Resolving the lineage relationship between malignant cells and vascular cells in glioblastomas

Glioblastoma multiforme (GBM), a highly malignant and heterogeneous brain tumor, contains various types of tumor and non-tumor cells. Whether GBM cells can trans-differentiate into non-neural cell types, including mural cells or endothelial cells (ECs), to support tumor growth and invasion remains controversial. Here we generated two genetic GBM models de novo in immunocompetent mouse brains, mimicking essential pathological and molecular features of human GBMs. Lineage-tracing and transplantation studies demonstrated that, although blood vessels in GBM brains underwent drastic remodeling, evidence of trans-differentiation of GBM cells into vascular cells was barely detected. Intriguingly, GBM cells could promiscuously express markers for mural cells during gliomagenesis. Furthermore, single-cell RNA sequencing showed that patterns of copy number variations (CNVs) of mural cells and ECs were distinct from those of GBM cells, indicating discrete origins of GBM cells and vascular components. Importantly, single-cell CNV analysis of human GBM specimens also suggested that GBM cells and vascular cells are likely separate lineages. Rather than expansion owing to trans-differentiation, vascular cell expanded by proliferation during tumorigenesis. Therefore, cross-lineage trans-differentiation of GBM cells is very unlikely to occur during gliomagenesis. Our findings advance understanding of cell lineage dynamics during gliomagenesis, and have implications for targeted treatment of GBMs.

A case of 5p15.1-5p15.33 duplication and literature review / 中华神经科杂志

Objective:To analyze the clinical and genetic features of the children with 5p15.1-5p15.33 duplication at the end of the short arm of chromosome 5 (5p).Methods:Clinical data of a 5p15.1-5p15.33 duplicative patient diagnosed in the Department of Pediatric Intensive Care Unit of West China Second University Hospital of Sichuan University in July 2021 were collected, and the characteristics of the patients of 5p duplication syndrome reported in the literatures were summarized and analyzed.Results:The boy was 1 year and 5 months old at the time of admission. The main clinical manifestations included growth restriction and developmental delay after birth, accompanied by craniofacial deformities. At 7 months old, he was diagnosed as epilepsy due to convulsive limbs. At present, he is 2 years old, still has recurrent convulsions, can not raise his head, sit alone, crawl and talk, with hypotonia. Repeated cranial magnetic resonance imaging showed agenesis of the corpus callosum. The child′s parents had normal phenotypes. His copy number variation sequencing results showed partial overlap of chromosome 5p15.1-5p15.33 (chr5:1934522-18905656), which was determined as pathogenic copy number variation according to copy number variations evaluation criteria, and no abnormality was detected in his parents. According to the retrieval strategy set in this study, 10 literatures (all in English, reporting 17 cases) were retrieved, and a total of 22 5p duplication syndrome patients (including this case and 4 cases included in databases) were included. Seventeen of the 22 patients were younger than 14 years old with a onset age of 7 (0, 18) years, and the male to female ratio was about 1.1∶1. Among the 22 patients, craniofacial malformation was found in 19 patients, developmental disorder in 18, bone/muscle dysplasia in 15, autism in 11, attention deficit hyperactivity disorder in 9, mental retardation in 8, obesity in 5, epilepsy in 5, congenital heart dysplasia in 2, hypotonia in 4, strabismus/hyperopia in 2, and corpus callosum dysplasia, endocrine dysfunction, inguinal hernia as well as umbilical hernia in 1, respectively. There were 19 cases of multiple malformation and 3 cases of single malformation.Conclusions:5p15.1-5p15.33 duplication may be the genetic cause of this child. Facial malformation, developmental delay, skeletal/muscular dysplasia, intellectual disability, autism spectrum disorder and attention deficit hyperactivity disorder are the main clinical phenotypes of 5p copy number duplication. Corpus callosum dysplasia may be an extended phenotype of chromosome duplication at this location.

