Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characteri...Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characterized by epigenetic reprogramming,while intergenerational and transgenerational epigenetic inheritance can influence the offspring’s development through the transmission of epigenetic features to the offspring via the germline.Therefore,the selec-tion of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers.We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.展开更多
BACKGROUND The molecular changes present in gastric neuroendocrine tumors(NETs)include a loss of heterozygosity or mutation of MEN1,CDKN1B gene mutation,P27 heterozygous mutation,and ATP4A gene missense mutation.We id...BACKGROUND The molecular changes present in gastric neuroendocrine tumors(NETs)include a loss of heterozygosity or mutation of MEN1,CDKN1B gene mutation,P27 heterozygous mutation,and ATP4A gene missense mutation.We identified and are the first to report a case of type 1 histamine-producing enterochromaffin-like cell NETs(ECL-cell NETs)with a BRCA2 gene germline mutation.CASE SUMMARY The patient had a history of iron-deficient anemia for 5 years,and gastroscopic examination indicated multiple gastric tumors.Then,the patient underwent distal gastrectomy.Microscopically,multifocal tumor cells were found in the mucosa and submucosa;tumor cells were organoid and arranged in nests and cords,and the stroma was rich in sinusoids.The surrounding gastric mucosa showed atrophy with mild intestinal metaplasia or pseudopyloric gland metaplasia.Neuroendocrine cells could be seen with diffuse linear,nodular,and adenomatous hyperplasia.Immunohistochemically,the tumor cells diffusely expressed cytokeratin,chromogranin,synaptophysin,and CD56.Whole-genome highthroughput molecular sequencing revealed a pathogenic germline mutation in the BRCA2 gene,a heterozygous germline frameshift mutation in exon 11,c.6443_6444del(p.S2148Yfs*2).The final diagnosis was gastric type 1 ECL-cell NETs with a BRCA2 gene germline mutation,accompanied by autoimmune gastritis.CONCLUSION This is the first report of a case of type 1 gastric ECL-cell NETs with a pathogenic germline mutation of the BRCA2 gene.The findings of this report will expand the germline mutation spectrum of gastric NETs and increase the understanding of the molecular changes present in these tumors for their improved diagnosis in the future.展开更多
Objective: Germline alterations in the breast cancer susceptibility genes type 1 and 2, BRCA1 and BRCA2, predispose individuals to hereditary cancers, including breast, ovarian, prostate, pancreatic, and stomach cance...Objective: Germline alterations in the breast cancer susceptibility genes type 1 and 2, BRCA1 and BRCA2, predispose individuals to hereditary cancers, including breast, ovarian, prostate, pancreatic, and stomach cancers.Accumulating evidence suggests inherited genetic susceptibility to lung cancer.The present study aimed to survey the prevalence of pathogenic germline BRCA mutations(gBRCAm) and explore the potential association between gBRCAm and disease onset in Chinese advanced non-small cell lung cancer(NSCLC) patients.Methods: A total of 6,220 NSCLC patients were screened using capture-based ultra-deep targeted sequencing to identify patients harboring germline BRCA1/2 mutations.Results: Out of the 6,220 patients screened, 1.03%(64/6,220) of the patients harbored the pathogenic gB RCAm, with BRCA2 mutations being the most predominant mutations(49/64, 76.5%).Patients who developed NSCLC before 50 years of age were more likely to carry gBRCAm(P = 0.036).Among the patients harboring classic lung cancer driver mutations, those with concurrent gBRCAm were significantly younger than those harboring the wild-type gBRCA(P = 0.029).By contrast, the age of patients with or without concurrent gBRCAm was comparable to those of patients without the driver mutations(P = 0.972).In addition, we identified EGFR-mutant patients with concurrent gBRCAm who showed comparable progression-free survival but significantly longer overall survival(P = 0.002) compared to EGFR-mutant patients with wild-type germline BRCA.Conclusions: Overall, our study is the largest survey of the prevalence of pathogenic gBRCAm in advanced Chinese NSCLC patients.Results suggested a lack of association between germline BRCA status and treatment outcome of EGFR-TKI.In addition,results showed a positive correlation between pathogenic gB RCAm and an early onset of NSCLC.展开更多
AIM: To explore germline hypermethylation of the tumor suppressor genes MLH1, CDH1 and P16INK4a in suspected cases of hereditary gastric cancer (GC). METHODS: A group of 140 Chinese GC patients in whom the primary can...AIM: To explore germline hypermethylation of the tumor suppressor genes MLH1, CDH1 and P16INK4a in suspected cases of hereditary gastric cancer (GC). METHODS: A group of 140 Chinese GC patients in whom the primary cancer had developed before the age of 60 or who had a familial history of cancer were screened for germline hypermethylation of the MLH1, CDH1 and P16INK4a tumor suppressor genes. GenomicDNA was extracted from peripheral blood leukocytes and modified by sodium bisulfite. The treated DNA was then subjected to bisulfi te DNA sequencing for a specif ic region of the MLH1 promoter. The methylation status of CDH1 or P16INK4a was assayed using methylation-specif ic PCR. Clonal bisulf ite allelic sequencing in positive samples was performed to obtain a comprehensive analysis of the CpG island methylation status of these promoter regions. RESULTS: Methylation of the MLH1 gene promoter was detected in the peripheral blood DNA of only 1/140 (0.7%) of the GC patient group. However, this methylation pattern was mosaic rather than the allelic pattern which has previously been reported for MLH1 in hereditary non-polyposis colorectal cancer (HNPCC) patients. We found that 10% of the MLH1 alleles in the peripheral blood DNA of this patient were methylated, consistent with 20% of cells having one methylated allele. No germline promoter methylation of the CDH1 or P16INK4a genes was detected. CONCLUSION: Mosaic germline epimutation of the MLH1 gene is present in suspected hereditary GC patients in China but at a very low level. Germline epimutation of the CDH1 or P16INK4a gene is not a frequent event.展开更多
Double sex and mab-3-related transcription factor 1(Dmrt1),which is expressed in goat male germline stem cells(mGSCs)and Sertoli cells,is one of the most conserved transcription factors involved in sex determination.I...Double sex and mab-3-related transcription factor 1(Dmrt1),which is expressed in goat male germline stem cells(mGSCs)and Sertoli cells,is one of the most conserved transcription factors involved in sex determination.In this study,we highlighted the role of Dmrt1 in balancing the innate immune response in goat mGSCs.Dmrt1 recruited promyelocytic leukemia zinc finger(Plzf),also known as zinc finger and BTB domain-containing protein 16(Zbtb16),to repress the Toll-like receptor 4(TLR4)-dependent inflammatory signaling pathway and nuclear factor(NF)-κB.Knockdown of Dmrt1 in seminiferous tubules resulted in widespread degeneration of germ and somatic cells,while the expression of proinflammatory factors were significantly enhanced.We also demonstrated that Dmrt1 stimulated proliferation of mGSCs,but repressed apoptosis caused by the immune response.Thus,Dmrt1 is sufficient to reduce inflammation in the testes,thereby establishing the stability of spermatogenesis and the testicular microenvironment.展开更多
