Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice

Age-Disturbed Vascular Extracellular Matrix Links to Abdominal Aortic Aneurysms

Abdominal aortic aneurysm (AAA) is a common but life-threatening vascular condition in men at an advanced age. However, the underlying mechanisms of age-increased incidence and mortality of AAA remain elusive. Here, we performed RNA sequencing (RNA-seq) of mouse aortas from males (young: 3-month, n = 4 vs old: 23-month, n = 4) and integrated with the data sets of human aortas (young: 20-39, n = 47 vs old: 60-79 years, n = 92) from GTEx project and the data set (GSE183464) for AAA to search for age-shifted aortic aneurysm genes, their relevant biological processes, and signaling pathways. Angiotensin II-induced AAA in mice was used to verify the critical findings. We found 1 001 genes transcriptionally changed with ages in both mouse and human. Most age-increased genes were enriched intracellularly and the relevant biological processes included mitochondrial function and translational controls, whereas the age-decreased genes were largely localized in extracellular regions and cell periphery and the involved biological processes were associated with extracellular matrix (ECM). Fifty-one were known genes for AAA and found dominantly in extracellular region. The common age-shifted vascular genes and known aortic aneurysm genes had shared functional influences on ECM organization, apoptosis, and angiogenesis. Aorta with angiotensin II-induced AAA exhibited similar phenotypic changes in ECM to that in old mice. Together, we present a conserved transcriptional signature for aortic aging and provide evidence that mitochondrial dysfunction and the imbalanced ribosomal homeostasis act likely as driven-forces for aortic aging and age-disturbed ECM is the substrate for developing AAA.

Integrative analysis of the transcriptome and metabolome reveals the importance of hepatokine FGF21 in liver aging

Aging is a contributor to liver disease. Hence, the concept of liver aging has become prominent and has attracted considerable interest, but its underlying mechanism remains poorly understood. In our study, the internal mechanism of liver aging was explored via multi-omics analysis and molecular experiments to support future targeted therapy. An aged rat liver model was established with d-galactose, and two other senescent hepatocyte models were established by treating HepG2 cells with d-galactose and H2O2. We then performed transcriptomic and metabolomic assays of the aged liver model and transcriptome analyses of the senescent hepatocyte models. In livers, genes related to peroxisomes, fatty acid elongation, and fatty acid degradation exhibited down-regulated expression with aging, and the hepatokine Fgf21 expression was positively correlated with the down-regulation of these genes. In senescent hepatocytes, similar to the results found in aged livers, FGF21 expression was also decreased. Moreover, the expressions of cell cycle-related genes were significantly down-regulated, and the down-regulated gene E2F8 was the key cell cycle-regulating transcription factor. We then validated that FGF21 overexpression can protect against liver aging and that FGF21 can attenuate the declines in the antioxidant and regenerative capacities in the aging liver. We successfully validated the results from cellular and animal experiments using human liver and blood samples. Our study indicated that FGF21 is an important target for inhibiting liver aging and suggested that pharmacological prevention of the reduction in FGF21 expression due to aging may be used to treat liver aging-related diseases.

Regulation of ENPP5, a senescence-associated secretory phenotype factor, prevents skin aging

Aging negatively affects the appearance and texture of the skin owing to the accumulation of senescent fibroblasts within the dermis. Senescent cells undergo abnormal remodeling of collagen and the extracellular matrix through an inflammatory histolytic senescence-associated secretory phenotype (SASP). Therefore, suppression of SASP in senescent cells is essential for the development of effective skin anti-aging therapies. Ectonucleotide pyrophosphatase/phosphodiesterase family member 5 (ENPP5), an extracellular signaling molecule, has been implicated in vascular aging and apoptosis; however, its role in SASP remains unclear. Therefore, this study aimed to investigate the role of ENPP5 in SASP and skin aging using molecular techniques. We investigated the effects of siRNA-mediated ENPP5 knockdown, human recombinant ENPP5 (rENPP5) treatment, and lentiviral overexpression of ENPP5 on SASP and aging in human skin fibroblasts. Additionally, we investigated the effect of siRNA-mediated ENPP5 knockdown on the skin of C57BL/6 mice. We found that ENPP5 was significantly expressed in replication-aged and otherwise DNA-damaged human skin fibroblasts and that treatment with human rENPP5 and lentiviral overexpression of ENPP5 promoted SASP and senescence. By contrast, siRNA-mediated knockdown of ENPP5 suppressed SASP and the expression of skin aging-related factors. Additionally, ENPP5 knockdown in mouse skin ameliorated the age-related reduction of subcutaneous adipose tissue, the panniculus carnosus muscle layer, and thinning of collagen fibers. Conclusively, these findings suggest that age-related changes may be prevented through the regulation of ENPP5 expression to suppress SASP in aging cells, contributing to the development of anti-aging treatments for the skin.

Effects of magnesium supplementation on improving hyperglycemia, hypercholesterolemia, and hypertension in type 2 diabetes: A pooled analysis of 24 randomized controlled trials

Background

Previous studies have demonstrated that diabetes is often accompanied with lower magnesium status. However, practical details regarding the influences of magnesium intervention on hyperglycemia, hypercholesterolemia, and hypertension in type 2 diabetes (T2D) need to be further investigated.

Methods

Web of Science, ScienceDirect, and PubMed were searched for relevant literatures published through April 30, 2022, and high-quality data were pooled to evaluate the effects of magnesium supplementation on glycemic, circulating lipids, and blood pressure control in T2D, and to explore the associated practical details.

Results

Pooled analyses of 24 randomized controlled trials with 1,325 T2D individuals revealed that subjects who received magnesium supplementation had statistically significant reductions in fasting plasma glucose, glycated hemoglobin, systolic blood pressure and diastolic blood pressure, with WMD values of -0.20 mM (95% CI: -0.30, -0.09), -0.22% (95% CI: -0.41, -0.03), -7.69 mmHg (95% CI: -11.71, -3.66) and -2.71 mmHg (95% CI: -4.02, -1.40), respectively. Detailed subgroup analyses demonstrated that health status of participants including age, body mass index, country, duration of disease, baseline magnesium level and baseline glycemic control condition as well as magnesium formulation, dosage and duration of intervention influenced the effects of magnesium addition. Dose-effect analysis showed that 279 mg/d for 116 d, 429 mg/d for 88 d and 300 mg/d for 120 d are the average optimal dosages and durations for improving glycemic, circulating lipids, and blood pressure controls, respectively.

Conclusion

Our findings provide clinically relevant information on the adjuvant therapy of magnesium for improving hyperglycemia, hypercholesterolemia, and hypertension in T2D.

A four-lncRNA risk signature for prognostic prediction of osteosarcoma

Aim: Osteosarcoma is the most common primary malignant tumor of bone. However, our understanding of the prognostic indicators and the genetic mechanisms of the disease progression are still incomplete. The aim of this study was to identify a long noncoding RNA (lncRNA) risk signature for osteosarcoma survival prediction. Methods: RNA sequencing data and relevant clinical information of osteosarcoma patients were downloaded from the database of Therapeutically Applicable Research to Generate Effective Treatments (TARGET). We analyzed the differentially expressed lncRNAs between deceased and living patients by univariate and multivariate Cox regression analysis to identify a risk signature. We calculated a prognostic risk score for each sample according to this prognosis signature, and divided patients into high-risk and low-risk groups according to the median value of the risk score (0.975). Kaplan-Meier analysis and receiver operating characteristic (ROC) curve statistics were used to evaluate the performance of the signature. Next, we analyzed the signature's potential function through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene-set enrichment analysis (GSEA). Lastly, qRT-PCR was used to validate the expression levels of the four lncRNAs in clinical samples. Results: Twenty-six differentially expressed lncRNAs were identified between deceased and living patients. Four of these lncRNAs (CTB-4E7.1, RP11-553A10.1, RP11-24N18.1, and PVRL3-AS1) were identified as independent prognostic factors, and a risk signature of these four lncRNAs for osteosarcoma survival prediction was constructed. Kaplan-Meier analysis showed that the five-year survival time in high-risk and low-risk groups was 33.1% and 82.5%, and the area under the curve (AUC) of the ROC was 0.784, which demonstrated that the prognostic signature was reliable and had the potential to predict the survival of patients with osteosarcoma. The expression level of the four lncRNAs in osteosarcoma tissues and cells was determined by qRT-PCR. Functional enrichment analysis suggested that the signature might be related to osteosarcoma through regulation of the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the extracellular matrix and also provided new insights into the study of osteosarcoma, including the role of papillomavirus infection, olfactory receptor activity, and olfactory transduction in osteosarcoma. Conclusion: We constructed a novel lncRNA risk signature that served as an independent biomarker for predicting the prognosis of osteosarcoma patients.

Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?

Introduction

Extracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.

Methods and results

In this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn's disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.

Discussion

These findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.

Role of microRNA-34b-5p in cancer and injury: how does it work?

MicroRNAs (miRNAs or miRs) are a class of noncoding single-stranded RNAs that can regulate gene expression by binding to the untranslated sequences at the 3 ' end of messenger RNAs. The microRNA-34 family is dysregulated in various human diseases. It is considered as a tumor-suppressive microRNA because of its synergistic effect with the well-known tumor suppressor p53. As a member of the miRNA-34 family, miR-34b-5p serves as a powerful regulator of a suite of cellular activities, including cell growth, multiplication, development, differentiation, and apoptosis. It promotes or represses disease occurrence and progression by participating in some important signaling pathways. This review aimed to provide an overview and update on the differential expression and function of miR-34b-5p in pathophysiologic processes, especially cancer and injury. Additionally, miR-34b-5p-mediated clinical trials have indicated promising consequences for the therapies of carcinomatosis and injury. With the application of the first tumor-targeted microRNA drug based on miR-34a mimics, it can be inferred that miR-34b-5p may become a crucial factor in the therapy of various diseases. However, further studies on miR-34b-5p should shed light on its involvement in disease pathogenesis and treatment options.

