Alterations of tumor-related genes do not exactly match the histopathological grade in gastric adenocarcinomas

AIM:To investigate the diverse characteristics of different pathological gradings of gastric adenocarcinoma (GA) using tumor-related genes.METHODS:GA tissues in different pathological gradings and normal tissues were subjected to tissue arrays.Expressions of 15 major tumor-related genes were detected by RNA in situ hybridization along with 3' terminal digoxin-labeled anti-sense single strandedoligonucleotide and locked nucleic acid modifying probe within the tissue array.The data obtained were processed by support vector machines by four different feature selection methods to discover the respective critical gene/gene subsets contributing to the GA activities of different pathological gradings.RESULTS:In comparison of poorly differentiated GA with normal tissues,tumor-related gene TP53 plays a key role,although other six tumor-related genes could also achieve the Area Under Curve (AUC) of the receiver operating characteristic independently by more than 80%.Comparing the well differentiated GA with normal tissues,we found that 11 tumor-related genes could independently obtain the AUC by more than 80%,but only the gene subsets,TP53,RB and PTEN,play a key role.Only the gene subsets,Bcl10,UVRAG,APC,Beclin1,NM23,PTEN and RB could distinguish between the poorly differentiated and well differentiated GA.None of a single gene could obtain a valid distinction.CONCLUSION:Different from the traditional point of view,the well differentiated cancer tissues have more alterations of important tumor-related genes than the poorly differentiated cancer tissues.

Characterization and distribution of novel alleles of the vernalization gene Vrn-A1 in Chinese wheat(Triticum aestivum L.) cultivars

The ability of wheat to adapt to a wide range of environmental conditions is determined mostly by allelic diversity among genes regulating vernalization requirement.Vrn-1 is a major regulator of this requirement.In this study,two novel alleles of Vrn-A1 were discovered in Chinese cultivars:vrn-A1n was identified in two landraces,Jiunong 2 and Ganchun 16,and Vrn-A1o was detected in Duanhongmangmai.Both novel alleles showed a linked duplication in the promoter region.The common copy of these two alleles was identical to the recessive allele vrn-A1.Compared with the recessive allele vrn-A1,the other copy of vrn-A1n contained a 54-bp deletion in the promoter region and the distinct copy of Vrn-A1o contained an11-bp deletion in the promoter region.In segregating populations in the greenhouse under nonvernalizing(20–25°C)and long-day(16 h light)conditions,plants with the novel vrn-A1n allele did not head earlier than those with the recessive vrn-A1 allele.However,plants that were either homozygous or heterozygous for the novel Vrn-A1o allele headed earlier than those with the recessive vrn-A1 allele.To identify the novel allele with the small-sized product and facilitate screening,a DNA marker for the novel dominant allele Vrn-A1o was designed.Analysis of the novel-allele distribution showed that two cultivars carrying the vrn-A1n allele were dispersed in the northwestern spring wheat zone,and 12 cultivars carrying the dominant Vrn-A1o allele were widely distributed in the northwestern spring wheat zone,Xinjiang winter and spring wheat zone,Yellow and Huai River valley winter wheat zone,and QinghaiTibetan Plateau spring and winter wheat zone.Our study identifies useful germplasm and a DNA marker for wheat breeding.

Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data

Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary study.Understanding lotus gene diversity is important for the study of molecular genetics and breeding.In this research,public RNA-seq data and the annotated reference genome were used to identify the genes in lotus.A total of 26,819 consensus and 1,081 novel genes were identified.Meanwhile,a comprehensive analysis of gene alternative splicing events was conducted,and a total of 19,983“internal”alternative splicing(AS)events and 14,070“complete”AS events were detected in 5,878 and 5,881 multi-exon expression genes,respectively.Observations made from the AS events show the predominance of intron retention(IR)subtype of AS events representing 33%.IR is followed by alternative acceptor(AltA),alternative donor(AltD)and exon skipping(ES),highlighting the universality of the intron definition model in plants.In addition,functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process,showing the key role for alternative splicing in influencing the growth and development of lotus.The results contribute to a better understanding of the current gene diversity in lotus,and provide an abundant resource for future functional genome analysis in lotus.

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

Background The genetic diversity of yak,a key domestic animal on the Qinghai-Tibetan Plateau(QTP),is a vital resource for domestication and breeding efforts.This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.Results We discovered 290 Mb of nonreference sequences and 504 new genes.Our pangenome-wide presence and absence variation(PAV)analysis revealed 5,120 PAV-related genes,highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations.Principal component analysis(PCA)based on binary gene PAV data classified yaks into three new groups:wild,domestic,and Jinchuan.Moreover,we pro-posed a‘two-haplotype genomic hybridization model'for understanding the hybridization patterns among breeds by integrating gene frequency,heterozygosity,and gene PAV data.A gene PAV-GWAS identified a novel gene(Bos-Gru3G009179)that may be associated with the multirib trait in Jinchuan yaks.Furthermore,an integrated transcrip-tome and pangenome analysis highlighted the significant differences in the expression of core genes and the muta-tional burden of differentially expressed genes between yaks from high and low altitudes.Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed m RNAs and lnc RNAs(between high-and low-altitude regions),especially in the heart and lungs,when comparing high-and low-altitude adaptations.Conclusions The yak pangenome offers a comprehensive resource and new insights for functional genomic studies,supporting future biological research and breeding strategies.