Effect of hexavalent chromium-induced ribosomal DNA copy number variation on DNA damage response in various cell lines / 预防医学

Objective@#To investigate the effect of ribosomal DNA (rDNA) copy number variation caused by hexavalent chromium exposure on DNA damage response in different cell lines, so as to provide insights into the involvement of hexavalent chromium-induced rDNA copy number variation in DNA damage responses. @*@#Methods Human lung epithelial BEAS-2B cells and human embryonic lung MRC-5 cells were treated with 2 μmol/L potassium dichromate for 24 hours, and then cells were transferred to fresh media for further incubation, while cells treated with the same volume of phosphate buffer solution served as controls. Cells treated with potassium dichromate for 24 hours, and 3 and 7 days post-detoxification, were harvested, and rDNA copy number was quantified in cells using a quantitative fluorescent real-time PCR assay. Cell cycle, apoptosis and DNA damage were detected using a Muse cell analyzer, and the DNA damage was evaluated with the proportion of ataxia telangiectasia-mutated (ATM) gene activation, proportion of double-strand DNA breaks and the percentage of the H2A.X variant histone phosphorylatio.@*@# Results The 45S and 5S rDNA copy numbers of were significantly higher in MRC-5 cells than in BEAS-2B cells [(1.54±0.26) vs. (1.02±0.18), P<0.05; (6.97±1.07) vs. (3.00±0.15), P<0.05]. The 45S rDNA copy number was lower in MRC-5 cells 3 days post-detoxification (0.80±0.04) than in controls (P<0.05), and was higher in BEAS-2B cells 3 days post-detoxification (1.43±0.07) than in controls (P<0.05) . G0/G1 phase arrest was found in MRC-5 cells 24 hours post-treatment, and the apoptotic rates were significantly higher in MRC-5 cells 3 and 7 days post-detoxification than in controls [(11.53±1.53)%, (18.33±0.70)% vs. (3.53±0.93)%, P<0.05]. The overall apoptotic rates 24 hours post-treatment and 3 days post-detoxification [(2.80±0.17)%, (3.33±0.57)% vs. (1.53±0.61)%, P<0.05], proportion of ATM gene activation 3 days post-detoxification [(3.37±0.67%) vs. (1.18±0.22)%, P<0.05], proportion of double-strand DNA breaks 3 days post-detoxification [(4.45±0.85)% vs. (0.97±0.21)%, P<0.05] and percentage of the H2A.X variant histone phosphorylation 3 days post-detoxification [(1.68±0.56)% vs. (0.29±0.06)%, P<0.05] in BEAS-2B cells were higher than in controls. @*Conclusions@#Hexavalent chromium-induced rDNA copy number variation affects DNA damage response in different cell lines. A stronger DNA damage response is found in BEAS-2B cells with a low rDNA copy number, and a relative stable response is observed in MRC-5 cells with a high rDNA copy number.

Genetic Analysis of a Chinese Pedigree with Hereditary Spherocytosis Caused by Copy Number Variation Deletion of SPTB Gene / 中国实验血液学杂志

OBJECTIVE@#To investigate the molecular mechanism of the disease based on the clinical characterization and genetic mutation analysis in a family with hereditary spherocytosis.@*METHODS@#The proband with jaundice and anemia was referred to Yidu Central Hospital of Weifang in May 2021. Peripheral blood samples were collected from six members of the family. Second-generation sequencing was used to screen the pathological mutations, and the clinically significant variant sites were selected. Then the relevant databases were used to analyze the variant sites, and RT-qPCR was used to detect the relative mRNA levels of candidate gene. The structure and function of SPTB protein were analyzed by UniProt and SMART databases.@*RESULTS@#We infer that the SPTB gene copy number variation (CNV) deletion was co-segregated with the phenotype of the patients in this family based on the results of second-generation sequencing (about 700 target genes). The UCSC Genome Browser demonstrated that the deleted region was mainly located in exon2-3 of SPTB gene. The results of RT-qPCR showed that the relative SPTB mRNA levels of all patients were lower than the healthy control. UniProt and SMART databases analysis showed that SPTB protein without CH1 and CH2 domains could not bind to erythrocyte membrane actin.@*CONCLUSION@#The CNV deletion of SPTB gene may be the reason for the hereditary spherocytosis in this family.