AIM:To give a comprehensive report of E-cadheringene (CDH1) variations in a population at a high risk for gastric cancer (GC).METHODS:The samples consisted of 178 men and 58 women with a mean age of 62.3 ± 9.4 ye...AIM:To give a comprehensive report of E-cadheringene (CDH1) variations in a population at a high risk for gastric cancer (GC).METHODS:The samples consisted of 178 men and 58 women with a mean age of 62.3 ± 9.4 years and an age range of 30-84 years.A total of 240 cancerfree controls were recruited (mean age of 61.8 ± 10.1 years,age range of 26-82 years).Samples were screened for CDH1 germline mutations by high-resolution melting analysis or directly sequencing.Luciferase reporter assay,RNA splicing assay and bioinformatic analysis were used to evaluate the effect of mutations.RESULTS:Four novel CDH1 sequence alterations were identified in GC patients including a G>T transition 49 bp before the start codon;a three-nucleotide deletion,c.44_46del TGC;one missense mutation,c.604G>A (V202I);and one variation in the intron,c.1320+7A>G.In addition,polymorphism frequencies were observed for CDH1-164delT,-161C>A,-73A>C,c.48+6C>T,c.48+62_48+63delinsCGTGCCCCAGCCC,c.894C>T (A298A),c.1224G>A (A408A),c.1888C>G (L630V),c.2076T>C (A692A),and c.2253C>T (N751N) which is similar to the data reported in http://www.ncbi.nlm.nih.gov/projects/SNP/.RNA splicing analysis suggested that the c.1320+7A>G and c.1224G>A variations did not affect exon splicing ability.Luciferase reporter assay demonstrated that the c.-49T variation might be helpful for E-cadherin transcription,though the increase in transcription activity is limited (only 33%).SIFT score and PolyPhen analysis both demonstrated that the L630V missense mutation probably damages protein function,while the V202I variant does not.CONCLUSION:This study reveals novel mutations in sporadic GC patients which had been poorly investigated for susceptibility genes.展开更多
Familial gastrointestinal stromal tumor(GIST) is a rare autosomal dominant disorder associated with mutations in the KIT gene in the majority of cases. Although, exon 11 appears to be the hot spot region for approxima...Familial gastrointestinal stromal tumor(GIST) is a rare autosomal dominant disorder associated with mutations in the KIT gene in the majority of cases. Although, exon 11 appears to be the hot spot region for approximately 95% of germline mutations, pathogenic variations have also been identified in exon 8, 13 and 17. Exon 13 germline mutations are extremely rare amongst familial GISTs and seven families with a germline mutation have been reported to date. Moreover, the role of imatinib mesylate in this rare familiar settings is not completely known so far. We describe here clinical, imaging, pathological and genetic findings of a family with four affected members; grandmother, his son and two grand-sons having a germline gain-of-function mutation of KIT in exon 13 and discuss the imatinib mesylate treatment surveillance outcomes towards disease management.展开更多
Dramatic progress has been made in the area of germline genetics of prostate cancer(PCa)in the past decade.Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice...Dramatic progress has been made in the area of germline genetics of prostate cancer(PCa)in the past decade.Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice-changing have been identified.For men with high risk PCa,the application of genetic testing for inherited pathogenic mutations is becoming standard of care.A major question exists about which additional populations of men to test,as men at all risk levels can potentially benefit by knowing their unique genetic profile of germline susceptibility variants.This article will provide a brief overview of some current issues in understanding inherited susceptibility for PCa.展开更多
Objective:Hereditary colorectal cancer(CRC)accounts for approximately 5%–10%of all CRC cases.The full profile of CRC-related germline mutations and the corresponding somatic mutational profile have not been fully det...Objective:Hereditary colorectal cancer(CRC)accounts for approximately 5%–10%of all CRC cases.The full profile of CRC-related germline mutations and the corresponding somatic mutational profile have not been fully determined in the Chinese population.Methods:We performed the first population study investigating the germline mutation status in more than 1,000(n=1,923)Chinese patients with CRC and examined their relationship with the somatic mutational landscape.Germline alterations were examined with a 58-gene next-generation sequencing panel,and somatic alterations were examined with a 605-gene panel.Results:A total of 92 pathogenic(P)mutations were identified in 85 patients,and 81 likely pathogenic(LP)germline mutations were identified in 62 patients,accounting for 7.6%(147/1,923)of all patients.MSH2 and APC was the most mutated gene in the Lynch syndrome and non-Lynch syndrome groups,respectively.Patients with P/LP mutations had a significantly higher ratio of microsatellite instability,highly deficient mismatch repair,family history of CRC,and lower age.The somatic mutational landscape revealed a significantly higher mutational frequency in the P group and a trend toward higher copy number variations in the non-P group.The Lynch syndrome group had a significantly higher mutational frequency and tumor mutational burden than the nonLynch syndrome group.Clustering analysis revealed that the Notch signaling pathway was uniquely clustered in the Lynch syndrome group,and the MAPK and cAMP signaling pathways were uniquely clustered in the non-Lynch syndrome group.Population risk analysis indicated that the overall odds ratio was 11.13(95%CI:8.289–15.44)for the P group and 20.68(95%CI:12.89–33.18)for the LP group.Conclusions:Distinct features were revealed in Chinese patients with CRC with germline mutations.The Notch signaling pathway was uniquely clustered in the Lynch syndrome group,and the MAPK and cAMP signaling pathways were uniquely clustered in the non-Lynch syndrome group.Patients with P/LP germline mutations exhibited higher CRC risk.展开更多
In mice,gene targeting by homologous recombination continues to play an essential role in the understanding of functional genomics.This strategy allows precise location of the site of transgene integration and is most...In mice,gene targeting by homologous recombination continues to play an essential role in the understanding of functional genomics.This strategy allows precise location of the site of transgene integration and is most commonly used to ablate gene expression("knock-out"),or to introduce mutant or modified alleles at the locus of interest("knock-in").The efficacy of producing live,transgenic mice challenges our understanding of this complex process,and of the factors which influence germline competence of embryonic stem cell lines.Increasingly,evidence indicates that culture conditions and in vitro manipulation can affect the germline-competence of Embryonic Stem cell(ES cell) lines by accumulation of chromosome abnormalities and/or epigenetic alterations of the ES cell genome. The effectiveness of ES cell derivation is greatly strain-dependent and it may also influence the germline transmission capability.Recent technical improvements in the production of germline chimeras have been focused on means of generating ES cells lines with a higher germline potential.There are a number of options for generating chimeras from ES cells (ES chimera mice);however,each method has its advantages and disadvantages.Recent developments in induced pluripotent stem(iPS)cell technology have opened new avenues for generation of animals from genetically modified somatic cells by means of chimera technologies.The aim of this review is to give a brief account of how the factors mentioned above are influencing the germline transmission capacity and the developmental potential of mouse pluripotent stem cell lines.The most recent methods for generating specifically ES and iPS chimera mice,including the advantages and disadvantages of each method are also discussed.展开更多