A pyroptosis-associated signature plays a role in prognosis prediction in clear cell renal cell carcinoma

Background

Approximately 90% of renal malignancies are RCCs (renal cell carcinomas), and the primary subtype in histology is ccRCC (clear cell RCC). In recent years, pyroptosis has been considered a kind of inflammation-related programmed cell death that participates in the invasion, metastasis, and proliferation of tumour cells, thereby influencing tumour prognosis. Nonetheless, the expression level of pyroptosis-associated genes in RCCs and their relationship with prognosis remain obscure.

Results

In our research, 44 regulators of pyroptosis that were differentially expressed between normal kidney and ccRCC tissues were identified. ccRCC cases were categorized into 2 subgroups according to prognostic-related DEGs (differentially expressed genes), and there was a significant difference in OS (overall survival) between them. The prognostic value of pyroptosis-associated genes was assessed as a signature based on a cohort from TCGA (The Cancer Genome Atlas). Following Cox regression with DEGs and LASSO (least absolute shrinkage and selection operator), a 6-gene signature was established, and all ccRCC cases in the cohort from TCGA were categorized into an LR (low-risk) or HR (high-risk) group (P < 0.001). In combination with clinical features, risk scores were considered a predictive factor of OS in ccRCC. KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses suggest increased immunity and enrichment of genes related to immunity in the HR group.

Conclusions

Our findings indicate that genes related to pyroptosis have an important role in tumour immunity and may be used to predict the prognosis of ccRCC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01339-0.

Genetic association of ANRIL with susceptibility to Ischemic stroke: A comprehensive meta-analysis

Background

Ischemic stroke (IS) is a complex polygenic disease with a strong genetic background. The relationship between the ANRIL (antisense non-coding RNA in the INK4 locus) in chromosome 9p21 region and IS has been reported across populations worldwide; however, these studies have yielded inconsistent results. The aim of this study is to clarify the types of single-nucleotide polymorphisms on the ANRIL locus associated with susceptibility to IS using meta-analysis and comprehensively assess the strength of the association.

Methods

Relevant studies were identified by comprehensive and systematic literature searches. The quality of each study was assessed using the Newcastle-Ottawa Scale. Allele and genotype frequencies were extracted from each of the included studies. Odds ratios with corresponding 95% confidence intervals of combined analyses were calculated under three genetic models (allele frequency comparison, dominant model, and recessive model) using a random-effects or fixed-effects model. Heterogeneity was tested using the chi-square test based on the Cochran Q statistic and I2 metric, and subgroup analyses and a meta-regression model were used to explore sources of heterogeneity. The correction for multiple testing used the false discovery rate method proposed by Benjamini and Hochberg. The assessment of publication bias employed funnel plots and Egger’s test.

Results

We identified 25 studies (15 SNPs, involving a total of 11,527 cases and 12,216 controls maximum) and performed a meta-analysis. Eight SNPs (rs10757274, rs10757278, rs2383206, rs1333040, rs1333049, rs1537378, rs4977574, and rs1004638) in ANRIL were significantly associated with IS risk. Six of these SNPs (rs10757274, rs10757278, rs2383206, rs1333040, rs1537378, and rs4977574) had a significant relationship to the large artery atherosclerosis subtype of IS. Two SNPs (rs2383206 and rs4977574) were associated with IS mainly in Asians, and three SNPs (rs10757274, rs1333040, and rs1333049) were associated with susceptibility to IS mainly in Caucasians. Sensitivity analyses confirmed the reliability of the original results. Ethnicity and individual studies may be the main sources of heterogeneity in ANRIL.

Conclusions

Our results suggest that some single-nucleotide polymorphisms on the ANRIL locus may be associated with IS risk. Future studies with larger sample numbers are necessary to confirm this result. Additional functional analyses of causal effects of these polymorphisms on IS subtypes are also essential.

A novel prognostic model for hepatocellular carcinoma based on 5 microRNAs related to vascular invasion

BACKGROUND

Hepatocellular carcinoma (HCC) is prevalent worldwide with a high mortality rate. Prognosis prediction is crucial for improving HCC patient outcomes, but effective tools are still lacking. Characteristics related to vascular invasion (VI), an important process involved in HCC recurrence and metastasis, may provide ideas on prognosis prediction.

METHODS

Tools, including R 4.0.3, Funrich version 3, Cytoscape 3.8.2, STRING 11.5, Venny 2.1.0, and GEPIA 2, were used to perform bioinformatic analyses. The VI-related microRNAs (miRNAs) were identified using Gene Expression Omnibus HCC miRNA dataset GSE67140, containing 81 samples of HCC with VI and 91 samples of HCC without VI. After further evaluated the identified miRNAs based on The Cancer Genome Atlas database, a prognostic model was constructed via Cox regression analysis. The miRNAs in this model were also verified in HCC patients. Moreover, a nomogram was developed by integrating risk score from the prognostic model with clinicopathological parameters. Finally, a potential miRNA-mRNA network related to VI was established through weighted gene co-expression network analysis of HCC mRNA dataset GSE20017, containing 40 samples of HCC with VI and 95 samples of HCC without VI.

RESULTS

A prognostic model of 5 VI-related miRNAs (hsa-miR-126-3p, hsa-miR-148a-3p, hsa-miR-15a-5p, hsa-miR-30a-5p, hsa-miR-199a-5p) was constructed. The area under receiver operating characteristic curve was 0.709 in predicting 5-year survival rate, with a sensitivity of 0.74 and a specificity of 0.63. The nomogram containing risk score could also predict prognosis. Moreover, a VI-related miRNA-mRNA network covering 4 miRNAs and 15 mRNAs was established.

CONCLUSION

The prognostic model and nomogram might be potential tools in HCC management, and the VI-related miRNA-mRNA network gave insights into how VI was developed.

The effects of gastrointestinal disturbances on the onset of depression and anxiety

Background

Stomach pain is an ailment that occurs frequently in the general population. It is not unusual if such stomach issues produce some amount of stress in an individual, but it can be worrying if these pains lead to significant mental health problems. The relationship between some abdominal pain, such as bowel syndrome, and depression or anxiety has been gaining much interest. However, previous studies that have empirically investigated this relationship are scarce.

Methods

To analyze the impact of having gastrointestinal problems, among other socioeconomic conditions, on the onset of depression and anxiety in the Spanish population, we compare treating gastrointestinal diseases as exogenous in a single-equation probit model with a bivariate probit model in which this variable is treated as endogenous. A likelihood-ratio test of the correlation coefficient of the disturbances suggests that gastrointestinal problems are endogenous. Thus, the approach taken herein allows the direct testing of the hypothesis that having gastrointestinal problems and the onset of mental illnesses such as depression and anxiety are jointly determined by certain socioeconomic factors. A cross-sectional analytical study was analyzed using data from a 2017 survey of health indicators and life conditions that was developed by the Statistics Spanish Office.

Results

The probability of having depression or anxiety increases with age, stress, daily limitations and gastrointestinal disorders. On the other hand, the probability is lower for men, married people and those who engage in exercise several times per week. Our findings estimate that having gastrointestinal problems increases the probability of having depression in 7% and the probability of anxiety in 8.8% of the sample.

Conclusions

Our empirical results suggest that not considering the endogeneity of gastrointestinal problems could result in an overestimate of the impact of this factor on the development of depression or anxiety.

Characterisation of insomnia as an environmental risk factor for asthma via Mendelian randomization and gene environment interaction

Asthma is a complex disease that is reportedly associated with insomnia. However, the causal directionality of this association is still unclear. We used asthma and insomnia-associated single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) summary statistics to test the causal directionality between insomnia and asthma via Mendelian randomization (MR) analysis. We also performed a cross-trait meta-analysis using UK Biobank GWAS summary statistics and a gene–environment interaction study using data from UK Biobank. The interaction of genetic risk score for asthma (GRS_asthma) with insomnia on asthma was tested by logistic regression. Insomnia was a risk factor for the incidence of asthma, as revealed by three different methods of MR analysis. However, asthma did not act as a risk factor for insomnia. The cross-trait meta-analysis identified 28 genetic loci shared between asthma and insomnia. In the gene–environment interaction study, GRS_asthma interacted with insomnia to significantly affect the risk of asthma. The results of this study highlight the importance of insomnia as a risk factor of asthma, and warrant further analysis of the mechanism through which insomnia affects the risk of asthma.

Genetic association between TNF-α G-308A and osteoarthritis in Asians: A case-control study and meta-analysis

BACKGROUND

Osteoarthritis (OA) is an important health issue in elderly people. Many studies have suggested that genetic factors are important risk factors for OA, of which tumor necrosis factor-α (TNF-α) is one of the most examined genes. Moreover, several studies have investigated the relationship between TNF-α G-308A polymorphisms and OA risk, but consistent results have not been obtained.

OBJECTIVE

This study examines the association between TNF-α G-308A polymorphisms and knee OA. Moreover, meta-analysis and trial sequential analysis (TSA) was used to determine whether this is a susceptibility gene for knee OA.