Effect of exposure to chrysotile on ribosomal DNA copy number variation and DNA damage response / 预防医学

Objective@#To investigate the effect of chrysotile exposure on ribosomal DNA (rDNA) copy number and DNA damage response, so as to provide insights into the mechanism of asbestos-induced carcinogenesis. @*Methods@#Human pleural mesothelial MeT-5A cells were treated with chrysotile suspensions at doses of 1.25, 2.5 and 5 μg/cm2 (low-, medium-, high-dose group), while PBS served as controls. MeT-5A cells were harvested 6, 24, 48 and 72 h post-treatment, and the rDNA copy numbers and the BIRC5, HRAS, GINS4 and RRM2 mRNA expression were determined using a quantitative real-time PCR (qPCR) assay. The apoptosis of MeT-5A cells and DNA damage were detected using Muse cell analyzer. The rDNA copy numbers, DNA damage responses and BIRC5, HRAS, GINS4 and RRM2 mRNA expression were compared in MeT-5A cells treated with different doses of chrysotile suspensions.@*Results@#There were significant differences in 45S rDNA copy numbers among low-, medium-, high-dose groups and the control groups 6, 48 and 72 h post-treatment with chrysotile suspensions, and significantly lower 45S rDNA copy numbers were measured in low-, medium- and high-dose groups than in the control group 6 h post-treatment, while significantly higher 45S rDNA copy numbers were found in the high-dose group than in low- and medium-dose groups 48 and 72 h post-treatment (all P<0.05). There were significant differences in 5S rDNA copy numbers among low-, medium-, high-dose groups and the control groups 24, 48 and 72 h post-treatment with chrysotile suspensions, and significantly lower 5S rDNA copy numbers were measured in medium- and high-dose groups than in the control group 24 and 48 h post-treatment, while significantly lower 5S rDNA copy numbers were found in medium- and high-dose groups than in the low-dose group 24, 72 h post-treatment (all P<0.05). There were significant differences in the overall apoptotic rate of MeT-5A cells among groups at different time points, and the overall apoptotic rate of MeT-5A cells were significantly higher in medium- and high-dose groups than in the control group (all P<0.05), with late-stage apoptosis predominantly detected. There were significant differences in the rates of ATM activation and DNA double-strand break in MeT-5A cells among groups 72 h post-treatment, and higher rates of ATM activation and DNA double-strand break were measured in medium- and high-dose groups than in the control group (all P<0.05). In addition, there were significant differences in the relative mRNA expression of BIRC5, HRAS, GINS4 and RRM2 genes among groups 24 and 48 h post-treatment, and significantly lower BIRC5, HRAS, GINS4 and RRM2 mRNA expression was quantified in medium- and high-dose groups than in the control group (all P<0.05).@*Conclusion@#Exposure to chrysotile may induce rDNA copy number variations and altered expression of nucleolar proteins in human pleural mesothelial cells, which may be involved in the regulation of DNA damage responses.

