RESULTS: In the screening analysis 143 miRNAs were detected for all samples. 27 were differentially expressed between the groups (false discovery p-value <0.01). 15 of these miRNAs individually demonstrated an area under the curve (AUC)>0.90 for distinguishing between between LS and non-LS strictures. 11-fold upregulation of MiR-155-5p specifically was found in LS vs. non-LS strictures (p<0.001, AUC = 1.0). In the validation analysis, 13 of the 15 miRNAs tested were confirmed to have differential expression (false discovery p-value <0.10). CONCLUSIONS: To our knowledge this is the first study evaluating miRNA expression profiles in LS and non-LS USD. We identified several miRNAs that are differentially expressed in USD caused by LS vs other etiologies, which could potentially serve as biomarkers of LS USD. The top eight differentially expressed miRNAs have been linked to immune response processes as well as involvement in wound healing, primarily angiogenesis and fibrosis.

Identification of Potential Genetic Biomarkers and Target Genes of Peri-Implantitis Using Bioinformatics Tools.

OBJECTIVES: To investigate potential genetic biomarkers of peri-implantitis and target genes for the therapy of peri-implantitis by bioinformatics analysis of publicly available data. METHODS: The GSE33774 microarray dataset was downloaded from the Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) between peri-implantitis and healthy gingival tissues were identified using the GEO2R tool. GO enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using the DAVID database and the Metascape tool, and the results were expressed as a bubble diagram. The protein-protein interaction network of DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) and visualized using Cytoscape. The hub genes were screened by the cytoHubba plugin of Cytoscape. The potential target genes associated with peri-implantitis were obtained from the DisGeNET database and the Open Targets Platform. The intersecting genes were identified using the Venn diagram web tool. RESULTS: Between the peri-implantitis group and the healthy group, 205 DEGs were investigated including 140 upregulated genes and 65 downregulated genes. These DEGs were mainly enriched in functions such as the immune response, inflammatory response, cell adhesion, receptor activity, and protease binding. The results of KEGG pathway enrichment analysis revealed that DEGs were mainly involved in the cytokine-cytokine receptor interaction, pathways in cancer, and the PI3K-Akt signaling pathway. The intersecting genes, including IL6, TLR4, FN1, IL1ß, CXCL8, MMP9, and SPP1, were revealed as potential genetic biomarkers and target genes of peri-implantitis. CONCLUSIONS: This study provides supportive evidence that IL6, TLR4, FN1, IL1ß, CXCL8, MMP9, and SPP1 might be used as potential target biomarkers for peri-implantitis which may provide further therapeutic potentials for peri-implantitis.

A New Definition of Pyroptosis-Related Gene Markers to Predict the Prognosis of Lung Adenocarcinoma.

Pyroptosis, the prototype of programmed cell death, is crucial to the development of multicellular organisms. Lung cancer is one of the most lethal cancers in the world. Because lung cancer progresses quickly, it is mostly found at an advanced stage, resulting in a very poor prognosis of lung cancer. At present, there is no treatment with good prognosis, but pyroptosis-based tumor therapy may be able to solve this problem. In the past few decades, it has been found that pyroptosis can affect the invasion, proliferation, and metastasis of tumor and apoptosis is an important system to resist cancer. Our study is aimed at constructing a prognostic model within pyroptosis-related genes. We developed a prognostic model by using TCGA and GEO database, and differentially expressed genes (DEGs) were identified. Five genes (NLRP1, NOD1, NLRC4, CASP9, and PLCG1) were identified to construct a prognostic model. According to the median risk score calculated by our formula, we divided patients into the high- and low-risk groups. Pyroptosis-related genes play important roles in tumor immunity and can be used to predict the prognosis of lung adenocarcinoma (LUAD).

Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis.

The complex pathology of Alzheimer's disease (AD) emphasises the need for comprehensive modelling of the disease, which may lead to the development of efficient treatment strategies. To address this challenge, we analysed transcriptome data of post-mortem human brain samples of healthy elders and individuals with late-onset AD from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) and Mayo Clinic (MayoRNAseq) studies in the AMP-AD consortium. In this context, we conducted several bioinformatics and systems medicine analyses including the construction of AD-specific co-expression networks and genome-scale metabolic modelling of the brain in AD patients to identify key genes, metabolites and pathways involved in the progression of AD. We identified AMIGO1 and GRPRASP2 as examples of commonly altered marker genes in AD patients. Moreover, we found alterations in energy metabolism, represented by reduced oxidative phosphorylation and ATPase activity, as well as the depletion of hexanoyl-CoA, pentanoyl-CoA, (2E)-hexenoyl-CoA and numerous other unsaturated fatty acids in the brain. We also observed that neuroprotective metabolites (e.g., vitamins, retinoids and unsaturated fatty acids) tend to be depleted in the AD brain, while neurotoxic metabolites (e.g., ß-alanine, bilirubin) were more abundant. In summary, we systematically revealed the key genes and pathways related to the progression of AD, gained insight into the crucial mechanisms of AD and identified some possible targets that could be used in the treatment of AD.