METHODS

Between 2015 and 2019, 591 knee OA cases and 536 healthy controls were recruited. The Kellgren-Lawrence grading system was used to identify the knee OA cases. A meta-analysis was conducted including related studies published until 2020 from PubMed, Embase, and previous meta-analysis to improve the evidence level of the current study. The results were expressed as odds ratios (ORs) with corresponding 95% confidence intervals (CI) to evaluate the effect of this polymorphism on knee OA risk. The TSA was used to estimate the sample sizes required in this issue.

RESULTS

A nonsignificant association was found between the AA genotype and knee OA [adjusted OR, 0.84; 95% CI, 0.62-1.15) in the recessive model] in the present case-control study, and analysis of other genetic models showed a similar trend. After adding the critical case-control samples for Asians, the TNF-α G-308A, AA genotype exhibited 2.57 times more risk of developing arthritis when compared with the GG + GA genotype (95% CI, 1.56-4.23), and the cumulative samples for TSA (n = 2182) were sufficient to obtain a definite conclusion.

CONCLUSIONS

The results of this meta-analysis revealed that the TNF-α G-308A, AA genotype is a susceptible genotype for OA in the Asian population. This study integrated all current evidence to arrive at this conclusion, suggesting that future studies on Asians are not required.

Association between nitric oxide synthase T-786C genetic polymorphism and chronic kidney disease: Meta-analysis incorporating trial sequential analysis

BACKGROUND

Several meta-analyses of the relationship between endothelial nitric oxide synthase (eNOS) T-786C gene polymorphism and chronic kidney disease (CKD) have been published. However, the results of these studies were inconsistent, and it is undetermined whether sample sizes are sufficient to reach a definite conclusion.

OBJECTIVE

To elucidate the relationship between T-786C and CKD by combining previous studies with our case-control sample and incorporate trial sequential analysis (TSA) to verify whether the sample size is adequate to draw a definite conclusion.

METHODS

PubMed and Embase databases were searched for relevant articles on eNOS T-786C and CKD before February 28, 2021. TSA was also incorporated to ascertain a conclusion. A total of 558 hemodialysis cases in the case-control study was recruited from nine dialysis centers in the northern area of Taiwan in 2020. Additionally, 640 healthy subjects of the control group, with estimated glomerular filtration rate (eGFR) ≥ 60 mL/min/1.73 m2, were selected from participants of the annual elderly health examination program at the Tri-Service General Hospital. The functional analysis was based on eQTL data from GTExPortal.

RESULTS

After screening with eligibility criteria, 15 papers were included and eventually combined in a meta-analysis. The result of the TSA showed that the sample size for Caucasians was adequate to ascertain the correlation between eNOS T-786C and CKD but was insufficient for Asians. Therefore, we added our case-control samples (n = 1198), though not associated with CKD (odds ratio [OR] = 1.01, 95% confidence interval [CI] = 0.69-1.46), into a meta-analysis, which supported that eNOS T-786C was significantly associated with CKD in Asians (OR = 1.39, 95% CI = 1.04-1.85) by using an adequate cumulative sample size (n = 4572) analyzed by TSA. Data of eQTL from GTEx showed that T-786C with the C minor allele exhibited relatively lower eNOS mRNA expression in whole blood, indicating the hazardous role of eNOS T-786C in CKD.

CONCLUSIONS

eNOS T-786C genetic polymorphism was of conclusive significance in the association with CKD among Asians in our meta-analysis. Our case-control samples play a decisive role in changing conclusions from indefinite to definite.

Macular corneal dystrophy related to novel mutations of CHST6 in a Chinese family and clinical observation after penetrating keratoplasty

BACKGROUND

Macular corneal dystrophy (MCD) is a rare corneal stromal dystrophy with bilateral progressive vision loss. The pathogenic gene of MCD is carbohydrate sulfotransferase 6 (CHST6). Herein, we report a novel missense mutation and a rare exon deletion mutation in the CHST6 gene in a Chinese family with MCD.

METHODS

Genomic DNA was extracted from the peripheral blood, and next generation sequencing was used to analyse the gene sequence. The pathogenic mutations were identified in all affected family members. The proband successively received binocular penetrating keratoplasty (PKP), and the corneas were examined by histopathology and colloidal iron staining to prove the diagnosis. A long-term follow-up was made to observe the changes after PKP.

RESULTS

Genetic analysis demonstrated hemizygous mutations in the proband, including a novel c.520A>C (p.K174Q) missense mutation and a rarely reported exon 3 deletion mutation, which were co-segregated with the MCD phenotypes in the pedigree. The positive colloidal iron staining confirmed the diagnosis of MCD in the proband. However, the clinical phenotype and pathological manifestation of both eyes were different from each other because of complicated keratitis in the left eye. During the nine years of follow-up, visual acuity was improved significantly, and the cornea was transparent without rejection and postoperative recurrence in both eyes.

CONCLUSIONS

The novel hemizygous mutations were thought to contribute to the loss of CHST6 function, which induced typical clinical and pathological features of MCD. PKP was an effective treatment for MCD.

Factors associated with health intentions and behaviour among health checkup participants in Japan

Health intentions and behaviours are essential for improving the health of individuals and society. This study used cross-sectional data from 20,155 health checkup participants in the Yamagata study to identify factors associated with health intentions and behaviours. Information regarding the current level of health intentions and behaviours was collected using a baseline survey questionnaire. Participants were categorised into three groups: having no intention (no intention), having intentions to improve but not acting on them (intention), and already active (action). The associations between background factors and the presence/absence of health intentions and behaviours were assessed using logistic regression analysis. Of the participants, 35.4%, 37.7%, and 26.9% belonged to the no intention, intention, and action groups, respectively. Multivariate analysis revealed that the factors associated with health intentions were being young, being female, longer duration of education, higher body mass index and abdominal circumference, diabetes, and dyslipidaemia. The factors associated with health behaviours were being older and male, not consuming alcohol, not smoking, performing daily exercise, and having diabetes. These results indicate that health guidance considering background factors, including age, gender, education, and comorbidities, may be useful for effectively promoting health intentions and health behaviours in the Japanese population.

Association study between genetic variants and the risk of schizophrenia in the Chinese population based on GWAS-implicated 6p21.3-23.1 human genome region: a case-control study

BACKGROUND

Schizophrenia is a polygenic disease; however, the specific risk genetic variants of schizophrenia are still largely unknown. Single nucleotide polymorphism (SNP) is important genetic factor for the susceptibility of schizophrenia. Investigating individual candidate gene contributing to disease risk remains important.

METHODS

In a case-control study, five SNPs located in 6p21.3-p23.1 including rs2021722 in human leukocyte antigen (HLA) locus and rs107822, rs383711, rs439205 and rs421446 within the upstream of microRNA-219a-1 were genotyped in 454 schizophrenia patients and 445 healthy controls to investigate the possible association between the loci and schizophrenia in a Han Chinese population.

RESULTS

Our results showed significant associations between the rs2021722 and schizophrenia in allele (A vs. G: adjusted OR = 1.661, 95%CI = 1.196-2.308), co-dominant (AG vs. GG: OR = 1.760, 95%CI = 1.234-2.510) and dominant genetic model (AG + AA vs. GG: OR = 1.756, 95%CI = 1.237-2.492), respectively. Haplotype analysis showed that TGGT and CAAC were protective factor for schizophrenia compared with TAAC haplotype (OR = 0.324, 95% CI = 0.157-0.672; OR = 0.423, 95% CI = 0.199-0.900).

CONCLUSIONS

These findings indicate that rs2021722 in HLA locus might be involved in pathogenesis of schizophrenia and that genotypes AG and allele A of the locus are risk factors for schizophrenia in the Han Chinese population, confirming the association between immune system and schizophrenia.

Budget constrained machine learning for early prediction of adverse outcomes for COVID-19 patients

The combination of machine learning (ML) and electronic health records (EHR) data may be able to improve outcomes of hospitalized COVID-19 patients through improved risk stratification and patient outcome prediction. However, in resource constrained environments the clinical utility of such data-driven predictive tools may be limited by the cost or unavailability of certain laboratory tests. We leveraged EHR data to develop an ML-based tool for predicting adverse outcomes that optimizes clinical utility under a given cost structure. We further gained insights into the decision-making process of the ML models through an explainable AI tool. This cohort study was performed using deidentified EHR data from COVID-19 patients from ProMedica Health System in northwest Ohio and southeastern Michigan. We tested the performance of various ML approaches for predicting either increasing ventilatory support or mortality. We performed post hoc analysis to obtain optimal feature sets under various budget constraints. We demonstrate that it is possible to achieve a significant reduction in cost at the expense of a small reduction in predictive performance. For example, when predicting ventilation, it is possible to achieve a 43% reduction in cost with only a 3% reduction in performance. Similarly, when predicting mortality, it is possible to achieve a 50% reduction in cost with only a 1% reduction in performance. This study presents a quick, accurate, and cost-effective method to evaluate risk of deterioration for patients with SARS-CoV-2 infection at the time of clinical evaluation.

The FSHR G-29A variant is not associated with the ovarian response to exogenous FSH stimulation

A common genetic variant in the follicle stimulating hormone receptor gene (FSHR) 5'-untranslated region has been previously reported to influence FSHR gene expression. However, studies on the ovarian response to exogenous gonadotropin stimulation are limited. The aim of this study was to evaluate the association of variants at positions -29 of the FSHR gene with the ovarian response to exogenous FSH stimulation in Chinese women. The genotypes of the FSHR gene were assayed using the Sequenom MassARRAY system. Total RNA and protein was extracted from granulosa cells, and FSHR expression at the mRNA and protein levels was assessed using quantitative PCR and western blotting. Our data revealed that there was no association between the FSHR genotype at the -29 position and the outcome of controlled ovarian stimulation. The expression of FSHR, at both the mRNA and protein levels, was similar amongst the different FSHR genotypes assessed, but was significantly reduced in the low responders. These results indicate that the variants caused by mutations at position -29 are not associated with ovarian response, and the low ovarian response to gonadotropin stimulation may be caused by decreased FSHR expression.

