Genetic variation at KIT locus may predispose to melanoma

As loss of KIT frequently occurs in melanoma progression, we hypothesized that KIT is implicated in predisposition to melanoma (MM). Thus, we sequenced the KIT coding region in 112 familial MM cases and 143 matched controls and genotyped tag single‐nucleotide polymorphisms (SNPs) in two cohorts of melanoma patients and matched controls. Five rare KIT substitutions, all predicted possibly or probably deleterious, were identified in five patients, but none in controls [RR = 2.26 (1.26–2.26)]. Expressed in melanocyte lines, three substitutions inhibited KIT signaling. Comparison with exomes database (7020 alleles) confirmed a significant excess of rare deleterious KIT substitutions in patients. Additionally, a common SNP, rs2237028, was associated with MM risk, and 6 KIT variants were associated with nevus count. Our data strongly suggest that rare KIT substitutions predispose to melanoma and that common variants at KIT locus may also impact nevus count and melanoma risk.     

Mutation Analysis of the RAD51C and RAD51D Genes in High-Risk Ovarian Cancer Patients and Families from the Czech Republic

Recent studies have conferred that the RAD51C and RAD51D genes, which code for the essential proteins involved in homologous recombination, are ovarian cancer (OC) susceptibility genes that may explain genetic risks in high-risk patients. We performed a mutation analysis in 171 high-risk BRCA1 and BRCA2 negative OC patients, to evaluate the frequency of hereditary RAD51C and RAD51D variants in Czech population. The analysis involved direct sequencing, high resolution melting and multiple ligation-dependent probe analysis. We identified two (1.2%) and three (1.8%) inactivating germline mutations in both respective genes, two of which (c.379_380insG, p.P127Rfs*28 in RAD51C and c.879delG, p.C294Vfs*16 in RAD51D) were novel. Interestingly, an indicative family cancer history was not present in four carriers. Moreover, the ages at the OC diagnoses in identified mutation carriers were substantially lower than those reported in previous studies (four carriers were younger than 45 years). Further, we also described rare missense variants, two in RAD51C and one in RAD51D whose clinical significance needs to be verified. Truncating mutations and rare missense variants ascertained in OC patients were not detected in 1226 control samples. Although the cumulative frequency of RAD51C and RAD51D truncating mutations in our patients was lower than that of the BRCA1 and BRCA2 genes, it may explain OC susceptibility in approximately 3% of high-risk OC patients. Therefore, an RAD51C and RAD51D analysis should be implemented into the comprehensive multi-gene testing for high-risk OC patients, including early-onset OC patients without a family cancer history.     

High-throughput sequencing of mGluR signaling pathway genes reveals enrichment of rare variants in autism

Identification of common molecular pathways affected by genetic variation in autism is important for understanding disease pathogenesis and devising effective therapies. Here, we test the hypothesis that rare genetic variation in the metabotropic glutamate-receptor (mGluR) signaling pathway contributes to autism susceptibility. Single-nucleotide variants in genes encoding components of the mGluR signaling pathway were identified by high-throughput multiplex sequencing of pooled samples from 290 non-syndromic autism cases and 300 ethnically matched controls on two independent next-generation platforms. This analysis revealed significant enrichment of rare functional variants in the mGluR pathway in autism cases. Higher burdens of rare, potentially deleterious variants were identified in autism cases for three pathway genes previously implicated in syndromic autism spectrum disorder, TSC1, TSC2, and SHANK3, suggesting that genetic variation in these genes also contributes to risk for non-syndromic autism. In addition, our analysis identified HOMER1, which encodes a postsynaptic density-localized scaffolding protein that interacts with Shank3 to regulate mGluR activity, as a novel autism-risk gene. Rare, potentially deleterious HOMER1 variants identified uniquely in the autism population affected functionally important protein regions or regulatory sequences and co-segregated closely with autism among children of affected families. We also identified rare ASD-associated coding variants predicted to have damaging effects on components of the Ras/MAPK cascade. Collectively, these findings suggest that altered signaling downstream of mGluRs contributes to the pathogenesis of non-syndromic autism.     