BACKGROUND Genetic testing is widely recommended for all epithelial ovarian cancer(EOC)patients.However,an increased probability of identifying germline mutations has been reported in selected patients with risk facto...BACKGROUND Genetic testing is widely recommended for all epithelial ovarian cancer(EOC)patients.However,an increased probability of identifying germline mutations has been reported in selected patients with risk factors such as a family history or personal history of cancer and high-grade serous carcinoma(HGSC)subtype.HGSC has been reported to be the most common subtype of EOC worldwide(approximately 70%).However,this subtype is less prevalent in Thai patients(reported as only 20%).The difference in the distribution of various subtypes of EOC may reflect the incidence of germline mutations in Thai EOC patients.AIM To evaluate the frequencies of germline mutations in EOC patients and to compare the frequencies in those with and without clinical risk factors for hereditary ovarian cancer.METHODS This cross-sectional study included 112 nonmucinous EOC patients who underwent primary surgery at our tertiary care hospital.Clinical risk factors for hereditary ovarian cancer were defined as follows:Age below 40 years,a significant family history of cancer,synchronous ovarian and endometrial cancer,and HGSC.Comprehensive germline mutations were detected by nextgeneration sequencing.RESULTS Of a total of 112 patients,82(73.2%)patients had≥1 risk factor and 30(26.8%)patients had no risk factors.Germline mutations were detected in 26 patients:20(17.8%)patients had BRCA1/2 mutations,but 6(5.4%)patients had mutations in other genes,including 1 in MLH1,1 in MSH2,1 in RAD51C,2 in ATM and 1 in CDH1.Germline mutations were only detected in patients with risk factors(26 of 82,31.7%),not in patients without risk factors(P<0.001).A significant family history of cancer and HGSC were the only two significant risk factors associated with a higher proportion of germline mutations(56.3%vs 10%for those with and without a history of cancer,respectively,40.8%vs 9.5%for those with and without HGSC).Germline BRCA mutations were detected in 38.8%of patients with HGSC but in only 1.6%of those with non-HGSC.An age below 40 years,personal history of breast cancer,and synchronous ovarian and endometrial cancer were not significant factors(14.3%vs 23.5%,33.3%vs 21%,22.2%vs 22.3%).CONCLUSION Approximately one-third of EOC patients with risk factors had germline mutations.Almost all germline BRCA mutations were found in patients with the HGSC subtype.Selected patients with HGSC and a family history of cancer should be initially considered for genetic analysis in Thailand.展开更多
BACKGROUND Familial gastrointestinal stromal tumors(GISTs)is a rare autosomal dominant disorder characterized by an array of clinical manifestations.Only 35 kindreds with germline KIT mutations and six with germline P...BACKGROUND Familial gastrointestinal stromal tumors(GISTs)is a rare autosomal dominant disorder characterized by an array of clinical manifestations.Only 35 kindreds with germline KIT mutations and six with germline PDGFRA mutations have been reported so far.It is often characterized by a series of manifestations,such as multiple lesions and hyperpigmentation.However,the effect of imatinib treatment in these patients is still uncertain.CASE SUMMARY Here,we report two patients(father and daughter)in a Chinese family(for the first time)with germline KIT mutation,and described their pathology,genetics and clinical manifestations.A 25-year-old Chinese woman went to hospital because of abdominal pain,and computed tomography showed multiple tumors in the small intestine.Small pigmented spots appeared on the skin within a few months after birth.Her father also had multiple pigmented spots and a history of multifocal GISTs.Multiple GISTs associated with diffuse interstitial Cajal cells(ICCs)hyperplasia were positive for CD117 and DOG-1.Gene sequencing revealed a germline mutation at codon 560 of exon 11(p.V560G)of KIT gene in these two patients.Imatinib therapy showed the long-lasting disease stability after resection.Remarkably,the hypopigmentation of the skin could also be observed.Luckily germline KIT mutation has not been identified yet in the 3-year-old daughter of the female patient.CONCLUSION Diagnosis of familial GISTs depends on combination of diffuse ICCs hyperplasia,germline KIT/PDGFRA mutation,hyperpigmentation and family history.展开更多
Objective To study the clinicopathological features of the Chinese hereditary non-polyposis colorectal cancer and its germline mutation of hMLH1 and hMSH2. Methods Thirteen typical Chinese hereditary non-polyposis col...Objective To study the clinicopathological features of the Chinese hereditary non-polyposis colorectal cancer and its germline mutation of hMLH1 and hMSH2. Methods Thirteen typical Chinese hereditary non-polyposis colorectal carcinoma (HNPC) C kindreds and 19 nontypical HNPCC families were registered and followed up. The germline mutation of the hMLH1 and hMSH2 of 12 index cases of 6 typical and 6 nontypical NHPCC were screened by PCR-SSCP. Samples with abnormal mobility were sequenced direcdy. Results The average age of typical HNPCC was 47, no difference existed between sexs. Location of the tumors of typical HNPCC represented 44.7% on the right half colon and non-typical HNPCC 65. 8% on the rectum. The rate of the metachronos cancer was 11.5%. The 3 - , 5 - and 10 -year survival rate was 64. 0%, 45. 3% and 31. 2% respectively. Among 12 cases, 8 showed abnormal mobility. Except for an intron polymorphinism, six exons abnormalities were found in 5 of 12 proband. Sequencing showed 4 missense,7展开更多
Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in ...Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.展开更多
Recently,an increasing number of young never-smokers are diagnosed with lung cancer.The aim of this study is to investigate the genetic predisposition of lung cancer in these patients and discover candidate pathogenic...Recently,an increasing number of young never-smokers are diagnosed with lung cancer.The aim of this study is to investigate the genetic predisposition of lung cancer in these patients and discover candidate pathogenic variants for lung adenocarcinoma in young never-smokers.Peripheral blood was collected from 123 never-smoking east-Asian patients diagnosed with lung adenocarcinoma before the age of 40.Whole-exome sequencing(WES)was conducted on genomic DNA extracted from peripheral blood cells.As a result,3,481 single nucleotide variants were identified.By bioinformatical tools and the published gene list associated with genetic predisposition of cancer,pathogenic variants were detected in ten germline genes:ATR,FANCD2,FANCE,GATA2,HFE,MSH2,PDGFRA,PMS2,SDHB,and WAS.Patients with pathogenic variants were more likely to occur in females(9/10,90.0%)and have stage IV lung adenocarcinoma(4/10,40%).Furthermore,germline muta-tions in 17 genes(ASB18,B3GALT5,CLEC4F,COL6A6,CYP4B1,C6orf132,EXO1,GATA4,HCK,KCP,NPHP4,PIGX,PPIL2,PPP1R3G,RRBP1,SALL4,and TTC28),which occurred in at least two patients,displayed potentially pathogenic effects.Gene ontology analysis further showed that these genes with germline mutations were mainly located in nucleo-plasm and associated with DNA repair-related biological processes.The study provides spectrum of pathogenic variants and functional explanation for genetic predisposition of lung adenocarcinoma in young never-smokers,which sheds a light on prevention and early diagnosis of lung cancer.展开更多