Parental origin of prenatally diagnosed pathogenic copy number variation in 56 pedigrees / 中华围产医学杂志

Objective:To investigate the prenatal management for pathogenic copy number variation (CNV) by analyzing the parental origin of CNV and pregnancy outcomes in 56 pedigrees.Methods:This study retrospectively analyzed the information of patients who received interventional prenatal diagnosis and chromosomal microarray analysis (CMA) at Guangzhou Women and Children's Medical Center from January 2015 to December 2020. The cases with pathogenic CNV indicated by CMA and receiving parental CMA for further verification were finally enrolled. Clinical data including prenatal diagnostic indications, chromosomal distribution of the pathogenic fragments and fragment sizes were collected and analyzed using t test. All cases were followed up by telephone and record review. Results:Fifty-six cases were included in this study. Pathogenic CNV in 13 (23.2%, 13/56) fetuses were inherited from one parent (eight from mothers and five from fathers), and mainly located in chromosomes 22 (3/13), 17 (3/11), 16 (2/7), 1 (2/4), and X (3/6) with fragment sizes all less than 3 Mb. The fragment size of inherited pathogenic CNV was significantly smaller than that of de novo CNV [1.69 (1.36-2.22) vs 7.54 (2.11-12.30) Mb, t=3.47, P=0.001]. Among the 43 cases with de novo pathogenic CNV, seven (16.3%) were lost to follow up and 35 (97.2%) terminated the pregnancy. The other one with a 0.58 Mb microruplication at 16p11.2 indicated at 37 gestational weeks gave birth to a baby weighting 2 900 g at 39 gestational weeks and no abnormalities were reported during an eight-month telephone follow-up. Two out of the 13 cases with inherited pathogenic CNV were lost to follow up and six pregnancies were terminated. The other five pregnancies were continued and babies were delivered with no abnormalities during a median follow-up period of 13 (4-15) months. Conclusion:Pathogenic CNV alone should not be the indication for pregnancy termination.

Comparative genomic analysis of esophageal squamous cell carcinoma and adenocarcinoma: New opportunities towards molecularly targeted therapy

Esophageal cancer is one of the most lethal cancers worldwide because of its rapid progression and poor prognosis. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are two major subtypes of esophageal cancer. ESCC predominantly affects African and Asian populations, which is closely related to chronic smoking and alcohol consumption. EAC typically arises in Barrett's esophagus with a predilection for Western countries. While surgical operation and chemoradiotherapy have been applied to combat this deadly cancer, molecularly targeted therapy is still at the early stages. With the development of large-scale next-generation sequencing, various genomic alterations in ESCC and EAC have been revealed and their potential roles in the initiation and progression of esophageal cancer have been studied. Potential therapeutic targets have been identified and novel approaches have been developed to combat esophageal cancer. In this review, we comprehensively analyze the genomic alterations in EAC and ESCC and summarize the potential role of the genetic alterations in the development of esophageal cancer. Progresses in the therapeutics based on the different tissue types and molecular signatures have also been reviewed and discussed.

Study on genetics and early diagnosis of early onset epileptic encephalopathy of unknown etiology / 中华实用儿科临床杂志

Objective:To explore the genetic etiology and the value of early diagnosis of early onset epileptic encephalopathy (EOEE) with unknown etiology.Methods:A total of 60 children with EOEE of unknown etiology were prospectively enrolled in the outpatient and inpatient departments of Fujian Provincial Hospital from January 2018 to January 2021.Peripheral blood was collected prospectively for whole-exome sequencing and copy number variation (CNV) detection to analyze the clinical characteristics and genetic sequencing results of the children.Results:Twenty-four patients with EOEE-related pathogenic or suspected pathogenic mutations were detected, including infantile spasms (10 cases), Dravet syndrome (3 cases), pyridoxine-dependent epilepsy (1 case) and ohtahara syndrome (1 case), and unknown epileptic encephalopathy (9 cases). The onset age of EOEE-related patients ranged from 1 day to 11 months (median age was 4.2 months), the treatment age ranged from 2 days to 4 years (median age was 10 months), and the age of diagnosis was controlled within 1 month after treatment.There were 20 cases (33.3%) single gene variants and 4 cases (6.7%) CNV variants.A total of 13 genes were involved: KCNQ2, SCN1A, SCN8A, CACNA1E, CDKL5, PPP3CA, PCDH19, TSC1, TSC2, ZEB2, ALDH7A1, DCX and HNRNPU.The 4 CNV abnormalities were 17p13.3 deletion, 11q23.3q25 deletion, 1q36.31-p36.33 deletion, 1q43-1q44 deletion and Xp22.33 duplication, respectively.Totally, 20 mutations were new loci reported for the first time at home and abroad; 11q23.3q25 deletion that resulted in infantile spasm was first reported at home and abroad.Infantile spasm caused by ZEB2 mutation and epileptic encephalopathy caused by PPP3CA gene were both reported for the first time in China. Conclusions:Gene and CNV are important potential causes of children suffering from EOEE.When the etiology is unclear, the combination of whole-exome sequencing and CNV sequencing technology can improve the diagnosis level of genetic etiology of children with EOEE.The early genetic detection of these children can early diagnose and accurately treat epilepsy.

