High-throughput screening of mouse gene knockouts identifies established and novel skeletal phenotypes

Screening gene function in vivo is a powerful approach to discover novel drug targets. We present high-throughput screening （HTS） data for 3 762 distinct global gene knockout （KO） mouse lines with viable adult homozygous mice generated using either gene-trap or homologous recombination technologies. Bone mass was determined from DEXA scans of male and female mice at 14 weeks of age and by microCT analyses of bones from male mice at 16 weeks of age. Wild-type （WT） cagemates/littermates were examined for each gene KO. Lethality was observed in an additional 850 KO lines. Since primary HTS are susceptible to false positive findings, additional cohorts of mice from KO lines with intriguing HTS bone data were examined. Aging, ovariectomy, histomorphometry and bone strength studies were performed and possible non-skeletal phenotypes were explored. Together, these screens identified multiple genes affecting bone mass： 23 previously reported genes （Calcr, Cebpb, Crtap, Dcstamp, Dkkl, Duoxa2, Enppl, Fgf23, Kissl/Kisslr, Kl （Klotho）, Lrp5, Mstn, Neol, Npr2, Ostml, Postn, Sfrp4, S1c30a5, Sic39a13, Sost, Sumf1, Src, Wnt10b）, five novel genes extensively characterized （Cldn18, Fam20c, Lrrkl, Sgpll, Wnt16）, five novel genes with preliminary characterization （Agpat2, RassfS, Slc10a7, Stc26a7, Slc30a10） and three novel undisclosed genes coding for potential osteoporosis drug targets.

Bioinformatics Analysis Raises Candidate Genes in Blood for Early Screening of Parkinson's Disease

Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.

Screening of Genes with Unique Mutations of Microcus

Yersinia pestis is the causative agent of bubonic and pneumonic plagues. Strains of Y. pestis are classified into four biovars： antiqua, mediaevalis, orientalis, and microtus[11. There are two microtus-related plague loci in China： the Microtus brandti plague focus in the Xilin Gol Grassland （focus L） and the Microtus fuscus plague focus in the Ojnghai-Tibet Plateau （focus M）.

Utilization of Gene Mapping and Candidate Gene Mutation Screening for Diagnosing Clinically Equivocal Conditions: A Norrie Disease Case Study

Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members..Mapping of the X chromosome and candidate gene mutation screening identified a c.C267A[p.F89L] mutation in NPD previously described as possibly causing Norrie disease..The detection of the c.C267A[p.F89L] variant in another unrelated family confirms the pathogenic nature of the mutation for the Norrie disease phenotype. Gene mapping, haplotype analysis, and candidate gene screening have been previously utilized in research applications but were applied here in a diagnostic setting due to the scarcity of available clinical information..The clinical diagnosis and mutation identification were critical for providing proper genetic counseling and prenatal diagnosis for this family.

Tay-Sachs carrier screening in the genomics age: Gene sequencing versus enzyme analysis in non-Jewish individuals

Purpose: To compare the sensitivity of Hexosaminidase A (HexA) enzyme-based testing to gene sequencing for carrier detection in non-Jewish individuals. Methods: Blood samples were obtained from parents and relatives of affected patients at an annual Tay-Sachs and Allied Diseases Foundation meeting. A family history was taken for each individual. Samples were analyzed for leukocyte HexA activity, serum HexA activity and subjected to extensive gene sequencing. The results from these analyses were combined with our previously published data describing 34 obligate Tay-Sachs disease (TSD) carriers. Results: Twelve additional TSD carriers were detected in this study. Gene sequencing successfully identified all 12 carriers whereas enzyme analysis identified 11 of 12 carriers. This individual is a carrier of the B1 variant that is known to cause false negative results with enzyme testing. Combined data from 46 non-Jewish TSD carriers revealed that gene sequencing had a higher sensitivity rate than HexA enzyme-based testing (94% versus 87%) in non-Jewish TSD carriers. In our series, approximately 4% of non-Jewish TSD carriers have this mutation. Conclusions: HexA gene sequencing provides a higher sensitivity for TSD carrier detection than HexA based enzyme analysis in non-Jewish patients primarily due to the presence of individuals with the B1 variant.