GATA-2, a transcription factor, is expressed in several types of blood cells and in the central nervous system (CNS), and regulates the differentiation of these cells. We have obtained five zebrafish transgenic germli...GATA-2, a transcription factor, is expressed in several types of blood cells and in the central nervous system (CNS), and regulates the differentiation of these cells. We have obtained five zebrafish transgenic germlines that carry and express the green fluorescent protein (GFP) gene ligated to various 5’ flanking sepuences of zebrafish GATA-2 gene. The spatial pattern of GFP expression varies, mainly depending on which regulatory sequence is used, among the germlines. In some of the germlines, the expression of GFP is restricted to the CNS and the enveloping layer (EVL) cells, while in some other lines GFP is observed only in the CNS. it is noted that the intensity of GFP in the transgenic fish remain unchanged after a six-generation passage of the transgenes. The transgenic fish could find its uses in the future in generating tissue-specific, even cellspecific mutant fish and in functional study of related genes through transgenesis.展开更多
Background:Inherited susceptibility accounts for nearly one-third of colorectal cancer(CRC)predispositions and has an 80%-100%lifetime risk of this disease.However,there are few data about germline mutations of heredi...Background:Inherited susceptibility accounts for nearly one-third of colorectal cancer(CRC)predispositions and has an 80%-100%lifetime risk of this disease.However,there are few data about germline mutations of hereditary CRC-related genes in Chinese patients with CRC.This study aimed to assess the prevalence of gene mutations related to cancer susceptibility among Chinese patients with CRC,differences between Chinese and Western patients,and the phenotypegenotype correlation.Methods:We retrospectively collected tumor samples from 526 patients with CRC under 70 years old who underwent hereditary CRC genetic testing.A series of bioinformatic analyses,as well as statistical comparisons,were performed.Results:We found that 77 patients(14.6%)harbored functional variants of the 12 genes.The mutation frequencies of the top 5 mutated genes were 6.5%for MutL homolog 1(MLH1),5.1%for MutS homolog 2(MSH2),1.0%for MSH6,0.8%for PMS1 homolog 2(PMS2),and 0.8%for APC regulator of the WNT signaling pathway(APC).Our data showed much higher rates of mutations of MSH6 and PMS2 genes among all mismatch repair(MMR)genes as compared with those in Western populations.Mutations in MLH1,MSH2,and MSH6 were found to be mutually exclusive.Patients with MLH1 or MSH2 mutations had higher frequencies of personal history of cancer(MLH1:20.6%vs.8.7%;MSH2:25.9%vs.8.6%)and family history of cancer than those without these mutations(MLH1:73.5%vs.48.4%;MSH2:70.4%vs.48.9%),and the lesions were more prone to occur on the right side of the colon than on the left side(MLH1:73.5%vs.29.3%;MSH2:56.0%vs.31.0%).The proportion of stage I/II disease was higher in patients with MLH1 mutations than in those without MLH1 mutations(70.6%vs.50.7%),and the rate of polyps was higher in patients withAPC mutations than in those with wild-type APC(75.0%vs.17.4%).Conclusion:These results provide a full-scale landscape of hereditary susceptibility over 12 related genes in CRC patients and suggest that a comprehensive multi-gene panel testing for hereditary CRC predisposition could be a helpful analysis in clinical practice.展开更多
Last year, the first attempt to genetically modify human embryos in the United States was reported and sparked a huge debate (Ma et al., 2017). Although the first human germline modification was only performed two yea...Last year, the first attempt to genetically modify human embryos in the United States was reported and sparked a huge debate (Ma et al., 2017). Although the first human germline modification was only performed two years ago, the study showed that rapid adva nces in tech no logy has allowed the rate of off-target effects and mosaicism to be reduced considerably (Liang et al., 2015). Recently, Vertex and CRISPR therapeutics collaborated and developed CTX001, the first CRISPR/Cas9-based therapy, targeting patients with P-thalassemia and have begun phase 1/2 clinical trials. With policies and technologies regarding genome editing both developing rapidly, explorations into the possibility of clinical gene editing for hundreds of hereditary diseases are starting to become achievable. Here, we address the progress of huma n embryo editi ng tech no logies so far and its promise and risks in advancing therapy for hereditary diseases.展开更多
DNA methylation plays essential homeostatic functions in eukaryotic genomes.In animals,DNA methylation is also developmentally regulated and,in turn,regulates development.In the past two decades,huge research effort h...DNA methylation plays essential homeostatic functions in eukaryotic genomes.In animals,DNA methylation is also developmentally regulated and,in turn,regulates development.In the past two decades,huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development,especially during sexual reproduction.The power of whole-genome sequencing and cell isolation techniques,as well as bioinformatics tools,have enabled recent studies to reveal dynamic changes in DNA methylation during germline development.Furthermore,the combination of these technological advances with genetics,developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines.In this review,we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.展开更多
Whether Fanconi anemia(FA)heterozygotes are predisposed to bone marrow failure and hematologic neoplasm is a crucial but unsettled issue in cancer prevention and family consulting.We retrospectively analyzed rare poss...Whether Fanconi anemia(FA)heterozygotes are predisposed to bone marrow failure and hematologic neoplasm is a crucial but unsettled issue in cancer prevention and family consulting.We retrospectively analyzed rare possibly significant variations(PSVs)in the five most obligated FA genes,BRCA2,FANCA,FANCC,FANCD2,and FANCG,in 788 patients with aplastic anemia(AA)and hematologic malignancy.Sixty-eight variants were identified in 66 patients(8.38%).FANCA was the most frequently mutated gene(n=29),followed by BRCA2(n=20).Compared with that of the ExAC East Asian dataset,the overall frequency of rare PSVs was higher in our cohort(P=0.016).BRCA2 PSVs showed higher frequency in acute lymphocytic leukemia(P=0.038),and FANCA PSVs were significantly enriched in AA and AML subgroups(P=0.020;P=0.008).FA-PSV-positive MDS/AML patients had a higher tumor mutation burden,higher rate of cytogenetic abnormalities,less epigenetic regulation,and fewer spliceosome gene mutations than those of FA-PSV-negative MDS/AML patients(P=0.024,P=0.029,P=0.024,and P=0.013).The overall PSV enrichment in our cohort suggests that heterozygous mutations of FA genes contribute to hematopoietic failure and leukemogenesis.展开更多
基金funded by the National Key R&D Program of China(2021YFD1200903)Seed Fund(CAU),Shandong Provincial Natural Science Foundation(ZR2021MC070)+3 种基金the National Key R&D Program of China(2021YFF1000701-06)Shandong Provincial Natural Science Foundation(ZR2020MC165)the Earmarked Fund for CARS-36.X.W.is funded by the“Hundred Talents Program”project of Hebei Province(E2020100019)the research project of Zhongnongtongchuang(ZNTC)group(ZNTC2019A10 and ZNTC2021B12)in China.