Lung disease network reveals impact of comorbidity on SARS-CoV-2 infection and opportunities of drug repurposing

BACKGROUND

Higher mortality of COVID-19 patients with lung disease is a formidable challenge for the health care system. Genetic association between COVID-19 and various lung disorders must be understood to comprehend the molecular basis of comorbidity and accelerate drug development.

METHODS

Lungs tissue-specific neighborhood network of human targets of SARS-CoV-2 was constructed. This network was integrated with lung diseases to build a disease-gene and disease-disease association network. Network-based toolset was used to identify the overlapping disease modules and drug targets. The functional protein modules were identified using community detection algorithms and biological processes, and pathway enrichment analysis.

RESULTS

In total, 141 lung diseases were linked to a neighborhood network of SARS-CoV-2 targets, and 59 lung diseases were found to be topologically overlapped with the COVID-19 module. Topological overlap with various lung disorders allows repurposing of drugs used for these disorders to hit the closely associated COVID-19 module. Further analysis showed that functional protein-protein interaction modules in the lungs, substantially hijacked by SARS-CoV-2, are connected to several lung disorders. FDA-approved targets in the hijacked protein modules were identified and that can be hit by exiting drugs to rescue these modules from virus possession.

CONCLUSION

Lung diseases are clustered with COVID-19 in the same network vicinity, indicating the potential threat for patients with respiratory diseases after SARS-CoV-2 infection. Pathobiological similarities between lung diseases and COVID-19 and clinical evidence suggest that shared molecular features are the probable reason for comorbidity. Network-based drug repurposing approaches can be applied to improve the clinical conditions of COVID-19 patients.

Integrative Network Analysis Revealed Genetic Impact of Pyruvate Kinase L/R on Hepatocyte Proliferation and Graft Survival after Liver Transplantation

Background

Pyruvate kinase L/R (PKLR) has been suggested to affect the proliferation of hepatocytes via regulation of the cell cycle and lipid metabolism. However, its impact on the global metabolome and its clinical implications remain unclear.

Aims

We aimed to clarify the genetic impact of PKLR on the metabolomic profiles of hepatoma cells and its potential effects on grafts for liver transplantation (LT).

Methods

Nontargeted and targeted metabolomic assays were performed in human hepatoma cells transfected with lentiviral vectors causing PKLR overexpression and silencing, respectively. We then constructed a molecular network based on integrative analysis of transcriptomic and metabolomic data. We also assessed the biological functions of PKLR in the global metabolome in LT grafts in patients via a weighted correlation network model.

Results

Multiomic analysis revealed that PKLR perturbations significantly affected the pyruvate, citrate, and glycerophospholipid metabolism pathways, as crucial steps in de novo lipogenesis (DNL). We also confirmed the importance of phosphatidylcholines (PC) and its derivative lyso-PC supply on improved survival of LT grafts in patients. Coexpression analysis revealed beneficial effects of PKLR overexpression on posttransplant prognosis by alleviating arachidonic acid metabolism of the grafts, independent of operational risk factors.

Conclusion

This systems-level analysis indicated that PKLR affected hepatoma cell viability via impacts on the whole process of DNL, from glycolysis to final PC synthesis. PKLR also improved prognosis after LT, possibly via its impact on the increased genesis of beneficial glycerophospholipids.

Prognostic nomogram for predicting 5-year overall survival in Chinese patients with high-grade osteosarcoma

This study aimed to construct a widely accepted prognostic nomogram in Chinese high-grade osteosarcoma (HOS) patients aged ≤ 30 years to provide insight into predicting 5-year overall survival (OS). Data from 503 consecutive HOS patients at our centre between 12/2012 and 05/2019 were retrospectively collected. Eighty-four clinical features and routine laboratory haematological and biochemical testing indicators of each patient at the time of diagnosis were collected. A prognostic nomogram model for predicting OS was constructed based on the Cox proportional hazards model. The performance was assessed by the concordance index (C-index), receiver operating characteristic curve and calibration curve. The utility was evaluated by decision curve analysis. The 5-year OS was 52.1% and 2.6% for the nonmetastatic and metastatic patients, respectively. The nomogram included nine important variables based on a multivariate analysis: tumour stage, surgical type, metastasis, preoperative neoadjuvant chemotherapy cycle, postoperative metastasis time, mean corpuscular volume, tumour-specific growth factor, gamma-glutamyl transferase and creatinine. The calibration curve showed that the nomogram was able to predict 5-year OS accurately. The C-index of the nomogram for OS prediction was 0.795 (range, 0.703–0.887). Moreover, the decision curve analysis curve also demonstrated the clinical benefit of this model. The nomogram provides an individualized risk estimate of the 5-year OS in patients with HOS aged ≤ 30 years in a Chinese population-based cohort.

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients

Coronavirus disease 2019 (COVID-19) is raging worldwide. This potentially fatal infectious disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the complete mechanism of COVID-19 is not well understood. Therefore, we analyzed gene expression profiles of COVID-19 patients to identify disease-related genes through an innovative machine learning method that enables a data-driven strategy for gene selection from a data set with a small number of samples and many candidates. Principal-component-analysis-based unsupervised feature extraction (PCAUFE) was applied to the RNA expression profiles of 16 COVID-19 patients and 18 healthy control subjects. The results identified 123 genes as critical for COVID-19 progression from 60,683 candidate probes, including immune-related genes. The 123 genes were enriched in binding sites for transcription factors NFKB1 and RELA, which are involved in various biological phenomena such as immune response and cell survival: the primary mediator of canonical nuclear factor-kappa B (NF-κB) activity is the heterodimer RelA-p50. The genes were also enriched in histone modification H3K36me3, and they largely overlapped the target genes of NFKB1 and RELA. We found that the overlapping genes were downregulated in COVID-19 patients. These results suggest that canonical NF-κB activity was suppressed by H3K36me3 in COVID-19 patient blood.

Expression of miR-192-5p in colon cancer serum and its relationship with clinicopathologic features

Colon cancer has a poor prognosis due to a lack of biomarkers for early diagnosis and prognosis. The present study analyzed serum miR-192-5p expression levels in colon cancer patients and their correlations with clinicopathologic features. Relative mRNA expression was assessed by real-time fluorescence-based quantitative PCR in the serum of 164 colon cancer patients and 60 healthy controls. Patients were enrolled in a high or low miR-192-5p group according to the cutoff value determined by ROC curve analysis. The Kaplan-Meier method and univariate and multivariate Cox regression models were applied to analyze the risk factors influencing the postoperative survival of colon cancer patients. miR-192-5p mRNA expression in the colon cancer group was significantly reduced compared with the control group (P<0.01). Low miR-192-5p expression was significantly associated with a poor differentiation degree, lymphatic metastasis, vascular invasion, and high TNM stage (P=0.027, 0.001, 0.010, and <0.001, respectively). Colon cancer patients in the low miR-192-5p group exhibited a low survival rate (P<0.001). The independent risk factors for postoperative survival included lymphatic metastasis, a high TNM stage, and miR-192-5p<1.16 (P=0.017, 0.025, and 0.008, respectively). miR-192-5p may represent a promising biomarker for early diagnosis and prognosis in colon cancer patients.

Tumor size may influence the prognosis of solitary hepatocellular carcinoma patients with cirrhosis and without macrovascular invasion after hepatectomy

Hepatocellular carcinoma (HCC) is usually associated with varying degrees of cirrhosis. Among cirrhotic patients with solitary HCC in the absence of macro-vascular invasion, whether tumor size drives prognosis or not after hepatectomy remains unknown. This study aimed to investigate the prognostic impact of tumor size on long-term outcomes after hepatectomy for solitary HCC patients with cirrhosis and without macrovascular invasion. A total of 813 cirrhotic patients who underwent curative hepatectomy for solitary HCC and without macrovascular invasion between 2001 and 2014 were retrospectively studied. We set 5 cm as the tumor cut-off value. Propensity score matching (PSM) was performed to minimize the influence of potential confounders including cirrhotic severity that was histologically assessed according to the Laennec staging system. Recurrence-free survival (RFS) and overall survival (OS) were compared between the two groups before and after PSM. Overall, 464 patients had tumor size ≤ 5 cm, and 349 had tumor size > 5 cm. The 5-year RFS and OS rates were 38.3% and 61.5% in the  ≤ 5 cm group, compared with 25.1% and 59.9% in the > 5 cm group. Long-term survival outcomes were significantly worse as tumor size increased. Multivariate analysis indicated that tumor size > 5 cm was an independent risk factor for tumor recurrence and long-term survival. These results were further confirmed in the PSM cohort of 235 pairs of patients. In cirrhotic patients with solitary HCC and without macrovascular invasion, tumor size may significantly affect the prognosis after curative hepatectomy.

Multi-factor regulatory network and different clusters in hypertrophic obstructive cardiomyopathy

BACKGROUND

Practical biosignatures and thorough understanding of regulatory processes of hypertrophic obstructive cardiomyopathy (HOCM) are still lacking.