Value of chromosomal microarray analysis for genetic evaluation of fetal ultrasound abnormality / 中国辐射卫生

Objective To evaluate the value of chromosomal microarray analysis (CMA) for genetic evaluation of fetal ultrasound abnormality. Methods A total of 180 pregnant women with fetal abnormality detected by prenatal ultrasound diagnosis in the first trimester during the period from January 2020 through May 2022 were enrolled as the study subjects. All prenatal fetal screening samples were subjected to G-band karyotyping and CMA. Results G-band karyotyping detected normal karyotypes in 168 samples (93.85%) and abnormal karyotypes in 11 samples (6.15%), and CMA detected 17 positive samples (9.44%) and 163 negative samples (90.56%). The seventeen positive samples included 11 pathogenic copy number variations (CNVs) and 6 variants of unknown significance (VOUS), and there were 11 CMA-positive results consistent with G-band karyotyping, and 6 additional pathogenic CNVs mainly included microdeletion and microduplication syndromes. The detection rates of pathogenic CNVs were 11.11%, 2.63%, 2.78%, 4.00%, 0, 0, 11.11% and 0 among the fetuses with abnormal structure of the cardiovascular system, the lymphatic system, the nervous system, the digestive system, the cranial and face system, the skeletal system, the urinary system, and other system (χ2 =8.188, P = 0.316). All eleven fetuses with pathogenic CNVs detected by CMA were all induced for abortion. Conclusion CMA improves the detection of genetic abnormality among fetuses with ultrasound abnormality in relative to G-band karyotyping, which is feasible for prenatal cytogenetic diagnosis among fetuses with ultrasound abnormality

Genetic analysis of a family with 6q22 microdeletion and 10p15.3p13 microduplication in two consecutive pregnancies / 中华检验医学杂志

Objective:Cytogenetic and molecular genetic analysis was performed on two consecutive antenatal abnormal fetuses and their parents in a family to clarify the copy number variation(CNV) and its mechanism.Methods:The karyotypes of two fetuses and their parents were analyzed by conventional karyotyping techniques, and CNVs of two fetuses and their mother were analyzed by low-coverage whole-genome copy number variation sequencing (CNV-seq) techniques.Results:The amniotic fluid karyotype results of fetus 1 and 2 were 46, XN, der(4)t(4;10)(q35;p13). The mother′s peripheral blood karyotype result was 46, XX, t(4;10)(q35;p13), and the father′s karyotype was normal. The CNV-seq results of fetus 1 and 2 were seq[hg19]6q22.31(122740000-125440000)X1; 10p15.3p13(120000-17260000)X3, suggesting that there was a heterozygous deletion of about 2 700 000 bp in fetal 6q22.31 and a duplication of about 17 140 000 bp in fetal 10p15.3p13. The CNV-seq result of their mother was seq[hg19]6q22.31(122740000-125440000)X1, suggesting that there was a heterozygous deletion of about 2 700 000 bp in 6q22.31. The pregnant woman and her family chose to terminate the pregnancy after genetic consulting.Conclusion:The combined application of karyotyping and CNV-Seq is significantly beneficial to detecting microdeletions or microduplications of fetal chromosomes and effectively preventing the birth of defective children.