文摘Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characterized by epigenetic reprogramming,while intergenerational and transgenerational epigenetic inheritance can influence the offspring’s development through the transmission of epigenetic features to the offspring via the germline.Therefore,the selec-tion of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers.We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
基金Supported by Natural Science Foundation of Zhejiang Province,No.LQ20H1600036 (to Wen X).
文摘BACKGROUND The molecular changes present in gastric neuroendocrine tumors(NETs)include a loss of heterozygosity or mutation of MEN1,CDKN1B gene mutation,P27 heterozygous mutation,and ATP4A gene missense mutation.We identified and are the first to report a case of type 1 histamine-producing enterochromaffin-like cell NETs(ECL-cell NETs)with a BRCA2 gene germline mutation.CASE SUMMARY The patient had a history of iron-deficient anemia for 5 years,and gastroscopic examination indicated multiple gastric tumors.Then,the patient underwent distal gastrectomy.Microscopically,multifocal tumor cells were found in the mucosa and submucosa;tumor cells were organoid and arranged in nests and cords,and the stroma was rich in sinusoids.The surrounding gastric mucosa showed atrophy with mild intestinal metaplasia or pseudopyloric gland metaplasia.Neuroendocrine cells could be seen with diffuse linear,nodular,and adenomatous hyperplasia.Immunohistochemically,the tumor cells diffusely expressed cytokeratin,chromogranin,synaptophysin,and CD56.Whole-genome highthroughput molecular sequencing revealed a pathogenic germline mutation in the BRCA2 gene,a heterozygous germline frameshift mutation in exon 11,c.6443_6444del(p.S2148Yfs*2).The final diagnosis was gastric type 1 ECL-cell NETs with a BRCA2 gene germline mutation,accompanied by autoimmune gastritis.CONCLUSION This is the first report of a case of type 1 gastric ECL-cell NETs with a pathogenic germline mutation of the BRCA2 gene.The findings of this report will expand the germline mutation spectrum of gastric NETs and increase the understanding of the molecular changes present in these tumors for their improved diagnosis in the future.
基金supported by grant from the National Natural Science Foundation of China (Grant No.81502699)
文摘Objective: Germline alterations in the breast cancer susceptibility genes type 1 and 2, BRCA1 and BRCA2, predispose individuals to hereditary cancers, including breast, ovarian, prostate, pancreatic, and stomach cancers.Accumulating evidence suggests inherited genetic susceptibility to lung cancer.The present study aimed to survey the prevalence of pathogenic germline BRCA mutations(gBRCAm) and explore the potential association between gBRCAm and disease onset in Chinese advanced non-small cell lung cancer(NSCLC) patients.Methods: A total of 6,220 NSCLC patients were screened using capture-based ultra-deep targeted sequencing to identify patients harboring germline BRCA1/2 mutations.Results: Out of the 6,220 patients screened, 1.03%(64/6,220) of the patients harbored the pathogenic gB RCAm, with BRCA2 mutations being the most predominant mutations(49/64, 76.5%).Patients who developed NSCLC before 50 years of age were more likely to carry gBRCAm(P = 0.036).Among the patients harboring classic lung cancer driver mutations, those with concurrent gBRCAm were significantly younger than those harboring the wild-type gBRCA(P = 0.029).By contrast, the age of patients with or without concurrent gBRCAm was comparable to those of patients without the driver mutations(P = 0.972).In addition, we identified EGFR-mutant patients with concurrent gBRCAm who showed comparable progression-free survival but significantly longer overall survival(P = 0.002) compared to EGFR-mutant patients with wild-type germline BRCA.Conclusions: Overall, our study is the largest survey of the prevalence of pathogenic gBRCAm in advanced Chinese NSCLC patients.Results suggested a lack of association between germline BRCA status and treatment outcome of EGFR-TKI.In addition,results showed a positive correlation between pathogenic gB RCAm and an early onset of NSCLC.
基金Supported by The National Natural Science Foundation of China, No. 30972535the Natural Science Foundation of Jiangsu, China, No. BK2008269the Fundamental Research Funds for the Central Universities of China, No. 1112021402
文摘AIM: To explore germline hypermethylation of the tumor suppressor genes MLH1, CDH1 and P16INK4a in suspected cases of hereditary gastric cancer (GC). METHODS: A group of 140 Chinese GC patients in whom the primary cancer had developed before the age of 60 or who had a familial history of cancer were screened for germline hypermethylation of the MLH1, CDH1 and P16INK4a tumor suppressor genes. GenomicDNA was extracted from peripheral blood leukocytes and modified by sodium bisulfite. The treated DNA was then subjected to bisulfi te DNA sequencing for a specif ic region of the MLH1 promoter. The methylation status of CDH1 or P16INK4a was assayed using methylation-specif ic PCR. Clonal bisulf ite allelic sequencing in positive samples was performed to obtain a comprehensive analysis of the CpG island methylation status of these promoter regions. RESULTS: Methylation of the MLH1 gene promoter was detected in the peripheral blood DNA of only 1/140 (0.7%) of the GC patient group. However, this methylation pattern was mosaic rather than the allelic pattern which has previously been reported for MLH1 in hereditary non-polyposis colorectal cancer (HNPCC) patients. We found that 10% of the MLH1 alleles in the peripheral blood DNA of this patient were methylated, consistent with 20% of cells having one methylated allele. No germline promoter methylation of the CDH1 or P16INK4a genes was detected. CONCLUSION: Mosaic germline epimutation of the MLH1 gene is present in suspected hereditary GC patients in China but at a very low level. Germline epimutation of the CDH1 or P16INK4a gene is not a frequent event.
基金This work was supported by the China National Basic Research Program(2016YFA0100203)National Natural Science Foundation of China(31572399Detail,32072806,32072815,32002246)+3 种基金State Key Lab of Reproductive Regulation&Breeding of Grassland Livestock(SKL-OT-201801)Science and Technology Major Project of Inner Mongolia Autonomous Region of China(ZDZX2018065)and Shaanxi Province Science and Technology Innovation Team(2019TD-036)The authors thank Dr.John Clotaire Daguia Zambe for helpful comments about this paper,Jia Fang for the PGL3-NF-κB luciferase reporter plasmid,and Dong-Xue Che for bioinformatics analysis.
文摘Double sex and mab-3-related transcription factor 1(Dmrt1),which is expressed in goat male germline stem cells(mGSCs)and Sertoli cells,is one of the most conserved transcription factors involved in sex determination.In this study,we highlighted the role of Dmrt1 in balancing the innate immune response in goat mGSCs.Dmrt1 recruited promyelocytic leukemia zinc finger(Plzf),also known as zinc finger and BTB domain-containing protein 16(Zbtb16),to repress the Toll-like receptor 4(TLR4)-dependent inflammatory signaling pathway and nuclear factor(NF)-κB.Knockdown of Dmrt1 in seminiferous tubules resulted in widespread degeneration of germ and somatic cells,while the expression of proinflammatory factors were significantly enhanced.We also demonstrated that Dmrt1 stimulated proliferation of mGSCs,but repressed apoptosis caused by the immune response.Thus,Dmrt1 is sufficient to reduce inflammation in the testes,thereby establishing the stability of spermatogenesis and the testicular microenvironment.