Cervical cancer screening: hTERC gene amplification detection by FISH in comparison with conventional methods

Aim: To assess the clinical significance of hTERC amplification for cervical cancer screening detected by fluorescence in situ hybridization (FISH) and compare it with that of current screening methods within the same group. Methods: A total of one hundred and nine women were recruited in this study. All of them had liquid-based thin-prep cytologic test (TCT), human papillomavirus (HPV) DNA testing and hTERC gene amplification analysis using interphase two-color FISH. In addition, colposcopically directed biopsy and/or cone biopsy were conducted for definite histopathologic diagnosis for each case. The optimal threashold of hTERC gene amplification by fluorescence in situ hybridization (FISH) were assecced by receiver operating characteristic (ROC) curve. The results of hTERC gene amplification analysis were compared with the cytological analysis, HPV DNA testing and those of subsequent biopsies. Results: Among the 109 patients, 18 were benign lesion, 17 were LSIL, 66 were HSIL and 8 were invasive carcinoma of cervix (ICC). Of them, hTERC-positive cases were found in 0.0% (0/18) of normal specimens, 11.8% (2/17) of LSIL, 72.7% (48/66) of HSIL and 100.0% (8/8) of ICC, respectively. The positive rate of hTERC gene amplification was significantly higher in HSIL and ICC compared with normal and LSIL (all P < 0.01).The optimal cut-off point of percentages of cells with hTERC amplification was determined as 5.5%. Using this threshold the hTERC test reached a much higher specificity(94.3%, 33/35) and a relatively lower sensitivity(77.0%, 57/74) to distinguish benign lesion and LSIL from HSIL and ICC in comparison with HR-HPV test (51.4%;91.9%) and TCT (74.3%;81.1%). Area Under the Curve revealed that hTERC amplification test performed more accurately (area under the curve = 0.857) compared to HPV test (area under the curve = 0.717) and cytology(area under the curve = 0.777) to discriminate HSIL or higher from LSIL or lower. This study also found a significant positive correlation between positive hTERC gain and HR-HPV infection, abnormal cytological or histopathologic lesions (all P < 0.01) in patients with cervical diseases. Conclusion: hTERC amplification testing may be a promising adjunct to screen women for cervical precancer or cancer with high specificity and accuracy.

Wolman Disease in Bulgarian Patients: Selective Genetic Screening in Two Presumable Endemic Regions

Wolman disease is a rare autosomal recessive disorder caused by mutations in the LIPA gene (10q23.31). The LIPA gene encodes lysosomal acid lipase (LAL), which plays a key role in hydrolysis of the cholesteryl esters and triglycerides. Two unrelated families from Bulgaria were referred for genetic testing with clinical diagnosis Wolman disease. Sanger sequencing of all coding exons and exon-intron boundaries of the LIPA gene was performed. The index patients were found to be homozygous for two different mutations in the LIPA gene: a missense mutation, c.260G > T, p.Gly87Val, which affects the enzyme active site and a splice-site change, c.822+1G > A, which most probably destroys the enzyme polypeptide chain. These two completely different types of mutations along the LIPA gene resulted in a very similar phenotype involving liver, kidney, gastrointestinal, muscle and blood disturbances. As consanguinity is not typical for the Bulgarian population, a possible explanation of the homozygosity could be presence of endemic regions for given mutations. To check this hypothesis, selective screening for these mutations was performed in two presumable endemic regions in Bulgaria. Altogether, 100 newborns were screened for p.Gly87Val mutation and the detected carrier frequency was about 1% (1/100), while in the group of 100 newborns screened for the c.822 + 1G > A mutation the detected carrier frequency was 2% (2/100). The results indicate a high recurrence risk of Wolman disease in these particular Bulgarian regions of about 1:10000. These findings are from crucial importance for the inhabitants of the corresponding parts of Bulgaria. They may benefit from early genetic testing and adequate genetic counselling during family planning.