An increased burden of rare exonic variants in NRXN1 microdeletion carriers is likely to enhance the penetrance for autism spectrum disorder

Autism spectrum disorder (ASD) is characterized by a complex polygenic background, but with the unique feature of a subset of cases (~15%-30%) presenting a rare large-effect variant. However, clinical interpretation in these cases is often complicated by incomplete penetrance, variable expressivity and different neurodevelopmental trajectories. NRXN1 intragenic deletions represent the prototype of such ASD-associated susceptibility variants. From chromosomal microarrays analysis of 104 ASD individuals, we identified an inherited NRXN1 deletion in a trio family. We carried out whole-exome sequencing and deep sequencing of mitochondrial DNA (mtDNA) in this family, to evaluate the burden of rare variants which may contribute to the phenotypic outcome in NRXN1 deletion carriers. We identified an increased burden of exonic rare variants in the ASD child compared to the unaffected NRXN1 deletion-transmitting mother, which remains significant if we restrict the analysis to potentially deleterious rare variants only (P = 6.07 × 10⁻⁵). We also detected significant interaction enrichment among genes with damaging variants in the proband, suggesting that additional rare variants in interacting genes collectively contribute to cross the liability threshold for ASD. Finally, the proband's mtDNA presented five low-level heteroplasmic mtDNA variants that were absent in the mother, and two maternally inherited variants with increased heteroplasmic load. This study underlines the importance of a comprehensive assessment of the genomic background in carriers of large-effect variants, as penetrance modulation by additional interacting rare variants to might represent a widespread mechanism in neurodevelopmental disorders.     

Endothelin 1 gene as a modifier in dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is a myocardial disease of unknown etiology with left ventricular dilatation and impaired myocardial contractility leading to heart failure. It is considered to be a multifactorial disorder with the interplay of both genetic and environmental factors. One of the possible genes implicated in DCM is endothelin 1 (EDN1). The genetic variants of EDN1 may be involved in the pathophysiology of DCM hence the entire EDN1 gene was screened to examine for the possible genotypic associations with DCM. A total of 115 DCM patients and 250 control subjects were included in the present study. PCR based SSCP analysis was carried out followed by commercial sequencing. Screening of EDN1 revealed two common and two rare polymorphisms. Allelic and genotypic frequencies were estimated in patient and control groups by appropriate statistical tests. The heterozygotes of insertion variation (+ 138A) were found to exhibit four-fold increase risk to DCM (OR = 4.12, 95% CI 2.10–8.08; p = 0.0001). The two rare variants (G>A transition (rs150035515) at c.90 and C>T transition (rs149399492) at c.119) observed in the present study were found to be unique in DCM. The secondary mRNA structures of these variations were found to have less free energy than wild type. The haplotype analysis revealed 4A–T to be risk haplotype for DCM (OR 5.90, 95% CI 2.29–15.25, p = 0.0001). In conclusion, EDN1 polymorphisms (+ 138A, A30A, T40I) appear to play a significant role in the pathogenesis of DCM, as they influence the stability of protein. The increased EDN1 production may lead to constriction of coronary arteries, reducing coronary blood flow which may in turn increase the load on left ventricle, impairing contractility of the heart resulting in a DCM phenotype, an end stage of heart failure.     