基金Supported by National Natural Science Foundation of China,No.30972535the Natural Science Foundation of Jiangsu,China,No.BK2012724the Fundamental Research Funds for the Cen-tral Universities of China,1112021402
文摘AIM:To give a comprehensive report of E-cadheringene (CDH1) variations in a population at a high risk for gastric cancer (GC).METHODS:The samples consisted of 178 men and 58 women with a mean age of 62.3 ± 9.4 years and an age range of 30-84 years.A total of 240 cancerfree controls were recruited (mean age of 61.8 ± 10.1 years,age range of 26-82 years).Samples were screened for CDH1 germline mutations by high-resolution melting analysis or directly sequencing.Luciferase reporter assay,RNA splicing assay and bioinformatic analysis were used to evaluate the effect of mutations.RESULTS:Four novel CDH1 sequence alterations were identified in GC patients including a G>T transition 49 bp before the start codon;a three-nucleotide deletion,c.44_46del TGC;one missense mutation,c.604G>A (V202I);and one variation in the intron,c.1320+7A>G.In addition,polymorphism frequencies were observed for CDH1-164delT,-161C>A,-73A>C,c.48+6C>T,c.48+62_48+63delinsCGTGCCCCAGCCC,c.894C>T (A298A),c.1224G>A (A408A),c.1888C>G (L630V),c.2076T>C (A692A),and c.2253C>T (N751N) which is similar to the data reported in http://www.ncbi.nlm.nih.gov/projects/SNP/.RNA splicing analysis suggested that the c.1320+7A>G and c.1224G>A variations did not affect exon splicing ability.Luciferase reporter assay demonstrated that the c.-49T variation might be helpful for E-cadherin transcription,though the increase in transcription activity is limited (only 33%).SIFT score and PolyPhen analysis both demonstrated that the L630V missense mutation probably damages protein function,while the V202I variant does not.CONCLUSION:This study reveals novel mutations in sporadic GC patients which had been poorly investigated for susceptibility genes.
文摘Familial gastrointestinal stromal tumor(GIST) is a rare autosomal dominant disorder associated with mutations in the KIT gene in the majority of cases. Although, exon 11 appears to be the hot spot region for approximately 95% of germline mutations, pathogenic variations have also been identified in exon 8, 13 and 17. Exon 13 germline mutations are extremely rare amongst familial GISTs and seven families with a germline mutation have been reported to date. Moreover, the role of imatinib mesylate in this rare familiar settings is not completely known so far. We describe here clinical, imaging, pathological and genetic findings of a family with four affected members; grandmother, his son and two grand-sons having a germline gain-of-function mutation of KIT in exon 13 and discuss the imatinib mesylate treatment surveillance outcomes towards disease management.
文摘Dramatic progress has been made in the area of germline genetics of prostate cancer(PCa)in the past decade.Both common and rare genetic variants with effects on risk ranging from barely detectable to outright practice-changing have been identified.For men with high risk PCa,the application of genetic testing for inherited pathogenic mutations is becoming standard of care.A major question exists about which additional populations of men to test,as men at all risk levels can potentially benefit by knowing their unique genetic profile of germline susceptibility variants.This article will provide a brief overview of some current issues in understanding inherited susceptibility for PCa.
基金This study was supported by the Special Funds for Strategic Emerging Industry Development of Shenzhen(Grant No.20170922151538732)the Science and Technology Project of Shenzhen(Grant No.JSGG20180703164202084)+2 种基金the Natural Science Foundation Project of China(Grant No.71573022)the National Natural Science Foundation Regional Projects(Grant No.82060440)the special health research projects of 2019 funded by the Chinese PLA General Hospital(Grant No.NLBJ-2019003).
文摘Objective:Hereditary colorectal cancer(CRC)accounts for approximately 5%–10%of all CRC cases.The full profile of CRC-related germline mutations and the corresponding somatic mutational profile have not been fully determined in the Chinese population.Methods:We performed the first population study investigating the germline mutation status in more than 1,000(n=1,923)Chinese patients with CRC and examined their relationship with the somatic mutational landscape.Germline alterations were examined with a 58-gene next-generation sequencing panel,and somatic alterations were examined with a 605-gene panel.Results:A total of 92 pathogenic(P)mutations were identified in 85 patients,and 81 likely pathogenic(LP)germline mutations were identified in 62 patients,accounting for 7.6%(147/1,923)of all patients.MSH2 and APC was the most mutated gene in the Lynch syndrome and non-Lynch syndrome groups,respectively.Patients with P/LP mutations had a significantly higher ratio of microsatellite instability,highly deficient mismatch repair,family history of CRC,and lower age.The somatic mutational landscape revealed a significantly higher mutational frequency in the P group and a trend toward higher copy number variations in the non-P group.The Lynch syndrome group had a significantly higher mutational frequency and tumor mutational burden than the nonLynch syndrome group.Clustering analysis revealed that the Notch signaling pathway was uniquely clustered in the Lynch syndrome group,and the MAPK and cAMP signaling pathways were uniquely clustered in the non-Lynch syndrome group.Population risk analysis indicated that the overall odds ratio was 11.13(95%CI:8.289–15.44)for the P group and 20.68(95%CI:12.89–33.18)for the LP group.Conclusions:Distinct features were revealed in Chinese patients with CRC with germline mutations.The Notch signaling pathway was uniquely clustered in the Lynch syndrome group,and the MAPK and cAMP signaling pathways were uniquely clustered in the non-Lynch syndrome group.Patients with P/LP germline mutations exhibited higher CRC risk.
基金Supported by Grants from EU FP6("MEDRAT"-LSHG-CT-2005-518240"Artemis",LSHM-CT-2006-037862+5 种基金"AGLAEA",LSHM-CT-2006-037554,"CLONET",MRTN-CT-2006-035468),EU FP7("PartnErS",PIAP-GA-2008-218205"InduHeart",EUFP7-PEOPL E-IRG-2008-234390"InduStem",PIAP-GA-2008-230675"Plurisys",HEALTH-F4-2009-223485)NKFP_07_1-ES2HEART-HU,No.OM-00202-2007 NKTH/ANRTET Franco-Hungarian Bilateral Scientific and Technological Collaborative Project"Plurabit"
文摘In mice,gene targeting by homologous recombination continues to play an essential role in the understanding of functional genomics.This strategy allows precise location of the site of transgene integration and is most commonly used to ablate gene expression("knock-out"),or to introduce mutant or modified alleles at the locus of interest("knock-in").The efficacy of producing live,transgenic mice challenges our understanding of this complex process,and of the factors which influence germline competence of embryonic stem cell lines.Increasingly,evidence indicates that culture conditions and in vitro manipulation can affect the germline-competence of Embryonic Stem cell(ES cell) lines by accumulation of chromosome abnormalities and/or epigenetic alterations of the ES cell genome. The effectiveness of ES cell derivation is greatly strain-dependent and it may also influence the germline transmission capability.Recent technical improvements in the production of germline chimeras have been focused on means of generating ES cells lines with a higher germline potential.There are a number of options for generating chimeras from ES cells (ES chimera mice);however,each method has its advantages and disadvantages.Recent developments in induced pluripotent stem(iPS)cell technology have opened new avenues for generation of animals from genetically modified somatic cells by means of chimera technologies.The aim of this review is to give a brief account of how the factors mentioned above are influencing the germline transmission capacity and the developmental potential of mouse pluripotent stem cell lines.The most recent methods for generating specifically ES and iPS chimera mice,including the advantages and disadvantages of each method are also discussed.