组织Gene-xpert MTB/RIF基因检测技术在结核病诊断中的应用研究

目的:探讨组织Gene-xpert MTB/RIF基因检测技术在结核病诊断中的应用价值。方法:选择2022年6月至2024年2月我院收治的130例疑似结核病患者作为研究对象,取研究对象晨间痰液样本分别进行痰涂片镜检、罗氏固体培养检测、支气管黏膜组织、胸膜组织Gene-xpert MTB/RIF基因快速检测。以罗氏固体培养检测结果为金标准,分析痰涂片镜检与不同组织Gene-xpert MTB/RIF基因快速检测对结核病诊断结果的一致性;比较不同检查方式对结核病诊断效能的差异。结果:罗氏固体培养检测发现130例疑似结核病患者中,确诊为结核病的患者共72例,非结核病患者共58例,阳性率与阴性率分别为55.38%、44.62%。Kappa检验分析结果显示,痰涂片镜检与胸膜组织Gene-xpert MTB/RIF基因快速检测对结核病的诊断结果与临床实际结果均存在一般的一致性,而支气管黏膜组织Gene-xpert MTB/RIF基因检测对结核病的诊断结果与临床实际结果有较高的一致性(Kappa值分别为0.679、0.722、0.925)。支气管黏膜组织Gene-xpert MTB/RIF基因检测对结核病的诊断效能数据明显高于胸膜组织检测与痰涂片镜检(P<0.05)。结论:支气管黏膜组织Gene-xpertMTB/RIF基因检测技术在结核病诊断中的应用更好,可为结核病的临床诊断提供更为准确的数据参考,对后续治疗方案的及早制定与实施均具有指导意义。

Kartagener综合征合并分泌性中耳炎患者的基因诊断

目的应用基因筛查技术进行kartagener综合征合并慢性分泌性中耳炎患者的基因诊断。方法将2010年1月至2013年12月就诊于解放军总医院耳鼻咽喉头颈外科的8例kartagener综合征合并慢性分泌性中耳炎患者作为研究对象。采集病史、绘制家系图,进行纯音测听、声导纳检查;应用sanger测序进行热点基因筛查,并对1例患者及其父母应用全外显子组测序进行基因筛查,应用Pomol软件对候选基因编码蛋白进行3D-蛋白结构模拟。结果 8例患者均伴有慢性分泌性中耳炎。应用sanger测序进行热点基因筛查的患者,均未发现所筛查位点基因突变;应用全外显子组测序的1例患者发现c.8030G>A(p.R2677Q)突变,位于基因DNAH5。结论慢性分泌性中耳炎患者应考虑kartagener综合征的可能性,以免漏诊误诊,基因筛查为该病提供了分子遗传学诊断证据。

A screening analysis of the GJB2 c.176 del 16 mutation responsible for hereditary deafness in a Chinese family

Objective:To determine whether a new-born child from a family carrying a deafness gene needs cochlear implantation to avoid dysphonia by screening and sequencing a deafness-related gene.Results:Both screening and sequencing results confirmed that the new born child had a normal GJB2 gene despite the fact that she has a brother suffering from hearing loss triggered by an allelic GJB2 c.176 del 16 mutation.We cloned the GJB2 genes derived from their respective blood genomic DNA into GFP fused plasmids and transfected those plasmids into the 293 T cell line to test for gene function.While the mutated GJB2gene(GJB2 c.176 del 16) of her deaf brother was found to be unable to form the gap junction structure between two adjacent cells,the baby girl’s GJB2 gene ran into no such problems.Conclusion:The screening and sequencing as well as the GJB2 gene function tests invariably showed results consistent with the ABR tested hearing phenotype,which means that the child,with a normal wild type GJB2 gene,does not need early intervention to prevent her from developing hearing loss and dysphonia at a later stage in life.