Five reasons why inbreeding may have considerable effect on post-reproductive human health

As the genetic architecture of common complex diseases of late onset is emerging through intensive research, it is intriguing to assess the predicted effect of inbreeding on those diseases. In this paper, we propose five reasons why we believe inbreeding may have a considerable effect on post-reproductive human health. (i) The joint effect of inbreeding depression on all polygenic quantitative phenotypes that confer risk for late-onset diseases is predicted to be multiplicative rather than additive. (ii) The "genetic load" of rare "Mendelian" variants with large deleterious effects in post-reproductive adults is unknown, but could be much greater than expected as these variants were invisible to selection through human history. (iii) Deleterious effects resulting from autozygosity in hundreds of affected rare recessive variants of small effect under common disease/rare variant (CD/RV) hypothesis could result in epistatic effects that could jointly impair capacity to compensate against environmental risks. (iv) Heterozygote advantage in loci under balancing selection could be reduced by inbreeding. (v) Published empirical evidence in animals and humans consistently report large inbreeding effects on late-onset traits. Since inbreeding is common in many populations and the effects of inbreeding depression could substantially contribute to disease burden and reduced life expectancy we believe there is now a clear need for further genetic epidemiological research in humans to investigate this issue.     

De novo <Emphasis Type="Italic">RRAGC</Emphasis> mutation activates mTORC1 signaling in syndromic fetal dilated cardiomyopathy

Idiopathic dilated cardiomyopathy (DCM) is a heritable, genetically heterogeneous disorder with variable age-dependent penetrance. We sought to identify the genetic underpinnings of syndromic, sporadic DCM in a newborn female diagnosed in utero. Postnatal evaluation revealed ventricular dilation and systolic dysfunction, bilateral cataracts, and mild facial dysmorphisms. Comprehensive metabolic and genetic testing, including chromosomal microarray, mitochondrial DNA and targeted RASopathy gene sequencing, and clinical whole exome sequencing for known cardiomyopathy genes was non-diagnostic. Following exclusion of asymptomatic DCM in the parents, trio-based whole exome sequencing was carried out on a research basis, filtering for rare, predicted deleterious de novo and recessive variants. An unreported de novo S75Y mutation was discovered in RRAGC, encoding Ras-related GTP binding C, an essential GTPase in nutrient-activated mechanistic target of rapamycin complex 1 (mTORC1) signaling. In silico protein modeling and molecular dynamics simulation predicted the mutation to disrupt ligand interactions and increase the GDP-bound state. Overexpression of RagC^S75Y rendered AD293 cells partially insensitive to amino acid deprivation, resulting in increased mTORC1 signaling compared to wild-type RagC. These findings implicate mTORC1 dysregulation through a gain-of-function mutation in RagC as a novel molecular basis for syndromic forms of pediatric heart failure, and expand genotype–phenotype correlation in RASopathy-related syndromes.     

Increased variation in mtDNA in patients with familial sensorineural hearing impairment

Analyses of mitochondrial DNA (mtDNA) sequences have revealed non-neutral patterns, suggesting that many amino acid mutations in animal mtDNA may be mildly deleterious, but this has not been verified in human clinical series. Since sensorineural hearing impairment (SNHI) is a common manifestation in many of the syndromes caused by mutations in mtDNA, this may be regarded as the phenotype of choice in attempts to detect mutations that may have a mildly deleterious effect on mitochondrial function. We selected 32 subjects from among 117 unrelated SNHI patients with SNHI in maternal relatives by means of family history, determined the entire coding region sequence of mtDNA and compared the sequence variation with that in 32 haplogroup-matched controls taken at random from 192 Finnish sequences. The 32 control sequences differed from the remaining 160 sequences by 36±9 substitutions (mean ± SD), while the difference for the 32 patients was 58±4 substitutions (P=0.005 for difference; Wilcoxon signed rank test). Differences were also found in the number of new haplotypes and new non-synonymous mutations or mutations in tRNA or rRNA genes. A total of 12 rare mtDNA variants were detected in the patients, and only 3 of these were considered to be neutral in effect. It is proposed that increased sequence variation in mtDNA may be a genetic risk factor for SNHI, and the increased frequency of rare haplotypes in these patients points to the presence of mildly deleterious mutations in mtDNA.     