文摘BACKGROUND Genetic testing is widely recommended for all epithelial ovarian cancer(EOC)patients.However,an increased probability of identifying germline mutations has been reported in selected patients with risk factors such as a family history or personal history of cancer and high-grade serous carcinoma(HGSC)subtype.HGSC has been reported to be the most common subtype of EOC worldwide(approximately 70%).However,this subtype is less prevalent in Thai patients(reported as only 20%).The difference in the distribution of various subtypes of EOC may reflect the incidence of germline mutations in Thai EOC patients.AIM To evaluate the frequencies of germline mutations in EOC patients and to compare the frequencies in those with and without clinical risk factors for hereditary ovarian cancer.METHODS This cross-sectional study included 112 nonmucinous EOC patients who underwent primary surgery at our tertiary care hospital.Clinical risk factors for hereditary ovarian cancer were defined as follows:Age below 40 years,a significant family history of cancer,synchronous ovarian and endometrial cancer,and HGSC.Comprehensive germline mutations were detected by nextgeneration sequencing.RESULTS Of a total of 112 patients,82(73.2%)patients had≥1 risk factor and 30(26.8%)patients had no risk factors.Germline mutations were detected in 26 patients:20(17.8%)patients had BRCA1/2 mutations,but 6(5.4%)patients had mutations in other genes,including 1 in MLH1,1 in MSH2,1 in RAD51C,2 in ATM and 1 in CDH1.Germline mutations were only detected in patients with risk factors(26 of 82,31.7%),not in patients without risk factors(P<0.001).A significant family history of cancer and HGSC were the only two significant risk factors associated with a higher proportion of germline mutations(56.3%vs 10%for those with and without a history of cancer,respectively,40.8%vs 9.5%for those with and without HGSC).Germline BRCA mutations were detected in 38.8%of patients with HGSC but in only 1.6%of those with non-HGSC.An age below 40 years,personal history of breast cancer,and synchronous ovarian and endometrial cancer were not significant factors(14.3%vs 23.5%,33.3%vs 21%,22.2%vs 22.3%).CONCLUSION Approximately one-third of EOC patients with risk factors had germline mutations.Almost all germline BRCA mutations were found in patients with the HGSC subtype.Selected patients with HGSC and a family history of cancer should be initially considered for genetic analysis in Thailand.
基金Supported by Shanghai Municipal Key 306 Clinical Specialty,No.shslczdzk01302.
文摘BACKGROUND Familial gastrointestinal stromal tumors(GISTs)is a rare autosomal dominant disorder characterized by an array of clinical manifestations.Only 35 kindreds with germline KIT mutations and six with germline PDGFRA mutations have been reported so far.It is often characterized by a series of manifestations,such as multiple lesions and hyperpigmentation.However,the effect of imatinib treatment in these patients is still uncertain.CASE SUMMARY Here,we report two patients(father and daughter)in a Chinese family(for the first time)with germline KIT mutation,and described their pathology,genetics and clinical manifestations.A 25-year-old Chinese woman went to hospital because of abdominal pain,and computed tomography showed multiple tumors in the small intestine.Small pigmented spots appeared on the skin within a few months after birth.Her father also had multiple pigmented spots and a history of multifocal GISTs.Multiple GISTs associated with diffuse interstitial Cajal cells(ICCs)hyperplasia were positive for CD117 and DOG-1.Gene sequencing revealed a germline mutation at codon 560 of exon 11(p.V560G)of KIT gene in these two patients.Imatinib therapy showed the long-lasting disease stability after resection.Remarkably,the hypopigmentation of the skin could also be observed.Luckily germline KIT mutation has not been identified yet in the 3-year-old daughter of the female patient.CONCLUSION Diagnosis of familial GISTs depends on combination of diffuse ICCs hyperplasia,germline KIT/PDGFRA mutation,hyperpigmentation and family history.
文摘Objective To study the clinicopathological features of the Chinese hereditary non-polyposis colorectal cancer and its germline mutation of hMLH1 and hMSH2. Methods Thirteen typical Chinese hereditary non-polyposis colorectal carcinoma (HNPC) C kindreds and 19 nontypical HNPCC families were registered and followed up. The germline mutation of the hMLH1 and hMSH2 of 12 index cases of 6 typical and 6 nontypical NHPCC were screened by PCR-SSCP. Samples with abnormal mobility were sequenced direcdy. Results The average age of typical HNPCC was 47, no difference existed between sexs. Location of the tumors of typical HNPCC represented 44.7% on the right half colon and non-typical HNPCC 65. 8% on the rectum. The rate of the metachronos cancer was 11.5%. The 3 - , 5 - and 10 -year survival rate was 64. 0%, 45. 3% and 31. 2% respectively. Among 12 cases, 8 showed abnormal mobility. Except for an intron polymorphinism, six exons abnormalities were found in 5 of 12 proband. Sequencing showed 4 missense,7
基金funded by the Laoshan Laboratory(No.LSKJ202203202)the National Natural Science Foundation of China(32270539,31922013,31961123002)+3 种基金the Natural Science Foundation of Shandong Province(ZR2020JQ13)Royal Society/NSFC International Exchanges Cost Share Project(IEC\NSFC\201024)National Institutes of Health(P40OD010964)the Fundamental Research Funds for the Central Universities(202141004).
文摘Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.
基金supported by the National Natural Science Foundation of China(81772466)Shanghai Rising-Star Program(21QC1400600)+1 种基金Ministry of Science and Technology of the People’s Republic of China(2017YFA0505500,2016YFA0501800)Science and Technology Commission of Shanghai Municipality(19XD1401300).
文摘Recently,an increasing number of young never-smokers are diagnosed with lung cancer.The aim of this study is to investigate the genetic predisposition of lung cancer in these patients and discover candidate pathogenic variants for lung adenocarcinoma in young never-smokers.Peripheral blood was collected from 123 never-smoking east-Asian patients diagnosed with lung adenocarcinoma before the age of 40.Whole-exome sequencing(WES)was conducted on genomic DNA extracted from peripheral blood cells.As a result,3,481 single nucleotide variants were identified.By bioinformatical tools and the published gene list associated with genetic predisposition of cancer,pathogenic variants were detected in ten germline genes:ATR,FANCD2,FANCE,GATA2,HFE,MSH2,PDGFRA,PMS2,SDHB,and WAS.Patients with pathogenic variants were more likely to occur in females(9/10,90.0%)and have stage IV lung adenocarcinoma(4/10,40%).Furthermore,germline muta-tions in 17 genes(ASB18,B3GALT5,CLEC4F,COL6A6,CYP4B1,C6orf132,EXO1,GATA4,HCK,KCP,NPHP4,PIGX,PPIL2,PPP1R3G,RRBP1,SALL4,and TTC28),which occurred in at least two patients,displayed potentially pathogenic effects.Gene ontology analysis further showed that these genes with germline mutations were mainly located in nucleo-plasm and associated with DNA repair-related biological processes.The study provides spectrum of pathogenic variants and functional explanation for genetic predisposition of lung adenocarcinoma in young never-smokers,which sheds a light on prevention and early diagnosis of lung cancer.