METHODS

Firstly, public data from GSE36961 and GSE89714 datasets of Gene Expression Omnibus (GEO), Gene database of NCBI (National Center of Biotechnology Information) and Online Mendelian Inheritance in Man (OMIM) database were merged into a candidate gene set of HOCM. Secondly, weighted gene co-expression network analysis (WGCNA) for the candidate gene set was carried out to determine premier co-expressed genes. Thirdly, significant regulators were found out by virtue of a multi-factor regulatory network of long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and transcription factors (TFs) with molecule interreactions from starBase v2.0 database and TRRUST v2 database. Ultimately, HOCM unsupervised clustering and "tsne" dimensionality reduction was employed to gain hub genes, whose classification performance was evaluated by a multinomial model of lasso logistic regression analysis binded with receiver operating characteristic (ROC) curve.

RESULTS

Two HOCM remarkably-interrelated modules were from WGCNA, followed by the recognition of 32 crucial co-expressed genes. The multi-factor regulatory network disclosed 7 primary regulatory agents, containing lncRNAs (XIST, MALAT1, and H19), TFs (SPI1 and SP1) and miRNAs (hsa-miR-29b-39 and has-miR-29a-3p). Four clusters of HOCM and 4 hub genes (COMP, FMOD, AEBP1 and SULF1) significantly expressing in preceding four subtypes were obtained, while ROC curve demonstrated satisfactory performance of clustering and 4 genes.

CONCLUSIONS

Our consequences furnish valuable resource which may bring about prospective mechanistic and therapeutic anatomization in HOCM.

A novel compound heterozygous variant of the SLC12A3 gene in Gitelman syndrome with diabetes and the choices of the appropriate hypoglycemic drugs: a case report

BACKGROUND

Gitelman syndrome (GS) is an autosomal recessive tubulopathy caused by mutations of the SLC12A3 gene. It is characterized by hypokalemic metabolic alkalosis, hypomagnesemia and hypocalciuria. It is universally known that both hypokalemia and hypomagnesemia can influence insulin secretion and insulin resistance, but the exact mechanisms require further study. We identified a novel deletion variant of the SLC12A3 gene and discussed the appropriate hypoglycemic drugs in Gitelman syndrome (GS) patients with type 2 diabetes.

CASE PRESENTATION

A 55-year-old diabetic female patient was hospitalized for evaluation because of paroxysmal general weakness and numbness of extremities for one year. We suspected that she was suffering from GS by initial estimation. Direct Sanger sequencing was used to analyze the causative gene SLC12A3 of GS. Oral glucose tolerance test (OGTT) was carried out to assess the glucose metabolism and insulin resistance status. Genetic analysis revealed that she was a compound heterozygote for a recurrent missense mutation c.179C > T and a novel deletion c.1740delC in SLC12A3, thus her diagnosis of GS was confirmed. The patient was treated with potassium chloride (3.0 g/d) and magnesium chloride (element magnesium 350 mg/d) on the basis of initial treatment of diabetes with hypoglycemic drug (Repaglinide, 3.0 mg/day). However, she developed frequent hypoglycemia after one week. OGTT showed that her glucose metabolism and insulin resistance much improved after potassium and magnesium supplemental therapy. Then we changed the hypoglycemic agent to a dipeptidyl peptidase-4 (DPP-4) inhibitor (Trajenta 5 mg/d), since then her blood glucose level remained normal during two-year of follow-up.

CONCLUSION

We have identified a novel deletion of the SLC12A3 gene and discussed the appropriate hypoglycemic drugs in Gitelman syndrome (GS) patients with type 2 diabetes. We suggested that attention need to be paid to blood glucose monitoring in GS patients, especially when hypokalemia and hypomagnesemia are corrected. Besides, the insufficient blood volume and serum electrolyte disturbance should also be taken into consideration in the selecting hypoglycemic drugs for GS patients.

The relationship between common mental disorders and incident diabetes among participants in the Kerala Diabetes Prevention Program (K-DPP)

This study aims to describe the prevalence of depression and anxiety among a population sample of people at high risk for type 2 diabetes in Kerala, India, and examine the relationship between depressive symptoms, anxiety, and incident Type 2 Diabetes Mellitus (T2DM) over a two-year period. We used data from the Kerala Diabetes Prevention Program, a cluster-randomized controlled trial for diabetes prevention among 1007 high-risk individuals. The prevalence of depression and anxiety were estimated using the 9-item Patient Health Questionnaire and the Generalized Anxiety Disorder 7-item scale, respectively. We calculated proportions for depression and anxiety and performed generalized estimating equations (GEE) to examine the relationship between baseline mental health status and incident T2DM. The prevalence of depression and anxiety at baseline were 7.5% and 5.5%, respectively. Compared with those reporting none/low symptoms, the odds ratio for incident diabetes was 1.07 (95% CI 0.54–2.12) for participants with moderate to severe depression and 0.73 (95% CI 0.23–2.28) for participants with moderate to severe anxiety, after adjusting for potential confounders. Our findings suggest that the prevalence of depression and anxiety were higher than those previously reported in the general population in India. However, among this sample of community-based adults at high risk of developing T2DM, the presence of moderate to severe depression and/or anxiety symptoms was not significantly associated with the risk of developing T2DM.

Trial registration: Australia and New Zealand Clinical Trials Registry ACTRN12611000262909. Registered 10 March 2011.

Circular noncoding RNA hsa_circ_0005986 as a prognostic biomarker for hepatocellular carcinoma

Circular RNAs (circRNAs) represent potential biomarkers because of their highly stable structure and robust expression pattern in clinical samples. The aim of this study was to evaluate the expression of a recently identified circRNA, hsa_circ_0005986; determine its clinical significance; and evaluate its potential as a biomarker of hepatocellular carcinoma (HCC). We evaluated hsa_circ_0005986 expression in 123 HCC tissue samples, its clinical significance, and its association with patients’ clinicopathological characteristics and survival. Hsa_circ_0005986 expression was downregulated in HCC tissues. Low hsa_circ_0005986 expression was more common in tumors larger than 5 cm [odds ratio (OR), 3.19; 95% confidence interval (CI), 1.51–6.76; p = 0.002], advanced TNM stage (III/IV; OR, 2.39; 95% CI, 1.16–4.95; p = 0.018), and higher BCLC stage (B/C; OR, 2.71; 95% CI, 1.30–5.65; p = 0.007). High hsa_circ_0005986 expression was associated with improved survival and was an independent prognostic factor for overall [hazard ratio (HR), 0.572; 95% CI, 0.339–0.966; p = 0.037] and progression-free (HR, 0.573; 95% CI, 0.362–0.906; p = 0.017) survival. Moreover, the circRNA–miRNA–mRNA network was constructed using RNA-seq/miRNA-seq data and clinical information from TCGA-LIHC dataset. Our findings indicate a promising role for hsa_circ_0005986 as a prognostic biomarker in patients with HCC.

Association of GSTP1 Ile105Val polymorphism with the risk of coronary heart disease: An updated meta-analysis

Background

Numerous case-control studies have investigated the association between GSTP1 Ile105Val polymorphism and CHD risk, but the results from published studies were inconclusive. The present meta-analysis was performed to derive a more precise estimation.

Methods

PubMed, EMBASE, and Web of Science database searches were conducted to retrieve relevant articles.

Results

Ultimately, 5,451 CHD cases and 5,561 controls from 15 studies were included. Pooled analysis did not yield any statistically significant association between GSTP1 Ile105Val polymorphism and CHD risk for the overall population (Val vs. Ile: OR, 1.05; 95% CI, 0.93 to 1.18; Val/Val vs. Ile/Ile: OR, 1.09; 95% CI, 0.83 to 1.42; Val/Ile vs. Ile/Ile: OR, 1.09; 95% CI, 0.93 to 1.28; Val/Val vs. Val/Ile+Ile/Ile: OR, 1.04; 95% CI, 0.83 to 1.30; Val/Val+Val/Ile vs. Ile/Ile: OR, 1.14; 95% CI, 0.97 to 1.33). Subgroup analyses and sensitivity analyses indicated that GSTP1 Ile105Val polymorphism was still not associated with an increased risk of CHD. After excluding studies detected by Galbraith plots as major sources of heterogeneity, these relationships were still not significant.

Conclusions

The overall results did not reveal a major role of the GSTP1 Ile105Val polymorphism in modulating CHD risk. Well-designed studies with large sample sizes are needed to validate our findings and explore the possible gene-gene or gene-environment interactions.

Comparison of dural grafts and methods of graft fixation in Chiari malformation type I decompression surgery

Suboccipital decompression with duraplasty is a widely accepted method for treating patients with Chiari malformation type I. However, important details of the duraplasty technique are still controversial. This retrospective study analyzes clinical and radiological outcomes after surgery depending upon the type of graft and methods of graft fixation. Seventy consecutive decompressions with duraplasty were analyzed. Two types of grafts, nonautologous (Non-AutoG; 60.0%) and autologous (AutoG; 40.0%), and two methods of graft fixation, suturing (S; 67.1%) and gluing (G; 32.9%), were used in four different combinations: (Non-AutoG+S: 31.4%; Non-AutoG+G: 28.6%; AutoG+S: 35.7%; AutoG+G: 4.3%) according to surgeon preference. The mean follow-up was 63.4 months. According to gestalt and Chicago Chiari Outcome Scales, satisfactory results were obtained in 72.9% and 78.6% of cases, respectively, in the long term. The outcomes were not related to the kind of graft (p = 0.44), fixation method (p = 0.89) or duraplasty pattern (p = 0.32). Decreased syringomyelia was observed in 88.9% of cases, and no associations with the kind of graft (p = 0.84), fixation method (p = 1) or duraplasty pattern were found (p = 0.96). Pseudomeningocele occurred 5 times more often in the Non-AutoG group than in the AutoG group (52.4% vs. 10.7%; p < 0.05), whereas their formations were not related to the fixation method (p = 0.34). Three cases (12.0%) required reoperation with reduraplasty. Autologous and nonautologous dural grafts can be sutured or glued with similar clinical results; however, the use of nonautologous grafts is linked with a much higher risk of pseudomeningocele formation.