Combined effects of the angiogenic genes polymorphisms on prostate cancer susceptibility and aggressiveness

The single-gene approaches in association studies of polygenic diseases are likely to provide limited value in predicting risk. The combined analysis of genetic variants that interact in the same pathway may amplify the effects of individual polymorphisms and enhance the predictive power. To evaluate higher order gene–gene interaction, we have examined the contribution of four angiogenic gene polymorphisms (VEGF-1154G/A; VEGF-634G/C; MMP9-1562C/T and TSP1-8831A/G) in combination to the risk of prostate cancer. For the combined analysis of VEGF and MMP9 SNPs, we found a significant gene–dosage effect for increasing numbers of potential high-risk genotypes. Compared to referent group (low-risk genotypes), individuals with one (OR = 2.79, P = 0.1), two (OR = 4.57, P = 0.02) and three high-risk genotypes (OR = 7.11, P = 0.01) had increasingly elevated risks of prostate cancer. Similarly, gene–gene interaction of VEGF and TSP1 polymorphisms increased risk of prostate cancer in additive manner (OR = 6.00, P = 0.03), although the TSP1 polymorphism itself was not associated with the risk. In addition, we examined the synergistic effect of these polymorphisms in relation to prostate cancer prognosis according to histopathological grade and clinical stage at diagnosis. Cross-classified analysis revealed potential higher order gene–gene interactions between VEGF and TSP1 polymorphisms in increasing the risk of developing an aggressive phenotype disease. Patients carrying three high-risk genotypes showed a 20-fold increased risk of high-grade tumor (OR = 20.75, P = 0.002). These results suggest that the gene–gene interaction of angiogenic gene polymorphisms’ increased risk of prostate cancer onset and aggressiveness.     

Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy

Dilated cardiomyopathy commonly causes heart failure and is the most frequent precipitating cause of heart transplantation. Familial dilated cardiomyopathy has been shown to be caused by rare variant mutations in more than 30 genes but only ~35% of its genetic cause has been identified, principally by using linkage-based or candidate gene discovery approaches. In a multigenerational family with autosomal dominant transmission, we employed whole-exome sequencing in a proband and three of his affected family members, and genome-wide copy number variation in the proband and his affected father and unaffected mother. Exome sequencing identified 428 single point variants resulting in missense, nonsense, or splice site changes. Genome-wide copy number analysis identified 51 insertion deletions and 440 copy number variants > 1 kb. Of these, a 8733 bp deletion, encompassing exon 4 of the heat shock protein cochaperone BCL2-associated athanogene 3 (BAG3), was found in seven affected family members and was absent in 355 controls. To establish the relevance of variants in this protein class in genetic DCM, we sequenced the coding exons in BAG3 in 311 other unrelated DCM probands and identified one frameshift, two nonsense, and four missense rare variants absent in 355 control DNAs, four of which were familial and segregated with disease. Knockdown of bag3 in a zebrafish model recapitulated DCM and heart failure. We conclude that new comprehensive genomic approaches have identified rare variants in BAG3 as causative of DCM.     

Germline mutations of the adenomatous polyposis coli (APC) gene in Algerian familial adenomatous polyposis cohort: first report

Background

Familial adenomatous polyposis (known also as classical or severe FAP) is a rare autosomal dominant colorectal cancer predisposition syndrome, characterized by the presence of hundreds to thousands of adenomatous polyps in the colon and rectum from an early age. In the absence of prophylactic surgery, colorectal cancer (CRC) is the inevitable consequence of FAP. The vast majority of FAP is caused by germline mutations in the adenomatous polyposis coli (APC) tumor suppressor gene (5q21). To date, most of the germline mutations in classical FAP result in truncation of the APC protein and 60% are mainly located within exon 15.

Material and methods

In this first nationwide study, we investigated the clinical and genetic features of 52 unrelated Algerian FAP families. We screened by PCR-direct sequencing the entire exon 15 of APC gene in 50 families and two families have been analyzed by NGS using a cancer panel of 30 hereditary cancer genes.