A new paradigm for leprosy diagnosis based on host gene expression.

Transcriptional profiling is a powerful tool to investigate and detect human diseases. In this study, we used bulk RNA-sequencing (RNA-Seq) to compare the transcriptomes in skin lesions of leprosy patients or controls affected by other dermal conditions such as granuloma annulare, a confounder for paucibacillary leprosy. We identified five genes capable of accurately distinguishing multibacillary and paucibacillary leprosy from other skin conditions. Indoleamine 2,3-dioxygenase 1 (IDO1) expression alone was highly discriminatory, followed by TLR10, BLK, CD38, and SLAMF7, whereas the HS3ST2 and CD40LG mRNA separated multi- and paucibacillary leprosy. Finally, from the main differentially expressed genes (DEG) and enriched pathways, we conclude that paucibacillary disease is characterized by epithelioid transformation and granuloma formation, with an exacerbated cellular immune response, while multibacillary leprosy features epithelial-mesenchymal transition with phagocytic and lipid biogenesis patterns in the skin. These findings will help catalyze the development of better diagnostic tools and potential host-based therapeutic interventions. Finally, our data may help elucidate host-pathogen interplay driving disease clinical manifestations.

Epigenetic Dysregulation of Mammalian Male Meiosis Caused by Interference of Recombination and Synapsis.

Meiosis involves a series of specific chromosome events, namely homologous synapsis, recombination, and segregation. Disruption of either recombination or synapsis in mammals results in the interruption of meiosis progression during the first meiotic prophase. This is usually accompanied by a defective transcriptional inactivation of the X and Y chromosomes, which triggers a meiosis breakdown in many mutant models. However, epigenetic changes and transcriptional regulation are also expected to affect autosomes. In this work, we studied the dynamics of epigenetic markers related to chromatin silencing, transcriptional regulation, and meiotic sex chromosome inactivation throughout meiosis in knockout mice for genes encoding for recombination proteins SPO11, DMC1, HOP2 and MLH1, and the synaptonemal complex proteins SYCP1 and SYCP3. These models are defective in recombination and/or synapsis and promote apoptosis at different stages of progression. Our results indicate that impairment of recombination and synapsis alter the dynamics and localization pattern of epigenetic marks, as well as the transcriptional regulation of both autosomes and sex chromosomes throughout prophase-I progression. We also observed that the morphological progression of spermatocytes throughout meiosis and the dynamics of epigenetic marks are processes that can be desynchronized upon synapsis or recombination alteration. Moreover, we detected an overlap of early and late epigenetic signatures in most mutants, indicating that the normal epigenetic transitions are disrupted. This can alter the transcriptional shift that occurs in spermatocytes in mid prophase-I and suggest that the epigenetic regulation of sex chromosomes, but also of autosomes, is an important factor in the impairment of meiosis progression in mammals.

Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus.

Flatheads in family Platycephalidae are ecologically and commercially important marine fish species in the Indo-West Pacific. Due to similar morphological characters, the taxonomy and phylogenetics of flatheads are in confusion. Studies on phylogenetics and molecular marker development are required to discriminate congeners of flatheads. In the present study, we performed whole genome survey sequencing of crocodile flathead Cociella crocodilus to provide genomic information and genetic markers of this species. In total, 54.03 Gb of clean genomic data were generated. The genome size was estimated to be 732.99 Mb with the heterozygosity ratio of 0.73% and the repeat sequence ratio of 33.48%. The preliminary assembled genome sequences were 794.07 Mb with contig N50 of 1504 bp. We detected 2 624 875 genome-wide SNPs with transition/transversion ratio of 1.422. A total of 313 842 microsatellite motifs were identified, most of which were dinucleotide motifs with a frequency of 74.89%. In addition, we assembled the complete mitogenome of C. crocodilus and subsequent phylogenetic analysis were performed. Phylogenetic analyses revealed numbers of polyphyletic groups in family Platycephalidae. The reported genomic data and genetic markers in our study should be useful in further phylogeny and phylogenomics studies of flathead species.

Using genetics to detangle the relationships between red cell distribution width and cardiovascular diseases: a unique role for body mass index.