文摘GATA-2, a transcription factor, is expressed in several types of blood cells and in the central nervous system (CNS), and regulates the differentiation of these cells. We have obtained five zebrafish transgenic germlines that carry and express the green fluorescent protein (GFP) gene ligated to various 5’ flanking sepuences of zebrafish GATA-2 gene. The spatial pattern of GFP expression varies, mainly depending on which regulatory sequence is used, among the germlines. In some of the germlines, the expression of GFP is restricted to the CNS and the enveloping layer (EVL) cells, while in some other lines GFP is observed only in the CNS. it is noted that the intensity of GFP in the transgenic fish remain unchanged after a six-generation passage of the transgenes. The transgenic fish could find its uses in the future in generating tissue-specific, even cellspecific mutant fish and in functional study of related genes through transgenesis.
基金This work was supported,in part,by the National Key Research and Development Program of China(2018YFC1313300,2017YFC1308900)National Natural Science Foundation of China(81930065,81872011,81903163)+4 种基金Science and Technology Program of Guangdong(2019B020227002)Science and Technology Program of Guangzhou(201904020046,201803040019,201704020228)Guangzhou Health and Medical Collaborative Innovation Project(201704020220)Guangdong Esophageal Cancer Institute Science and Technology Program(M201905)the Sun Yat-sen University Clinical Research 5010 Program(2018014).
文摘Background:Inherited susceptibility accounts for nearly one-third of colorectal cancer(CRC)predispositions and has an 80%-100%lifetime risk of this disease.However,there are few data about germline mutations of hereditary CRC-related genes in Chinese patients with CRC.This study aimed to assess the prevalence of gene mutations related to cancer susceptibility among Chinese patients with CRC,differences between Chinese and Western patients,and the phenotypegenotype correlation.Methods:We retrospectively collected tumor samples from 526 patients with CRC under 70 years old who underwent hereditary CRC genetic testing.A series of bioinformatic analyses,as well as statistical comparisons,were performed.Results:We found that 77 patients(14.6%)harbored functional variants of the 12 genes.The mutation frequencies of the top 5 mutated genes were 6.5%for MutL homolog 1(MLH1),5.1%for MutS homolog 2(MSH2),1.0%for MSH6,0.8%for PMS1 homolog 2(PMS2),and 0.8%for APC regulator of the WNT signaling pathway(APC).Our data showed much higher rates of mutations of MSH6 and PMS2 genes among all mismatch repair(MMR)genes as compared with those in Western populations.Mutations in MLH1,MSH2,and MSH6 were found to be mutually exclusive.Patients with MLH1 or MSH2 mutations had higher frequencies of personal history of cancer(MLH1:20.6%vs.8.7%;MSH2:25.9%vs.8.6%)and family history of cancer than those without these mutations(MLH1:73.5%vs.48.4%;MSH2:70.4%vs.48.9%),and the lesions were more prone to occur on the right side of the colon than on the left side(MLH1:73.5%vs.29.3%;MSH2:56.0%vs.31.0%).The proportion of stage I/II disease was higher in patients with MLH1 mutations than in those without MLH1 mutations(70.6%vs.50.7%),and the rate of polyps was higher in patients withAPC mutations than in those with wild-type APC(75.0%vs.17.4%).Conclusion:These results provide a full-scale landscape of hereditary susceptibility over 12 related genes in CRC patients and suggest that a comprehensive multi-gene panel testing for hereditary CRC predisposition could be a helpful analysis in clinical practice.
基金National Key R&D Program of China (2016YFC1000601)National Natural Science Foundation of China (Grant Nos. 81570101, 81728002, 81741006 and 81871162)+1 种基金Guan gdo ng Province Science and Tech no logy Project (2017A020214005)the Guangzhou Science and Technology Project (201803010048).
文摘Last year, the first attempt to genetically modify human embryos in the United States was reported and sparked a huge debate (Ma et al., 2017). Although the first human germline modification was only performed two years ago, the study showed that rapid adva nces in tech no logy has allowed the rate of off-target effects and mosaicism to be reduced considerably (Liang et al., 2015). Recently, Vertex and CRISPR therapeutics collaborated and developed CTX001, the first CRISPR/Cas9-based therapy, targeting patients with P-thalassemia and have begun phase 1/2 clinical trials. With policies and technologies regarding genome editing both developing rapidly, explorations into the possibility of clinical gene editing for hundreds of hereditary diseases are starting to become achievable. Here, we address the progress of huma n embryo editi ng tech no logies so far and its promise and risks in advancing therapy for hereditary diseases.
文摘DNA methylation plays essential homeostatic functions in eukaryotic genomes.In animals,DNA methylation is also developmentally regulated and,in turn,regulates development.In the past two decades,huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development,especially during sexual reproduction.The power of whole-genome sequencing and cell isolation techniques,as well as bioinformatics tools,have enabled recent studies to reveal dynamic changes in DNA methylation during germline development.Furthermore,the combination of these technological advances with genetics,developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines.In this review,we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.
基金supported by a grant from the Shandong Nature Science Fund(No.ZR2016HP02).
文摘Whether Fanconi anemia(FA)heterozygotes are predisposed to bone marrow failure and hematologic neoplasm is a crucial but unsettled issue in cancer prevention and family consulting.We retrospectively analyzed rare possibly significant variations(PSVs)in the five most obligated FA genes,BRCA2,FANCA,FANCC,FANCD2,and FANCG,in 788 patients with aplastic anemia(AA)and hematologic malignancy.Sixty-eight variants were identified in 66 patients(8.38%).FANCA was the most frequently mutated gene(n=29),followed by BRCA2(n=20).Compared with that of the ExAC East Asian dataset,the overall frequency of rare PSVs was higher in our cohort(P=0.016).BRCA2 PSVs showed higher frequency in acute lymphocytic leukemia(P=0.038),and FANCA PSVs were significantly enriched in AA and AML subgroups(P=0.020;P=0.008).FA-PSV-positive MDS/AML patients had a higher tumor mutation burden,higher rate of cytogenetic abnormalities,less epigenetic regulation,and fewer spliceosome gene mutations than those of FA-PSV-negative MDS/AML patients(P=0.024,P=0.029,P=0.024,and P=0.013).The overall PSV enrichment in our cohort suggests that heterozygous mutations of FA genes contribute to hematopoietic failure and leukemogenesis.