Results

Among 52 FAP index cases, 36 had 100 or more than 100 polyps, 37 had strong family history of FAP, 5 developed desmoids tumors, 15 had extra colonic manifestations and 21 had colorectal cancer. We detected 13 distinct germline mutations in 17 FAP families. Interestingly, 4 novel APC germline pathogenic variants never described before have been identified in our study.

Conclusions

The accumulating knowledge about the prevalence and nature of APC variants in Algerian population will contribute in the near future to the implementation of genetic testing and counseling for FAP patients.

     

Construction of a prognostic signature in Ewing's sarcoma: Based on metabolism-related genes

ObjectiveBy combining the expression profiles of metabolism-related genes (MRGS) with clinical information, the expression quantities of MRGS and the influence on development and prognosis were systematically analyzed, so as to provide a theoretical basis for the clinical study on the prognosis of Ewing's sarcoma.MethodsMRGs expression profiles of 64 patients with Ewing's sarcoma were obtained from GEO dataset. Univariate Cox regression analysis was used to identify metabolization-related differentially expressed genes (DEGs) related with prognosis in Ewing's sarcoma patients. Then, multivariate Cox analysis was used to calculate novel prognostic markers based on metabolism-related DEGs. Besides, We validate the model using ICGC datasets. Finally, the new prognostic index was verified on the basis of the prognostic models.ResultsMultivariate Cox regression analysis identified 74 metabolization-related DEGs, 25 of which were associated with Ewing's sarcoma patients' overall survival. Subsequently, we used 25 DEGs to construct metabolism-related prognostic signature for patients with Ewing's sarcoma. Based on the 18 DEGs regression coefficient, we propose the formula of each patient's risk score, and then divided the patients into high-risk group and low-risk group. The results indicated that the survival rate and survival time were higher in the low-risk group and lower in the high-risk group. Multivariate Cox analysis showed that risk score index was an independent prognostic factor for Ewing's sarcoma.ConclusionThe experimental results suggest that the 18 metabolism-related DEGs marker may be effective in predicting the prognosis of Ewing's sarcoma to some extent, helping to individualize treatment of patients at different risks.     

Gemcabene,a first-in-class lipid-lowering agent in late-stage development,down-regulates acute-phase C-reactive protein via C/EBP-δ-mediated transcriptional mechanism

The marked clinical and genetic heterogeneity seen in hypertrophic (HCM) and dilated cardiomyopathies (DCM) suggests involvement of disease modifiers and environmental factors in the pathophysiology of these diseases. In the current study, we examined association of single nucleotide polymorphisms (SNPs) of three candidate genes, ACE2 (rs6632677), TNNI3K (rs49812611) and CALM3 (rs13477425) with clinical phenotypes of HCM and DCM patients of North Indian ethnicity. Prevalence of ACE2 (7160726 C>G) variant genotypes (CG and GG) was significantly higher in DCM subjects as compared to controls. Prevalence of TNNI3K (3784 C>T) and CALM3 (?34T>A) variant homozygous genotype were significantly higher in HCM and DCM subjects as compared to controls. DCM patients with CT genotype showed significant decrease in LVEF as compared to CC genotype (p < 0.03). There was significant gene–gene interaction between these SNPs and three-way SNP combination of ACE2 C>G, TNN13K C>T, CALM3 A>T gene variants and was associated with high risk of HCM and DCM. Presence of ACE2 (7160726 C>G) and CALM3 (?34T>A) variant genotypes in HCM Patients with mutations (sarcomeric or non sarcomeric genes) was associated with increased mean septal thickness, further suggesting a role of these gene variants in modifying disease phenotype. Our results suggest that ACE2, TNNI3K and CALM3 polymorphisms are associated with increased risk of HCM and DCM and may act as disease modifiers of these diseases.     