OBJECTIVE: Red cell distribution width (RDW) is an enigmatic biomarker associated with the presence and severity of multiple cardiovascular diseases (CVDs). It is unclear whether elevated RDW contributes to, results from, or is pleiotropically related to CVDs. We used contemporary genetic techniques to probe for evidence of aetiological associations between RDW, CVDs, and CVD risk factors. METHODS: Using an electronic health record (EHR)-based cohort, we built and deployed a genetic risk score (GRS) for RDW to test for shared genetic architecture between RDW and the cardiovascular phenome. We also created GRSs for common CVDs (coronary artery disease, heart failure, atrial fibrillation, peripheral arterial disease, venous thromboembolism) and CVD risk factors (body mass index (BMI), low-density lipoprotein, high-density lipoprotein, systolic blood pressure, diastolic blood pressure, serum triglycerides, estimated glomerular filtration rate, diabetes mellitus) to test each for association with RDW. Significant GRS associations were further interrogated by two-sample Mendelian randomisation (MR). In a separate EHR-based cohort, RDW values from 1-year pre-gastric bypass surgery and 1-2 years post-gastric bypass surgery were compared. RESULTS: In a cohort of 17 937 subjects, there were no significant associations between the RDW GRS and CVDs. Of the CVDs and CVD risk factors, only genetically predicted BMI was associated with RDW. In subsequent analyses, BMI was associated with RDW by multiple MR methods. In subjects undergoing bariatric surgery, RDW decreased postsurgery and followed a linear relationship with BMI change. CONCLUSIONS: RDW is unlikely to be aetiologically upstream or downstream of CVDs or CVD risk factors except for BMI. Genetic and clinical association analyses support an aetiological relationship between BMI and RDW.

Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis).

BACKGROUND: High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions. RESULTS: Compared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in "Glycolysis/Gluconeogenesis" (ko00010), "Cutin, suberine and wax biosynthesis" (ko00073), and "phenylpropanoid biosynthesis" (ko00940) in Sujiang 1419, although "cysteine/methionine metabolism" (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties. CONCLUSIONS: These findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis.

Free-fall landing and interval running have different effects on trabecular bone mass and microarchitecture, serum osteocalcin, biomechanical properties, SOST expression and on osteocyte-related characteristics.

The effects of treadmill interval training (IT) and free-fall exercise were evaluated on bone parameters including osteocyte related characteristics. Thirty-eight 4-month-old male Wistar rats were randomly divided into a control (C) group and exercise groups: IT, 10 free-fall impacts/day with a 10-s (FF10) or 20-s interval between drops (FF20), 5 days/week, for 9 weeks. We assessed bone mineral density (BMD); microarchitecture by µCT; mechanical strength by a 3-point bending test; density and occupancy of the osteocyte lacunae by toluidine blue staining; osteocalcin and NTx systemic levels by ELISA; and bone tissue Sost messenger RNA (mRNA) expression by RT-PCR. NTx levels were significantly lower in exercise groups as compared with the C group. In exercise groups the Sost mRNA expression was significantly lower than in C. Tb.N was significantly higher for IT and FF20 compared with the C group. Tb.Sp was significantly lower in FF10 compared with the C group. Both IT and FF20 were associated with higher tibial lacunar density as compared with FF10. compared with FF10, IT fat mass was lower, while tibial osteocyte lacunae occupancy and systemic osteocalcin level were higher. All exercise modes were efficient in reducing bone resorption. Both IT and free-fall impact with appropriate recovery periods, which may be beneficial for bone health and osteocyte-related characteristics. Novelty: Interval training is beneficial for bone mineral density. Exercises decreased both bone resorption and inhibition of bone formation (Sost mRNA). Longer interval recovery time favors osteocyte lacunae density.

Highly sensitive duplex MSI test and BAT40 germline polymorphism.

Tumors exhibiting DNA mismatch repair (MMR) deficiency and microsatellite instability (MSI) are responsive to immune checkpoint blockade. MSI is frequently diagnosed using five quasimonomorphic mononucleotide (pentaplex) markers; however, the assays have several technical limitations, including the lack of sensitivity of some of the markers. Although markers with increased sensitivity, such as CAT25 and BAT40, have been introduced, the majority of multiplex MSI tests have only been studied in Western populations and require further evaluation in an Asian cohort. This study tested the efficacy of BAT26, CAT25, and BAT40 mononucleotide MSI markers via triplex PCR on 300 samples from patients with advanced cancers from a Korean clinical population. The results were directly compared with those of a pentaplex MSI test and tumor mutation burden (TMB) status, and an additional 60 MSI-H cancers were used for further validation. Four (1.3%) out of 300 advanced tumors were MSI-high (MSI-H). In the pentaplex PCR assay, two colorectal cancers (0.7%) exhibited instability only with the BAT25 mononucleotide marker and were interpreted as MSI-low (MSI-L). In the triplex PCR assay, BAT40 was unstable in 64 cases (21%) and the results did not overlap with those of MSI-L from pentaplex. Given the high frequency of isolated BAT40 instability, we performed the same triplex PCR with DNA obtained from normal controls and found BAT40 polymorphisms in 37 cases (90%). Interestingly, the median TMB of the cases with BAT40 polymorphism was significantly higher (7.0 mt/Mb) than that of BAT40 wild-type cases (5.5 mt/Mb) (p = 0.003). The triplex PCR results from 60 additional MSI-H cancers correlated perfectly (100%) with those of pentaplex PCR, and the results were consistent for two (BAT26 and CAT25) markers. BAT40 germline polymorphism is common in the Korean population and is associated with higher TMB values. The simple duplex (BAT26 and CAT25) MSI test provided the same sensitivity and specificity as pentaplex PCR tests.