Nomogram and a predictive model for postoperative hemorrhage in preoperative patients of laparoscopic pancreaticoduodectomy

To develop a predictive model and a nomogram for predicting postoperative hemorrhage in preoperative patients undergoing laparoscopic pancreaticoduodenectomy (LPD). A total of 409 LPD patients that underwent LPD by the same surgical team between January 2014 and December 2020 were included as the training cohort. The preoperative data of patients were statistically compared and analyzed for exploring factors correlated with postoperative hemorrhage. The predictive model was developed by multivariate logistic regression and stepwise (stepAIC) selection. A nomogram based on the predictive model was developed. The discriminatory ability of the predictive model was validated using the receiver operating characteristic (ROC) curve and leave-one-out method. The statistical analysis was performed using R 3.5.1 (www.r-project.org). The predictive model including the risk-associated factors of postoperative hemorrhage was as follows: 2.695843 − 0.63056 × (Jaundice = 1) − 1.08368 × (DM = 1) − 2.10445 × (Hepatitis = 1) + 1.152354 × (Pancreatic tumor = 1) + 1.071354 × (Bile duct tumor = 1) − 0.01185 × CA125 − 0.04929 × TT − 0.08826 × APTT + 26.03383 × INR − 1.9442 × PT + 1.979563 × WBC − 2.26868 × NEU − 2.0789 × LYM − 0.02038 × CREA + 0.00459 × AST. A practical nomogram based on the model was obtained. The internal validation of ROC curve was statistically significant (AUC = 0.7758). The validation by leave-one-out method showed that the accuracy of the model and the F measure was 0.887 and 0.939, respectively. The predictive model and nomogram based on the preoperative data of patients undergoing LPD can be useful for predicting the risk degree of postoperative hemorrhage.

Combined prognostic nutritional index and albumin-bilirubin grade to predict the postoperative prognosis of HBV-associated hepatocellular carcinoma patients

This study aims to evaluate the predictive value of the prognostic nutritional index (PNI) and albumin-bilirubin grade (ALBI) for the postoperative prognosis of hepatitis B virus-associated hepatocellular carcinoma (HBV-HCC) patients undergoing radical hepatectomy (RH). Besides, we seek to identify novel prognosis indicators for HBV-HCC patients. Between April 2009 and March 2015, this work enrolled 868 patients diagnosed with HBV-HCC and undergoing RH in the Liver Surgery Department, West China Hospital, Sichuan University (WCHSU). The basic information, laboratory examination indicators, pathological reports, and follow-up data of patients were included. SPSS 22.0 statistical software was used for statistical data analyses. Platelet (PLT), alpha-fetoprotein (AFP), maximum diameter (max-D), number of tumors (Number), degree of differentiation (DD), Microvascular invasion situation (MVI), satellite focus situation (SF), PNI, and ALBI were the independent risk factors for both overall survival (OS) and disease-free survival (DFS) of HBV-HCC patients undergoing RH. Taking PNI = 46 and ALBI = - 2.80 as cut-off values, the OS and DFS of the PNI-high group were significantly higher than those of the PNI-low group. Meanwhile, the OS and DFS of the ALBI-low group were significantly higher than those of the ALBI-high group; the OS and DFS of the PNI-high + ALBI-low group were significantly higher than those of the PNI-low + ALBI-high group. Xie prognostic index (XPI) was the independent risk factor for both OS and DFS of HBV-HCC patients undergoing RH. The OS and DFS of the XPI-high group were significantly higher than those of the XPI-low group. This paper reveals that preoperative PNI and ALBI can predict the OS and DFS of HBV-HCC patients undergoing RH. Their impact on the prognosis of HBV-HCC patients is insignificant, however, it cannot be ignored. XPI can precisely predict the prognosis of HBV-HCC patients undergoing RH, nonetheless, its effect requires additional research for validation.

Clinical, epidemiological aspects, and trends of Hepatitis B in Brazil from 2007 to 2018

Hepatitis B virus (HBV) infection is a concern for public health due to its high prevalence, high infectivity, morbidity, and mortality worldwide. Brazil presents a low HBV prevalence, but has considerable heterogeneity among its geographic regions. Here, we describe the epidemiological profile of HBV infection in different regions of Brazil during 2007-2018, as well as the historical trends associated with the infection. We conducted an observational, ecological time-series study using secondary data collected from the National Notifiable Diseases Information System (SINAN). Our findings suggest that HBV infection was more likely to occur in young, sexually active adults. Individuals from Northeast and Midwest regions were more likely to present acute HBV infection, while individuals from South region were more likely to present chronic HBV infection, reinforcing that specific strategies are required for each particular region. Additionally, we observed a general decreasing trend of infection starting in 2014, however there was an increasing trend of infection in men and in individuals over 40 years old. Although we observed a decreasing trend in HBV infection, active surveillance is needed to prevent HBV spread and possible epidemics, as well as encouraging the vaccination of adults, especially young adult males. Our findings can inform the conduct of large-scale observational studies to evaluate clinical, economical, and social impacts of HBV infections, leading to improved social policies. Finally, our results highlight the need to improve data quality and completeness of epidemiological data, minimizing eventual errors that can make prevention and control strategies difficult.

Impact of surgical resection of butterfly glioblastoma on survival: a meta-analysis based on comparative studies

Butterfly glioblastoma (bGBM) is a rare brain tumor that invades both hemispheres by crossing the corpus callosum. bGBM is associated with a dismal prognosis with a median survival time of a few months. Surgical resection is a rare treatment option due to the unfavorable location and assumed poor risk-to-benefit ratio. Therefore, a biopsy-alone approach is considered the main treatment option. This meta-analysis aimed to systematically evaluate whether resection of bGBM is associated with improved overall survival compared with biopsy alone. We searched three databases to find studies that compare resection with biopsy in 6-, 12- and 18-months overall survival in patients with bGBM. We calculated the pooled relative risk (RR) of mortality using a random-effects model. Five studies with 194 patients were included in the meta-analysis. Mortality was decreased for resection compared with biopsy at 6-months (RR 0.63 [95% CI 0.44-0.91]). No significant differences in overall survival were found at 12 (RR 0.76 [95% CI 0.50-1.14]) and 18-months (RR 0.84 [95% CI 0.56-1.26]). Surgical resection of bGBM is associated with an improved 6-months overall survival compared with biopsy alone. We have not found strong evidence supporting the superiority of resection over biopsy alone in overall survival at 12 and 18-months.

The structure-based cancer-related single amino acid variation prediction

Single amino acid variation (SAV) is an amino acid substitution of the protein sequence that can potentially influence the entire protein structure or function, as well as its binding affinity. Protein destabilization is related to diseases, including several cancers, although using traditional experiments to clarify the relationship between SAVs and cancer uses much time and resources. Some SAV prediction methods use computational approaches, with most predicting SAV-induced changes in protein stability. In this investigation, all SAV characteristics generated from protein sequences, structures and the microenvironment were converted into feature vectors and fed into an integrated predicting system using a support vector machine and genetic algorithm. Critical features were used to estimate the relationship between their properties and cancers caused by SAVs. We describe how we developed a prediction system based on protein sequences and structure that is capable of distinguishing if the SAV is related to cancer or not. The five-fold cross-validation performance of our system is 89.73% for the accuracy, 0.74 for the Matthews correlation coefficient, and 0.81 for the F1 score. We have built an online prediction server, CanSavPre ( http://bioinfo.cmu.edu.tw/CanSavPre/ ), which is expected to become a useful, practical tool for cancer research and precision medicine.

Association of NOS2A gene polymorphisms with susceptibility to bovine tuberculosis in Chinese Holstein cattle

Bovine tuberculosis (bTB) is a global zoonotic disease that has detrimental economic impacts worldwide. The NOS2A gene plays a key role in immunological control of many infectious diseases. However, research on the association between NOS2A polymorphisms and bTB infection in Holstein cattle reared on the Yunnan-Guizhou plateau of China is scarce. This study investigated a possible linkage between NOS2A polymorphisms and risk of developing bTB in Chinese Holstein cattle. The NOS2A gene was genotyped in 144 bTB-infected Holstein cows and 139 healthy controls were genotyped through nucleotide sequencing. Ten single-nucleotide polymorphisms (SNPs) were detected, six of which were associated with susceptibility/resistance patterns of bTB. Furthermore, the C/T genotypes of 671 and 2793, and T/T genotype of E22 (+15) were significantly associated with susceptibility risk; the G/A genotype of 2857, T/T genotype of E9 (+65), and C/C genotype of E9 (+114) probably increased resistance to bTB. In addition, the haplotypes of NOS2A-2 and NOS2A-9 were risk factors for bTB susceptibility, while the NOS2A-5 and NOS2A-8 haplotypes were contributing protective variants against tuberculosis. There is a significant association between variation in SNPs of NOS2A and tuberculosis susceptibility/resistance pattern. These findings suggest that substitution of genetic selection would be helpful for eradicating bTB. However, further investigation is required to study the underlying mechanism through which NOS2A polymorphisms affect bTB infection.