Rare BRCA1 haplotypes including 3’UTR SNPs associated with breast cancer risk

Genetic markers identifying women at an increased risk of developing breast cancer exist, yet the majority of inherited risk remains elusive. While numerous BRCA1 coding sequence mutations are associated with breast cancer risk, BRCA1 mutations account for less then 5% of breast cancer risk. Since 3' untranslated region (3'UTR) polymorphisms disrupting microRNA (miRNA) binding can be functional and can act as genetic markers of cancer risk, we tested the hypothesis that such polymorphisms in the 3'UTR of BRCA1 and haplotypes containing these functional polymorphisms may be associated with breast cancer risk. We sequenced the BRCA1 3'UTR from breast cancer patients to identify miRNA disrupting polymorphisms. We further evaluated haplotypes of this region including the identified 3'UTR variants in a large population of controls and breast cancer patients (n=221) with known breast cancer subtypes and ethnicities. We identified three 3'UTR variants in BRCA1 that are polymorphic in breast cancer populations, and haplotype analysis including these variants revealed that breast cancer patients harbor five rare haplotypes not generally found among controls (9.50% for breast cancer chromosomes, 0.11% for control chromosomes, p=0.0001). Three of these rare haplotypes contain the rs8176318 BRCA1 3'UTR functional variant. These haplotypes are not biomarkers for BRCA1 coding mutations, as they are found rarely in BRCA1 mutant breast cancer patients (1/129 patients= 0.78%). These rare BRCA1 haplotypes and 3'UTR SNPs may represent new genetic markers of breast cancer risk.     

滇池中溶藻细菌的分离鉴定及其溶藻效应

【背景】藻类水华或赤潮在世界范围内频发,带来各种危害,亟需找到有效途径控制水华或赤潮。溶藻细菌具有杀死藻类控制藻类生物量的能力,可以作为防治水华和赤潮的有效工具。【目的】分离并鉴定滇池中的铜绿微囊藻(Microcystisaeruginosa)及其溶藻细菌,对溶藻菌作用于铜绿微囊藻的溶藻效应进行研究,初步了解其溶藻特性与溶藻机制。【方法】采用LB平板稀释涂布,再经多次划线分离纯化细菌,测定16SrRNA基因序列以鉴定细菌种类;采用毛细管分离的方法分离铜绿微囊藻,并测定其cpcBA基因序列以鉴定蓝藻种类;采用热乙醇法提取叶绿素a,从而计算溶藻效率;基于过氧化氢酶(CAT)、还原型谷胱甘肽(GSH)和丙二醛(MDA)探究藻细胞在溶藻菌处理下的抗氧化系统响应。【结果】共分离获得11株微囊藻和17株针对铜绿微囊藻的高效溶藻菌。选取其中一株生长速度最快的铜绿微囊藻DCM4和一株溶藻效果最好的溶藻菌Sp37 (Bacillus siamensis)进行后续研究。Sp37对DCM4的4 d溶藻率达到92.4%±1.5%,且对微囊藻属的水华微囊藻(M. flos-aquae)和惠氏微囊藻(M.wesenbergii)均有溶藻效果,而对绿藻没有溶藻效果。Sp37的原菌液和无菌滤液对DCM4的4d溶藻率分别为86.8%±4.3%和81.1%±2.2%,两者没有显著差异(P0.05)。Sp37菌体对DCM4的溶藻率为25.4%±7.3%。Sp37无菌滤液经不同温度和pH处理之后的溶藻率与未经处理的无菌滤液的溶藻率无明显差异。Sp37无菌滤液处理藻细胞会使藻细胞的CAT、GSH和MDA含量发生变化。【结论】菌株Sp37对铜绿微囊藻DCM4具有高效的溶藻作用,而且对微囊藻属具有一定的溶藻特异性。Sp37是通过分泌胞外物质间接溶藻,且溶藻物质具有热稳定性和酸碱稳定性。Sp37无菌滤液处理藻细胞会触发藻细胞抗氧化系统,并且会损伤藻细胞膜。Sp37无菌滤液很可能是通过对藻细胞造成氧化胁迫,最终导致藻细胞死亡的。     