Research progress and application of the CRISPR/Cas9 gene-editing technology based on hepatocellular carcinoma

Hepatocellular carcinoma(HCC)is now a common cause of cancer death,with no obvious change in patient survival over the past few years.Although the traditional therapeutic modalities for HCC patients mainly involved in surgery,chemotherapy,and radiotherapy,which have achieved admirable achievements,challenges are still existed,such as drug resistance and toxicity.The emerging gene therapy of clustered regularly interspaced short palindromic repeat/CRISPR-associated nuclease 9-based(CRISPR/Cas9),as an alternative to traditional treatment methods,has attracted considerable attention for eradicating resistant malignant tumors and regulating multiple crucial events of target gene-editing.Recently,advances in CRISPR/Cas9-based anti-drugs are presented at the intersection of science,such as chemistry,materials science,tumor biology,and genetics.In this review,the principle as well as statues of CRISPR/Cas9 technique were introduced first to show its feasibility.Additionally,the emphasis was placed on the applications of CRISPR/Cas9 technology in therapeutic HCC.Further,a broad overview of non-viral delivery systems for the CRISPR/Cas9-based anti-drugs in HCC treatment was summarized to delineate their design,action mechanisms,and anticancer applications.Finally,the limitations and prospects of current studies were also discussed,and we hope to provide comprehensively theoretical basis for the designing of anti-drugs.

Gene-XpertMTB/RIF技术在HIV合并结核分枝杆菌感染筛查中的应用

目的探讨新技术(Gene-XpertMTB/RIF,简称为Xpert)在人类免疫缺陷病毒(HIV)合并结核分枝杆菌感染筛查中的临床应用,期望为HIV/TB的感染者找到快捷、准确的检测方法或者检测方法组合。方法收集云南省传染病医院2017年3月至2018年12月收治的HIV住院患者278例痰液标本,每例患者痰液标本均用Xpert、罗氏培养法和直接涂片萋-纳抗酸染色法三种方法进行检测。结果Xpert、罗氏培养和直接涂片萋-纳抗酸染色法三种检测方法的阳性率分别为15.8%、12.6%、10.8%,Xpert与其他两种方法一致性评价,均为Kappa>0.75,一致性较好。结论Gene-XpertMTB/RIF技术是一种快速、安全、高效的分子生物学检测方法,并且能够同时检测利福平的耐药性,对艾滋病合并结核病的早期筛查具有重要意义。

Identifcation of up-regulated genes in human uterine leiomyoma by sup-pression subtractive hybridization

In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.

TGFBI and CHST6 gene analysis in Chinese stromal corneal dystrophies

AIM:To investigate whether mutations in TGFBI gene or CHST6 gene correlated with stromal corneal dystrophies(CD) in 8 Chinese probands.· METHODS:Eight unrelated patients with stromal corneal dystrophies were recruited in this study;all affected members were assessed by completely ophthalmologic examinations.Genomic DNA was extracted from peripheral leukocytes,17 exons of TGFBI gene and the exon of CHST6 gene were amplified by polymerase chain reaction(PCR),sequenced directly and compared with the reference database.· RESULTS:Three heterozygous mutations in TGFBI gene were identified in six patients:c.370C>T(p.Arg124Cys) was found in exon 4 of TGFBI gene in three members,c.371G>A(p.Arg124His) was found in one patient;c.1663C>T(p.Arg555Trp) was found in exon 12 in other two members.In addition,four polymorphisms with the nucleotide changes rs1442,rs1054124,rs4669,and rs35151677 were found in TGFBI gene.Mutations were not identified in the rest of 2 affected individuals in TGFBI gene or CHST6 gene.· CONCLUSION:Within these patients,R124C,R124H and R555W mutations were co-segregated with the disease phenotypes and were specific mutations for lattice corneal dystrophy type I(LCD I),Avellino corneal dystrophy(ACD,GCDⅡ),granular corneal dystrophy type I(GCD I),respectively.Our study highlights the prevalence of codon 124 and codon 555 mutations in the TGFBI gene among the Chinese stromal corneal dystrophies patients.·