A defective interleukin-17 receptor A1 causes weight loss and intestinal metabolism-related gene downregulation in Japanese medaka, Oryzias latipes

In the intestine, the host must be able to control the gut microbiota and efficiently absorb transiently supplied metabolites, at the risk of enormous infection. In mammals, the inflammatory cytokine interleukin (IL)-17A/F is one of the key mediators in the intestinal immune system. However, many functions of IL-17 in vertebrate intestines remain unclarified. In this study, we established a gene-knockout (KO) model of IL-17 receptor A1 (IL-17RA1, an IL-17A/F receptor) in Japanese medaka (Oryzias latipes) using genome editing technique, and the phenotypes were compared to wild type (WT) based on transcriptome analyses. Upon hatching, homozygous IL-17RA1-KO medaka mutants showed no significant morphological abnormality. However, after 4 months, significant weight decreases and reduced survival rates were observed in IL-17RA1-KO medaka. Comparison of gene-expression patterns in WT and IL-17RA1-KO medaka revealed that various metabolism- and immune-related genes were significantly down-regulated in IL-17RA1-KO medaka intestine, particularly genes related to mevalonate metabolism (mvda, acat2, hmgcs1, and hmgcra) and genes related to IL-17 signaling (such as il17c, il17a/f1, and rorc) were found to be decreased. Conversely, expression of genes related to cardiovascular system development, including fli1a, sox7, and notch1b in the anterior intestine, and that of genes related to oxidation-reduction processes including ugp2a, aoc1, and nos1 in posterior intestine was up-regulated in IL-17RA1-KO medaka. These findings show that IL-17RA regulated immune- and various metabolism-related genes in the intestine for maintaining the health of Japanese medaka.

Genetic association study between TAB2 polymorphisms and noise-induced-hearing-loss in a Han Chinese population

Noise-induced-hearing-loss(NIHL) is a common occupational disease caused by various environmental and biological factors. To investigate the association between TAB2 and the susceptibility of NIHL of people exposed to occupational environments, a genetic association study was performed on selected companies with 588 cases and 537 healthy control subjects. Five selected single nucleotide polymorphisms (SNPs) in TAB2,incoluding rs2744434, rs521845, rs652921, rs7896, rs9485372, were genotyped after a collection of DNA samples. Evident differences in participants between the case group and the control group reveals the result that people with the TAB2 has a high probability of getting NIHL. The results show that rs521845 is deeply associated with the risk of NIHL and is available for the diagnosis in the future.

A five metastasis-related long noncoding RNA risk signature for osteosarcoma survival prediction

BACKGROUND

Osteosarcoma is a highly malignant and common bone tumour with an aggressive disease course and a poor prognosis. Previous studies have demonstrated the relationship between long noncoding RNAs (lncRNAs) and tumorigenesis, metastasis, and progression.

METHODS

We utilized a large cohort from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database osteosarcoma project to identify potential lncRNAs related to the overall survival of patients with osteosarcoma by using univariate and multivariate Cox proportional hazards regression analyses. Kaplan-Meier curves were generated to evaluate the overall survival difference between patients in the high-risk group and the low-risk group. A time-dependent receiver operating characteristic curve (ROC) was employed, and the area under the curve (AUC) of ROC was measured to assess the sensitivity and specificity of the multi-lncRNA signature.

RESULTS

Five lncRNAs (RP11-128N14.5, RP11-231|13.2, RP5-894D12.4, LAMA5-AS1, RP11-346L1.2) were identified, and a five-lncRNA signature was constructed. The AUC for predicting 5-year survival was 0.745, which suggested good performance of the five-lncRNA signature. In addition, functional enrichment analysis of the five-lncRNA-correlated protein-coding genes (PCGs) was performed to show the biological function of the five lncRNAs. Additionally, PPI network suggested RTP1 is a potential biomarker that regulates the prognosis of osteosarcoma.

CONCLUSIONS

We developed a five-lncRNA signature as a potential prognostic indicator for osteosarcoma.

Genetic network and gene set enrichment analyses identify MND1 as potential diagnostic and therapeutic target gene for lung adenocarcinoma

This study aimed to characterize the key survival-specific genes for lung adenocarcinoma (LUAD) using machine-based learning approaches. Gene expression profiles were download from gene expression omnibus to analyze differentially expressed genes (DEGs) in LUAD tissues versus healthy lung tissue and to construct protein–protein interaction (PPI) networks. Using high-dimensional datasets of cancer specimens from clinical patients in the cancer genome atlas, gene set enrichment analysis was employed to assess the independent effect of meiotic nuclear divisions 1 (MND1) expression on survival status, and univariate and multivariate Cox regression analyses were applied to determine the associations of clinic-pathologic characteristics and MND1 expression with overall survival (OS). A set of 495 DEGs (145 upregulated and 350 downregulated) was detected, including 63 hub genes with ≥ 10 nodes in the PPI network. Among them, MND1 was participated in several important pathways by connecting with other genes via 17 nodes in lung cancer, and more frequently expressed in LUAD patients with advancing stage (OR = 1.68 for stage III vs. stage I). Univariate and multivariate Cox analyses demonstrated that the expression level of MND1 was significantly and negatively correlated with OS. Therefore, MND1 is a promising diagnostic and therapeutic target for LUAD.

COL3A1 rs1800255 polymorphism is associated with pelvic organ prolapse susceptibility in Caucasian individuals: Evidence from a meta-analysis

Background

The collagen 3 alpha 1 (COL3A1) rs1800255 polymorphism has been reported to be associated with women pelvic organ prolapse (POP) susceptibility, but the results of these previous studies have been contradictory. The objective of current study is to explore whether COL3A1 rs1800255 polymorphism confers risk to POP.

Methods

Relevant literatures were searched by searching databases including Pubmed, Embase, Google academic, the Cochrane library, China National Knowledge Infrastructure (CNKI). Search time is from database foundation to March 2021.

Results

A total of seven literatures were enrolled in the present meta-analysis, including 1642 participants. Overall, no significant association was found by any genetic models. In subgroup analysis based on ethnicity, significant associations were demonstrated in Caucasians by allele contrast (A vs. G: OR = 1.34, 95%CI = 1.03–1.74,), homozygote comparison (AA vs. GG: OR = 3.25, 95%CI = 1.39–7.59), and recessive genetic model (AA vs. GG/GA: OR = 3.22, 95%CI = 1.40–7.42).

Conclusions

The present meta-analysis suggests that the COL3A1 is a candidate gene for POP susceptibility. Caucasian individuals with A allele and AA genotype have a higher risk of POP. The COL3A1 rs1800255 polymorphism may be risk factor for POP in Caucasian population.

Providing an optimized model to detect driver genes from heterogeneous cancer samples using restriction in subspace learning

Extracting the drivers from genes with mutation, and segregation of driver and passenger genes are known as the most controversial issues in cancer studies. According to the heterogeneity of cancer, it is not possible to identify indicators under a group of associated drivers, in order to identify a group of patients with diseases related to these subgroups. Therefore, the precise identification of the related driver genes using artificial intelligence techniques is still considered as a challenge for researchers. In this research, a new method has been developed using the subspace learning method, unsupervised learning, and with more constraints. Accordingly, it has been attempted to extract the driver genes with more precision and accurate results. The obtained results show that the proposed method is more to predict the driver genes and subgroups of driver genes which have the highest degree of overlap due to p-value with known driver genes in valid databases. Driver genes are the benchmark of MsigDB which have more overlap compared to them as selected driver genes. In this article, in addition to including the driver genes defined in previous work, introduce newer driver genes. The minister will define newer groups of driver genes compared to other methods the p-value of the proposed method was 9.21e-7 better than previous methods for 200 genes. Due to the overlap and newer driver genes and driver gene group and subgroups. The results show that the p value of the proposed method is about 2.7 times less than the driver sub method due to overlap, indicating that the proposed method can identify driver genes in cancerous tumors with greater accuracy and reliability.

Gene network and biological pathways associated with susceptibility to differentiated thyroid carcinoma

Variants identified in earlier genome-wide association studies (GWAS) on differentiated thyroid carcinoma (DTC) explain about 10% of the overall estimated genetic contribution and could not provide complete insights into biological mechanisms involved in DTC susceptibility. Integrating systems biology information from model organisms, genome-wide expression data from tumor and matched normal tissue and GWAS data could help identifying DTC-associated genes, and pathways or functional networks in which they are involved. We performed data mining of GWAS data of the EPITHYR consortium (1551 cases and 1957 controls) using various pathways and protein-protein interaction (PPI) annotation databases and gene expression data from The Cancer Genome Atlas. We identified eight DTC-associated genes at known loci 2q35 (DIRC3), 8p12 (NRG1), 9q22 (FOXE1, TRMO, HEMGN, ANP32B, NANS) and 14q13 (MBIP). Using the EW_dmGWAS approach we found that gene networks related to glycogenolysis, glycogen metabolism, insulin metabolism and signal transduction pathways associated with muscle contraction were overrepresented with association signals (false discovery rate adjusted p-value < 0.05). Additionally, suggestive association of 21 KEGG and 75 REACTOME pathways with DTC indicate a link between DTC susceptibility and functions related to metabolism of cholesterol, amino sugar and nucleotide sugar metabolism, steroid biosynthesis, and downregulation of ERBB2 signaling pathways. Together, our results provide novel insights into biological mechanisms contributing to DTC risk.