Radiation dose and cancer risks from radiation exposure during abdominopelvic computed tomography (CT) scans: comparison of diagnostic and radiotherapy treatment planning CT scans

In the present study, radiation doses and cancer risks resulting from abdominopelvic radiotherapy planning computed tomography (RP-CT) and abdominopelvic diagnostic CT (DG-CT) examinations are compared. Two groups of patients who underwent abdominopelvic CT scans with RP-CT (n = 50) and DG-CT (n = 50) voluntarily participated in this study. The two groups of patients had approximately similar demographic features including mass, height, body mass index, sex, and age. Radiation dose parameters included CTDI_vol, dose–length product, scan length, effective tube current, and pitch factor, all taken from the CT scanner console. The ImPACT software was used to calculate the patient-specific radiation doses. The risks of cancer incidence and mortality were estimated based on the BEIR VII report of the US National Research Council. In the RP-CT group, the mean ± standard deviation of cancer incidence risk for all cancers, leukemia, and all solid cancers was 621.58 ± 214.76, 101.59 ± 27.15, and 516.60 ± 189.01 cancers per 100,000 individuals, respectively, for male patients. For female patients, the corresponding risks were 742.71 ± 292.35, 74.26 ± 20.26, and 667.03 ± 275.67 cancers per 100,000 individuals, respectively. In contrast, for DG-CT cancer incidence risks were 470.22 ± 170.07, 78.23 ± 18.22, and 390.25 ± 152.82 cancers per 100,000 individuals for male patients, while they were 638.65 ± 232.93, 62.14 ± 13.74, and 575.73 ± 221.21 cancers per 100,000 individuals for female patients. Cancer incidence and mortality risks were greater for RP-CT than for DG-CT scans. It is concluded that the various protocols of abdominopelvic CT scans, especially the RP-CT scans, should be optimized with respect to the radiation doses associated with these scans.

     

Development and Validation of a DNA Methylation-related Classifier of Circulating Tumour Cells to Predict Prognosis and to provide a therapeutic strategy in Lung Adenocarcinoma

Background: A significant factor influencing the prognosis of lung adenocarcinoma (LUAD) is tumor metastasis. Studies have shown that abnormal DNA methylation in circulating tumor cells (CTCs) is associated with tumour metastasis. Based on the genes expressed in CTCs that play an important role in DNA methylation, we hope to build a risk model to predict prognosis and provide a therapeutic strategy in LUAD.Methods: The CTC sequencing data for LUAD were obtained from {"type":"entrez-geo","attrs":{"text":"GSE74639","term_id":"74639"}}GSE74639, which contains 10 CTC samples and 6 primary tumour samples. To carefully assess the clinical value, functional status, involvement of the tumor microenvironment (TME) based on the risk model, and genetic variants based on based on data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), a reliable risk model was successfully built.Results: Three differentially methylated genes (DMGs) of CTCs for LUAD, including mitochondrial ribosomal protein L51 (MRPL51), STE20-like kinase (SLK), and protein regulator of cytokinesis 1(PRC1), were effectively used to construct a risk model. Both the training and validation cohorts'' stability and accuracy of the risk model were evaluated. Each patient in the TCGA-LUAD cohort received a risk score, and based on the median score, they were divided into high- and low-risk groups. The tumors in the high-risk group in this study were classified as "cold" and immunosuppressed, which may be linked to a poor prognosis. The tumors in the low-risk group, however, were deemed "hot" and had immune hyperfunction linked to a positive prognosis. Additionally, patients in the low-risk group showed greater sensitivity to immunotherapy than those in the high-risk group.Conclusions: Based on DMGs of CTCs from LUAD, we successfully developed a predictive risk model and discovered differences in biological function, TME, genetic variation, and clinical outcomes between those at high and low risk group.     

Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such putative mutations was larger than has been previously reported; this yield was in part due to the comprehensive and uniform coverage afforded by WGS. Deleterious variants were found in four unrecognized, nine known, and eight candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to FMR1, which is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.     

有核红细胞数在白血病患者危险度分层评估中的意义

摘要 目的：探讨有核红细胞数(nucleated red blood cell count,NRBCs)在白血病患者危险度分层评估中的意义。方法：选择2016年2月到2019年7月在厦门大学附属成功医院(本院)诊治的急性髓系白血病(Acute myeloid leukemia,AML)患者120例,检测其NRBCs并进行危险度分层,回顾分析患者的临床资料并与其NRBCs进行相关性分析。结果：120例患者中,危险度分层为低危40例,中危60例,高危20例。低危组和中高危组的患者年龄、性别、核仁磷酸蛋白(nucleophosmin,NPM1)突变、骨髓原始细胞等对比差异无统计学意义(P>0.05),其外周血原始细胞、FMS 样酪氨酸激酶-3(FMS-like tyrosinekinase 3,FLT3)突变、急性生理和慢性健康状况Ⅱ(acute physiology andchron ic health evaluationⅡ,APACHEⅡ)评分、白细胞（white blood cell,WBC）、血红蛋白（hemoglobin,Hb）、血小板（platelet,PLT） 、白蛋白（albumin,ALB）与丙氨酸氨基转移酶（alanine aminotransferase,ALT）值等对比差异有统计学意义(P<0.05)。低危组的NRBCs为3.94±0.29个,显著低于中高危组(11.87±2.11个,P=0.000)。Pearson相关分析显示危险度分层与NRBCs、外周血原始细胞、APACHEⅡ评分、FLT3突变、PLT有显著相关性(r=0.823、0.566、0.494、0.578、0.781,P<0.05)。logistic回归分析显示NRBCs、外周血原始细胞、APACHEⅡ评分、FLT3突变、PLT为影响急性髓系白血病患者危险度分层的主要因素(P<0.05)。结论：不同危险度分层的白血病患者的NRBCs具有显著差异,其与患者的病理特征显著相关,也是影响患者危险度分层的主要因素。     

α-Synuclein genetic variants predict faster motor symptom progression in idiopathic Parkinson disease

Currently, there are no reported genetic predictors of motor symptom progression in Parkinson's disease (PD). In familial PD, disease severity is associated with higher α-synuclein (SNCA) expression levels, and in postmortem studies expression varies with SNCA genetic variants. Furthermore, SNCA is a well-known risk factor for PD occurrence. We recruited Parkinson's patients from the communities of three central California counties to investigate the influence of SNCA genetic variants on motor symptom progression in idiopathic PD. We repeatedly assessed this cohort of patients over an average of 5.1 years for motor symptom changes employing the Unified Parkinson's Disease Rating Scale (UPDRS). Of 363 population-based incident PD cases diagnosed less than 3 years from baseline assessment, 242 cases were successfully re-contacted and 233 were re-examined at least once. Of subjects lost to follow-up, 69% were due to death. Adjusting for covariates, risk of faster decline of motor function as measured by annual increase in motor UPDRS exam score was increased 4-fold in carriers of the REP1 263bp promoter variant (OR 4.03, 95%CI:1.57-10.4). Our data also suggest a contribution to increased risk by the G-allele for rs356165 (OR 1.66; 95%CI:0.96-2.88), and we observed a strong trend across categories when both genetic variants were considered (p for trend = 0.002). Our population-based study has demonstrated that SNCA variants are strong predictors of faster motor decline in idiopathic PD. SNCA may be a promising target for therapies and may help identify patients who will benefit most from early interventions. This is the first study to link SNCA to motor symptom decline in a longitudinal progression study.