THE CLONING OF HRNT-1 USING A COMBINATION OF cDNA LIBRARY SCREENING WITH BIOTIN-LABELED PROBE AND RAPID AMPLIFICATION OF cDNA ENDS

Objective: To clone the human counterpart of rat ZA73, EST cloned from rat tracheal epithelial (RTE) neoplastic transformed cell model induced by (a-particles radiation by using mRNA differential display. Methods: According to the sequence of rat ZA73, a probe was biotin-labeled to screen human cDNA library, and then the gene sequence was extended by RACE (rapid amplification of cDNA ends). Result: Human gene HRNT-1 (GenBank Accession Number: AF223393) is 4.256 kb in length, with an ORF located in the region between 254 and 3013 bp. 5′ UTS (untranslated sequences) is 253 bp, 3′ UTS is 1243 bp. Conclusion: The combination of cDNA library screening with biotin-labeled probes and RACE is an effective method to clone full-length cDNA, especially for sequences longer than 2 kb.

Incidence of Sickle Cell Disease and Other Hemoglobinopathies in Burkina Faso: Results of a Five-Year Systematic Neonatal Screening (2015-2019) in Four Urban Hospitals

Hemoglobinopathies, mainly Sickle cell disease (SCD), are the most common monogenic disorders in Africa. In Burkina Faso, data on these diseases are scarce, mainly hospital-based in Ouagadougou and its surroundings. In order to assess the incidence and allelic frequencies of the main hemoglobinopathies in newborns in Burkina Faso, we conducted a cross-sectional study from 2015 to 2019 in four hospitals. The study included babies of both sexes, regardless of ethnic group and parents’ hemoglobin status. It was a newborn screening and hemoglobin variants were detected using isoelectric focusing on cord blood samples and confirmed using hemoglobin electrophoresis by high-performance liquid chromatography. The proportions and cumulative incidences of the different hemoglobinopathies were computed. Hardy-Weinberg equilibrium law was applied to calculate genotypic and allelic frequencies. The significant level was p < 0.05. Out of 11,337 newborns included, 47.8% were males and 60.2% were from Bobo-Dioulasso. Abnormal hemoglobin was found in 27.1%, representing a cumulative incidence of 1:4 newborns. The incidence of SCD was 1.9% (1:53 newborns) with 27.9% of homozygous SS. Homozygous CC and compound heterozygous Cβ-Thalassemia accounted for 1.1%. SCD cases were 1.51 times higher in Bobo-Dioulasso (OR = 1.51;95% CI [1.09 - 2.10]: p = 0.013). The observed genotype frequencies were significantly different from the expected ones (p 0.001). The βS and βC alleles represented 5.1 and 9.9%, respectively. This study showed a high incidence of hemoglobinopathies. Such results raise the question of control strategies for these hemoglobinopathies in our country.

山药块茎生长膨大相关基因的筛选与分析

为筛选山药块茎生长膨大相关基因,采用生物信息学方法,对山药块茎发育前期和中期构建的不同发育阶段抑制性消减杂交(suppression subtractive hybridization,SSH)文库进行分析。结果表明:山药块茎发育前期与中期差异表达基因(differential expression genes,DEGs)序列主要涉及九大类,其中发育调控占比最大(27.1%),其他依次为细胞组织结构(14.0%)、物质代谢(11.2%)、生物合成(4.7%)等。初步筛选出泛素-连接酶体(F-box associated,F-box)、碳酸酐酶(carbonic anhydrase,CAs)、核苷二磷酸激酶(nucleoside diphosphate kinase,NDPK)、氨基酸透性酶(amino acid permease)、糖基转移酶(glycosyl transferase)、α-淀粉酶(α-amylase,AMY)等候选基因,它们可能与细胞增殖、细胞伸长、激素代谢、酸碱环境调节及功能物质代谢物等功能有关,参与调控山药块茎的生长膨大。