Mining the plasma-proteome associated genes in patients with gastro-esophageal cancers for biomarker discovery

Gastro-esophageal (GE) cancers are one of the major causes of cancer-related death in the world. There is a need for novel biomarkers in the management of GE cancers, to yield predictive response to the available therapies. Our study aims to identify leading genes that are differentially regulated in patients with these cancers. We explored the expression data for those genes whose protein products can be detected in the plasma using the Cancer Genome Atlas to identify leading genes that are differentially regulated in patients with GE cancers. Our work predicted several candidates as potential biomarkers for distinct stages of GE cancers, including previously identified CST1, INHBA, STMN1, whose expression correlated with cancer recurrence, or resistance to adjuvant therapies or surgery. To define the predictive accuracy of these genes as possible biomarkers, we constructed a co-expression network and performed complex network analysis to measure the importance of the genes in terms of a ratio of closeness centrality (RCC). Furthermore, to measure the significance of these differentially regulated genes, we constructed an SVM classifier using machine learning approach and verified these genes by using receiver operator characteristic (ROC) curve as an evaluation metric. The area under the curve measure was > 0.9 for both the overexpressed and downregulated genes suggesting the potential use and reliability of these candidates as biomarkers. In summary, we identified leading differentially expressed genes in GE cancers that can be detected in the plasma proteome. These genes have potential to become diagnostic and therapeutic biomarkers for early detection of cancer, recurrence following surgery and for development of targeted treatment.

Construction and validation of a metabolic risk model predicting prognosis of colon cancer

Metabolic genes have played a significant role in tumor development and prognosis. In this study, we constructed a metabolic risk model to predict the prognosis of colon cancer based on The Cancer Genome Atlas (TCGA) and validated the model by Gene Expression Omnibus (GEO). We extracted 753 metabolic genes and identified 139 differentially expressed genes (DEGs) from TCGA database. Then we conducted univariate cox regression analysis and Least Absolute Shrinkage and Selection Operator Cox regression analysis to identify prognosis-related genes and construct the metabolic risk model. An eleven-gene prognostic model was constructed after 1000 resamples. The gene signature has been proved to have an excellent ability to predict prognosis by Kaplan-Meier analysis, time-dependent receiver operating characteristic, risk score, univariate and multivariate cox regression analysis based on TCGA. Then we validated the model by Kaplan-Meier analysis and risk score based on GEO database. Finally, we performed a weighted gene co-expression network analysis and protein-protein interaction network on DEGs, and Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology enrichment analyses were conducted. The results of functional analyses showed that most significantly enriched pathways focused on metabolism, especially glucose and lipid metabolism pathways.

Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease

This investigation seeks to dissect coronary artery disease molecular target candidates along with its underlying molecular mechanisms. Data on patients with CAD across three separate array data sets, GSE66360, GSE19339 and GSE97320 were extracted. The gene expression profiles were obtained by normalizing and removing the differences between the three data sets, and important modules linked to coronary heart disease were identified using weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and genomes (KEGG) pathway enrichment analyses were applied in order to identify statistically significant genetic modules with the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool (version 6.8; http://david.abcc.ncifcrf.gov ). The online STRING tool was used to construct a protein-protein interaction (PPI) network, followed by the use of Molecular Complex Detection (MCODE) plug-ins in Cytoscape software to identify hub genes. Two significant modules (green-yellow and magenta) were identified in the CAD samples. Genes in the magenta module were noted to be involved in inflammatory and immune-related pathways, based on GO and KEGG enrichment analyses. After the MCODE analysis, two different MCODE complexes were identified in the magenta module, and four hub genes (ITGAM, degree = 39; CAMP, degree = 37; TYROBP, degree = 28; ICAM1, degree = 18) were uncovered to be critical players in mediating CAD. Independent verification data as well as our RT-qPCR results were highly consistent with the above finding. ITGAM, CAMP, TYROBP and ICAM1 are potential targets in CAD. The underlying mechanism may be related to the transendothelial migration of leukocytes and the immune response.

Identification of oxytocin-related lncRNAs and assessment of their expression in breast cancer

Oxytocin is a neuropeptide released by the central nervous system. A number of studies have demonstrated the role of this neuropeptide in the pathogenesis of breast cancer. In the present project, we have identified mRNA coding genes and long non-coding RNAs (lncRNAs) that are associated with this pathway through an in-silico strategy, and measured their expression in a cohort of Iranian females affected with this type of malignancy. Expression levels of OXTR, FOS, ITPR1, RCAN1, CAMK2D, CACNA2D and lnc_ZFP161 were significantly down-regulated in breast cancer tissues compared with nearby non-cancerous tissues. On the other hand, expression of lnc_MTX2 was higher in breast cancer tissues compared with controls. Expression of lnc_TNS1 and lnc_FOXF1 were not different between these two kinds of samples. Expression of CACNA2D was associated with mitotic rate and PR status (P values = 3.02E−02 and 2.53E−02, respectively). Expression of other oxytocin-related genes was not associated with clinicopathological parameters. FOS and ITPR1 had the highest AUC value among the oxytocin-related genes. Combination of expression profiles of all oxytocin-related genes increased the AUC value to 0.75. However, the combinatorial sensitivity and specificity values were lower than some individual genes. In the breast cancer tissues, the most robust correlations have been detected between lnc_ZFP161/ lnc_FOXF1, CAMK2D/ lnc_ZFP161 and CAMK2D / lnc_FOXF1 (r = 0.86, 0.71 and 0.64 respectively). In the non-cancerous tissues, the strongest correlation was detected between lnc_FOXF1/lnc_MTX2 and lnc_ZFP161/CAMK2D respectively (r = 0.78 and 0.65). Taken together, oxytocin-associated genes have been dysregulated in breast cancer tissues. Moreover, the correlation ratio between these genes is connected with the existence of cancer.

Association of NAT2 genetic polymorphism with the efficacy of Neurotropin® for the enhancement of aggrecan gene expression in nucleus pulposus cells: a pilot study

BACKGROUND

Intervertebral disc degeneration, one of the major causes of low-back pain, results from altered biosynthesis/turnover of extracellular matrix in the disc. Previously, we reported that the analgesic drug Neurotropin® (NTP) had an anabolic effect on glycosaminoglycan synthesis in cultured nucleus pulposus (NP) cells via the stimulation of chondroitin sulfate N-acetylgalactosaminyltransferase 1. However, its effect on the aggrecan core protein was not significantly detected, because of the data variance. A microarray analysis suggested that the effect of NTP on aggrecan was correlated with N-acetyltransferase 2 (NAT2), a drug-metabolizing enzyme. Specific NAT2 alleles are known to correlate with rapid, intermediate, and slow acetylation activities and side effects of various drugs. We investigated the association between the efficacy of NTP on aggrecan expression and the NAT2 genotype in cell donors.

METHODS

NP cells were isolated from intervertebral disc tissues donated by 31 Japanese patients (28-68 years) who underwent discectomy. NTP was added to the primary cell cultures and its effect on the aggrecan mRNA was analyzed using real-time quantitative PCR. To assess acetylator status, genotyping was performed based on the inferred NAT2 haplotypes of five common single-nucleotide polymorphisms using allele-specific PCR.

RESULTS

The phenotype frequencies of NAT2 in the patients were 0%, 42.0%, and 58.0% for slow, intermediate, and rapid acetylators, respectively. The proportions of responders to NTP treatment (aggrecan upregulation, ≥ 1.1-fold) in the intermediate and rapid acetylators were 76.9% and 38.9%, respectively. The odds ratio of the comparison of the intermediate acetylator status between responders and nonresponders was 5.2 (95% CI 1.06-26.0, P = 0.036), and regarding the 19 male patients, this was 14.0 (95% CI 1.54-127.2, P = 0.012). In the 12 females, the effect was not correlated with NAT2 phenotype but seemed to become weaker along with aging.

CONCLUSIONS

An intermediate acetylator status significantly favored the efficacy of NTP treatment to enhance aggrecan production in NP cells. In males, this tendency was detected with higher significance. This study provides suggestive data of the association between NAT2 variants and the efficacy of NTP treatment. Given the small sample size, results should be further confirmed.

A Chinese multicenter retrospective study of isolated increased nuchal translucency associated chromosome anomaly and prenatal diagnostic suggestions

Extensive researches involving fetuses with multiple ultrasound anomalies have been conducted over the years, but only few were focused on the isolated increased nuchal translucency (NT). On top of that, these limited number of researches were all designed as single-arm studies and the control group was missing. In this study, we conducted a multicenter, retrospective study using amniotic fluid samples collected from 1197 pregnant women having fetuses with isolated increased NT (INT group) or normal NT values (NNT group). Copy number variation sequencing (CNV-seq) was performed to determine their chromosome status and pathogenic variations were validated using SNP array. Overall, 59 chromosome aneuploidies, 34 pathogenic CNVs and 23 copy number variants of unknown significance (VOUS CNVs) were discovered. the INT group had a significantly higher proportion of aneuploidy (19.44%) and pathogenic CNV (8.33%) than the control group (3.49% and 2.30% respectively), and 88.89% of the pathogenic CNVs were related to heart defects. Additionally, more male fetuses were presented in the INT group (68.51%), but they did not have a higher risk (Relative Risk = 1.03) of carrying pathogenic chromosome variations than female fetuses. Our results demonstrated that fetuses with isolated increased NT had a distinct pattern of chromosome abnormality and majority of detected pathogenic CNVs could be linked to the congenital heart disease. Furthermore, because a considerable proportion of pathogenic CNVs were detected, we strongly recommend to perform a joint test of karyotyping and CNV analysis in prenatal diagnosis for fetuses with isolated increased NT in order to decrease the incident of missed diagnosis.