Novel rearrangements between different chromosomes with direct impact on the diagnosis of 5p- syndrome

Abstract Objectives Copy Number Variations (CNVs) in the human genome account for common populational variations but can also be responsible for genetic syndromes depending on the affected region. Although a deletion in 5p is responsible for a syndrome with highly recognizable phenotypical features, other chromosomal abnormalities might overlap phenotypes, especially considering that most studies in 5p use traditional cytogenetic techniques and not molecular techniques. Methods The authors have investigated 29 patients with clinical suspicion of 5p- syndrome using Chromosomal Microarray (CMA), and have gathered information on previous tests, clinical signs, symptoms, and development of the patients. Results The results showed 23 pure terminal deletions, one interstitial deletion, one deletion followed by a 3 Mb duplication in 5p, three cases of 5p deletion concomitant to duplications larger than 20 Mb in chromosomes 2, 9, and 18, and one 5p deletion with a chromosome Y deletion. CMA showed relevant CNVs not typically associated with 5p- that may have contributed to the final phenotype in these patients. Conclusions The authors have identified three novel rearrangements between chromosomes 5 and 2 (Patient 27), 5 and 18 (Patient 11), and 5 and Y (Patient 22), with breakpoints and overlapped phenotypes that were not previously described. The authors also highlight the need for further molecular investigation using CMA, in different chromosomes beyond chromosome 5 (since those cases did not show only the typical deletion expected for the 5p- syndrome) to explain discordant chromosomal features and overlapped phenotypes to unravel the cause of the syndrome in atypical cases. HIGHLIGHTS The authors The authors have described three novel rearrangements between chromosomes 5 and 2, 5 and 18, and 5 and Y with chromosomal breakpoints and overlapped phenotypes that were not previously described. One of the main atypical features for 5p- syndrome that the authors report was the presence of seizures that was found in the three patients with rearrangements between different chromosomes and in a patient with a deletion followed by duplication in 5p. The authors suggest physicians conduct further molecular investigation in the presence of atypical clinical features for patients with 5p- syndrome suspicion.

Avances genómicos de la última década y su influencia en el enfoque diagnóstico de la discapacidad intelectual / Genomic advances in the last decade and their influence in the diagnosis of intellectual disability

RESUMEN La inteligencia humana es un rasgo poligénico (~1000 genes) con una influencia de cada gen aproximadamente ascendente al 0,1%. Es un atributo indispensable para el desarrollo personal, familiar, social y económico y tiene, además, una relación directamente proporcional al mantenimiento de la salud y a una mayor esperanza de vida. La discapacidad intelectual, consecuentemente, afecta todas estas áreas y constituye un problema de salud pública en varios países de Latinoamérica en los que exhibe una prevalencia mayor al 10%. La etiología de la discapacidad intelectual sea aislada o sindrómica, es genética hasta en un 85% de los casos; se diagnostica mediante las nuevas tecnologías de búsqueda en el genoma, tales como la secuenciación masiva y el análisis cromosómico por micromatrices. El diagnóstico etiológico de la discapacidad intelectual permite la selección de terapias específicas, la determinación del pronóstico y de riesgos de recurrencia familiar e individual.

SUMMARY Human intelligence is a polygenic trait (~1000 genes), with an approximate influence of 0.1% per every individual gen. It is an indispensable attribute for personal, familial, social, and economic development; furthermore, it is directly proportional to health maintenance and a longer life expectancy. Consequently, intellectual disability affects all these areas, and constitutes a public health problem in several Latin American countries where it shows a >10%. In ~85% of the patients, the etiology of intellectual disability, be that isolated or syndromic; it is mostly diagnosed through the new technological search studies of the genome, such as new generation sequencing and/or chromosomal microarray analysis. The clinical and etiological diagnosis of intellectual disability, when duly confirmed, allows the choice of specific treatment modalities, the precise determination of prognosis, and the estimation of individual or familial recurrence risks.

Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Copy number variations (CNVs), which can affect the role of long non-coding RNAs (lncRNAs), are important genetic changes seen in some malignant tumors. We analyzed lncRNAs with CNV to explore the relationship between lncRNAs and prognosis in bladder cancer (BLCA). Messenger RNA (mRNA) expression levels, DNA methylation, and DNA copy number data of 408 BLCA patients were subjected to integrative bioinformatics analysis. Cluster analysis was performed to obtain different subtypes and differently expressed lncRNAs and coding genes. Weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression gene and lncRNA modules. CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve. Multi-omics integration analysis revealed five prognostic lncRNAs with CNV, namely

Application of genome copy number variation sequencing combined with chromosome karyotype analysis in prenatal diagnosis / 中国医师进修杂志

Objective:To explore the application value of copy number variation sequencing(CNV-seq) combined with chromosome karyotyping technology based on next-generation sequencing technology in prenatal diagnosis.Methods:The subjects of the study were 329 pregnant women who underwent prenatal diagnosis at Dalian Municipal Women and Children′s Medical Center from January 2019 to June 2020. The amniotic fluid samples of these pregnant women were submitted for chromosome karyotype analysis, and CNV-seq testing was performed at the same time to compare the test results of the two methods.Results:A total of 53 cases of abnormal chromosomes were detected using CNV-seq combined with chromosome karyotyping technology, with an abnormal detection rate of 16.11%(53/329). Among them, 26 cases had consistent detection results, including 22 cases of aneuploidy, 2 cases of structural abnormalities and 2 cases of mosaic; CNV-seq detected 23 cases of chromosome copy number variations that were missed by karyotyping, including 17 cases of microdeletion and 6 cases of microduplication; chromosome karyotype analysis detected 4 cases of chromosome structural abnormalities that were missed by CNV-seq, including 3 cases balanced translocation and 1 case of inversion.Conclusions:CNV-seq has obvious advantages in detecting copy number variations of small fragments, which can make up for the lack of resolution of karyotyping analysis; CNV-seq combined with chromosome karyotyping analysis can improve the detection rate of abnormal chromosomes, which is important for prenatal diagnosis meaning.

Cellular mesenchymal epithelial transition (C-MET) gene copy number variation in gastric adenocarcinoma: A pilot search for new marker for targeted therapy in HER-2/neu resistance

Increasing HER-2/neu resistance in gastric carcinoma has encouraged search for new biomarkers for targeted therapy. Cellular mesenchymal epithelial transition (C-MET) is one such tyrosine kinase inhibitor proposed for personalized salvage treatment. We determined frequency of C-MET gene copy number variation (CNV) by Fluorescent in-situ hybridization (FISH) in gastric adenocarcinoma (GAC) and sought its correlation with conventional clinicopathologic parameters. Dual-coloured FISH was done on 32 GAC cases. C-MET gene and centromere 7 signals were counted under fluorescent microscope and ratio was calculated for each case. Correlation between C-MET CNV and conventional clinic-pathologic parameters was done by Fischer exact test. CNV was identified in the form of amplification and polysomy (3.1% each) and associated with poorer prognostic parameters. Our pilot study highlights limited subset of patients that may benefit from anti-C-MET-targeted therapy and thus could be a novel biomarker for targeted intervention in GAC.