川东北地区3089例育龄期人群地中海贫血基因筛查结果分析

目的通过分析地中海贫血基因筛查结果,了解川东北地区育龄期人群中地中海贫血基因携带情况,为本地区地中海贫血的一级和二级防控提供实验室依据。方法回顾性分析2023年度在川北医学院附属医院进行地中海贫血基因筛查的3089例育龄期男女的基因检测、血常规和血红蛋白电泳结果,对地贫基因检测阴性而后两种方法检测结果异常者行罕见地中海贫血基因测序;选取其中22例血常规和血红蛋白电泳结果正常而本院基因检测结果提示为-ɑ3.7杂合缺失的标本进行HKɑɑ及ɑ三联体检测。结果3089标本中共检出370例地中海贫血基因携带者,阳性率为11.98%(370/3089),ɑ-地贫基因携带者194例(52.43%),β-地贫基因携带者166例(44.86%),最常见的基因型为--^(SEA)/ɑɑ、-ɑ^(3.7)/ɑɑ、β^(CD41-42M)/β^(N)、β^(CD17M)/β^(N)和β^(IVS-II-654M)/β^(N);罕见地贫基因测序标本中有1例为ɑɑɑ^(anti4.2),1例为β^(IVS-II-654M)杂合变异,4例为δ-地贫,1例为δ-地贫复合nd-HPFH,3例为结构异常血红蛋白,1例为HBB基因良性变异;PCR结果提示22例待测标本中有4例HKɑɑ。结论本地区育龄人群中的地中海贫血基因携带率较高,基因型复杂,应重视罕见地中海贫血基因和HKɑɑ的检测。

Screening and molecular classification of low-temperature protease from Antarctic microorganism and its characterization

107 strains producing protease were screened from 260 strains of Antarctic psychrophilic bacteria, among which proteolytic activity of five strains was more than 45 U ml^-1. The 16S rRNA gcne sequences homology and phylogcnetic analysis of five Antarctic psychrophillc bacteria showed that NJ276, NJS-9, NJ16-70,NJ345 belonged tO the described genus Pseudoalteromonas and NJ341 belonged to the genus Colwellia. The growth and the protease characteristic of four Antarctic psychrophilic bacteria had been studied, and the result showed that the 6ptimal temperature for growth and protease-produeing of four strains was about 10℃. Their growth and protease-produeing were still high during incubatlng 2-5 days. The maximum proteolytic activity occurred at pH 9 for four Antarctic psychrophilic bacteria. The optimal temperature of protease action of both strains NJ276 and NJ5-9 was about 50℃, however, the optimal temperature of protease aetlon of both strains NJ341 and NJ345 was about 40 ℃, and their proteolytic activity under 0℃ exhibited nearly 30% of the maximum activity, but their thermal stabilities were weaker. These results indicated that proteases from NJ341 and NJ345 were low-temperature proteases.

Two mutations in the truncated Rep gene RBR domain delayed the Wheat dwarf virus infection in transgenic barley plants

Wheat dwarf virus （WDV）, an important cereal pathogen, is closely related to Maize streak virus （MSV）, a model virus of the Mastrevirus genus. Based on its similarity to known MSV resistance strategies, a truncated part of the WDV replication- associated （RepA） gene （WDVRepA215） and the WDV RepA gene with a mutated retinoblastoma-related protein （RBR） interaction domain （WDVRepA215RBRre^t） were cloned into the plPKb002 expression vector and transformed into immature embryos of spring barley cv. Golden Promise plants through Agrobacterium-mediated transformation. A detailed study of T1-generation plants infected by leafhoppers （Psammotettix alienus） fed on infection sources of variable strength was performed over a 5-week period encompassing the initial stages of virus infection. A DNA WDV TaqMan qPCR assay normalized using the DNA puroindoline-b SYBR Green qPCR assay for samples on a per week basis revealed an approximately 2-week delay in WDVRepA215RBR^mut plants to WDVRepA215 plants before significant increases in the WDV viral levels occurred. Both WDVRepA215 and WDVRepA215RBR^mut plants showed similar levels of transgenic transcripts over the screened period; however, the transgenic plants also showed increased numbers of infected plants compared to the control plants.