Diagnosis of one case of Williams-Beuren syndrome presenting with hypothyroidism by low-coverage massively parallel CNV sequencing / 中华内分泌代谢杂志

Objective@#To explore the clinical phenotypes and the genetic causes for a 5 years old boy with unexplained growth retardation, developmental delay, special face, and hypothyroidism.@*Methods@#Routine G-banding was performed to analyze the karyotype of the patient and his parents. In addition, whole exome sequencing and low-coverage massively parallel CNV sequencing (CNV-seq) were used to determine the potentially pathogenic variants as well as the copy number variations (CNVs).@*Results@#The child′s karyotype was 46, XY, and his parents′ karyotypes were normal.However, CNV-seq identified a heterozygous deletion of 1.56 Mb on chromosome region 7q11.23 in the patient, including 24 protein-coding genes, which were associated with Williams-Beuren syndrome. His parents′ results of CNV-seq were normal, indicating a de novo CNVs.@*Conclusion@#A Williams-Beuren syndrome child presenting with hypothyroidism was diagnosed by CNV-seq, which would contribute to further understanding the clinical phenotypes and pathogenesis of this disease.

A study of susceptibility genes in rare monozygotic twins with generalized aggressive periodontitis / 口腔疾病防治

Objective@#Exploring the effects of susceptibility genes on aggressive periodontitis during its occurrence and development lays a foundation for further research on its genetic pathogenesis.@*Methods@#Medical history and clini⁃ cal indicators were collected from monozygotic twins with generalized aggressive periodontitis. Susceptibility genes were detected by polymerase chain reaction⁃restriction fragment length polymorphisms, and the exon gene components were analyzed by whole⁃exome sequencing. @*Results @#The severity of generalized aggressive periodontitis in the twins was dif⁃ ferent (P < 0.05). Florida diagnosis results showed that the younger sister’ s explored clinical depth (probing depth, PD) and clinical attachment loss (CAL) were higher than those for the elder sister, but her clinical bleeding index (bleeding on probing, BOP) was lower than that of the elder sister. In addition, their responses to periodontal basic treatment were different (P < 0.05). After treatment, the improvement of CAL and decline in BOP were more obvious in the elder sister,and the proportion of different periodontal pocket depths in the elder sister decreased after treatment, while the de⁃ crease was slighter in the younger sister. Genetic tests revealed that the twins had the same genotypes at target suscepti⁃ bility genes (IL⁃1β⁃511, IL⁃1β+3953, TNF⁃α⁃308, FcγR⁃IIIb, VDR, and ER) and differential exon gene components, and that the suspected differential genes, e.g. ZFPM1, PTH2, ZFYVE16, and LY6G6C, might be related to their pheno⁃ typic differences.@* Conclusion@#These monozygotic twins had different phenotypes of generalized aggressive periodonti⁃ tis. Their shared susceptibility genes increased the risk of disease, and their different genetic mutations affected the phe⁃ notype of the disease

Progress on Copy Number Variation and Its Application in Forensic Medicine / 法医学杂志

Recently, researches on copy number variation （CNV） have extended to every field, such as etiological exploration and precise treatment of complex diseases, as well as genetic breeding and evolution. The unique genetic characteristics of CNV have made people gradually believe that it could be used as a biological genetic marker to solve related problems. With the development of detection technology, application of CNV in forensic medicine will increase gradually. In this paper, the concept and development of CNV, as well as its application in forensic medicine are summarized, to provide new ideas for the practical application of CNV in the future.

Minor temperature shifts do not affect chromosomal ploidy but cause transcriptomic changes in Leishmania braziliensis promastigotes in vitro

BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment.

Relationship between gene copy number variation of PI3K/AKT signaling pathway and thyroid cancer: a recent advance / 中华地方病学杂志

At present,more and more studies have shown that gene copy number variation can be involved in the occurrence,development and outcome of thyroid cancer.The studies on the copy number variation of genes related to phosphatidylinositol-3 kinase/protein kinase B (PI3K/AKT) signaling pathways can serve as molecular bases for further understanding the gene map of thyroid cancer subtypes,as well as the accurate diagnosis of thyroid cancer and the development of precise molecular targeted therapy.This review summarizes recent advances on correlation between PI3K/AKT pathway-related gene copy number variation and thyroid cancer.