Functional analysis of the novel mitochondrial tRNA^(Trp)and tRNA^(Ser(AGY))variants associated with type 2 diabetes mellitus

BACKGROUND Mutations in mitochondrial tRNA(mt-tRNA)genes that result in mitochondrial dysfunction play important roles in type 2 diabetes mellitus(T2DM).We previously reported a large Chinese pedigree with maternally inherited T2DM that harbors novel mt-tRNA^(Trp)A5514G and tRNA^(Ser(AGY))C12237T variants,however,the effects of these mt-tRNA variants on T2DM progression are largely unknown.AIM To assess the potential pathogenicity of T2DM-associated m.A5514G and m.C12237T variants at genetic,molecular,and biochemical levels.METHODS Cytoplasmic hybrid(cybrid)cells carrying both m.A5514G and m.C12237T variants,and healthy control cells without these mitochondrial DNA(mtDNA)variants were generated using trans-mitochondrial technology.Mitochondrial features,including mt-tRNA steady-state level,levels of adenosine triphosphate(ATP),mitochondrial membrane potential(MMP),reactive oxygen species(ROS),mtDNA copy number,nicotinamide adenine dinucleotide(NAD+)/NADH ratio,enzymatic activities of respiratory chain complexes(RCCs),8-hydroxy-deoxyguanine(8-OhdG),malondialdehyde(MDA),and superoxide dismutase(SOD)were examined in cell lines with and without these mt-tRNA variants.RESULTS Compared with control cells,the m.A5514G variant caused an approximately 35%reduction in the steady-state level of mt-tRNA^(Trp)(P<0.0001);however,the m.C12237T variant did not affect the mt-tRNA^(Ser(AGY))steady-state level(P=0.5849).Biochemical analysis revealed that cells with both m.A5514G and m.C12237T variants exhibited more severe mitochondrial dysfunctions and elevated oxidative stress than control cells:ATP,MMP,NAD+/NADH ratio,enzyme activities of RCCs and SOD levels were markedly decreased in mutant cells(P<0.05 for all measures).By contrast,the levels of ROS,8-OhdG and MDA were significantly increased(P<0.05 for all measures),but mtDNA copy number was not affected by m.A5514G and m.C12237T variants(P=0.5942).CONCLUSION The m.A5514G variant impaired mt-tRNA^(Trp)metabolism,which subsequently caused mitochondrial dysfunction.The m.C12237T variant did not alter the steady-state level of mt-tRNA^(Ser(AGY)),indicating that it may be a modifier of the m.A5514G variant.The m.A5514G variant may exacerbate the pathogenesis and progression of T2DM in this Chinese pedigree.

Novel mutation in the ligand-binding domain of the androgen receptor gene （1790p） associated with complete androgen insensitivity syndrome

Mutations in the X-linked androgen receptor （AR） gene cause androgen insensitivity syndrome （AIS）, resulting in an impaired embryonic sex differentiation in 46,XY genetic men. Complete androgen insensitivity （CAIS） produces a female external phenotype, whereas cases with partial androgen insensitivity （PALS） have various ambiguities of the genitalia. Mild androgen insensitivity （MAIS） is characterized by undermasculinization and gynecomastia. Here we describe a 2-month-old 46,XY female patient, with all of the characteristics of CAIS. Defects in testosterone （T） and dihydrotestosterone （DHT） synthesis were excluded. Sequencing of the AR gene showed the presence in exon 6 of a T to C transition in the second base of codon 790, nucleotide position 2369, causing a novel missense Leu790Pro mutation in the ligand-binding domain of the AR protein. The identification of a novel AR mutation in a girl with CAIS provides significant information due to the importance of missense mutations in the ligand-binding domain of the AR, which are able to induce functional abnormalities in the androgen binding capability, stabilization of active conformation, or interaction with coactivators.

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.

Cloning and characterization of a novel gene (C17orf25) from the deletion region on chromosome 17p13.3 in hepatocelular carcinoma

Using a combination of hybridization of PAC to a cDNA library and RACE technique, we isolated a novel cDNA, designated as C17orf25 (Chromosome 17 open rea(ling frame 25, previously named it HC71A), from the deletion region on chromosome 17p13.3. The cDNA encodes a protein of 313 amino acids with a calculated molecular mass of 34.8 kDa. C17orf25 is divided into 10 exons and 9 introns, spanning 23 kb of genomic DNA. Northern blot analysis showed that the mRNA expression of C17orf25 was decreased in hepatocellular carcinoma samples as compared to adjacent noncancerous liver tissues from the same patients. The transfection of C17or25 into the hepatocellular carcinoma cell SMMC7721 and overexpression could inhibit the cell growth. The above results indicate that C17orf25 is a novel human gene, and the cloning and preliminary characterization of C17orf25 is a prerequisite for further functional analysis of this novel gene in human hepatocellular carcinoma.

Novel Association of Killer Cell Immunoglobulin-like Receptor Genes with EBV-infectious Diseases in Children

Killer cell immunoglobulin-like receptors （KIRs） which are mainly expressed on natural killer （NK） cells are implicated in many virus infections. However, it is unclear whether or not KIRs are associated with susceptibility to Epstein-Barr virus （EBV） infection related diseases. Therefore, the purpose of our study was to investigate possible correlation between polymorphisms of KIR genes and infectious mononucleosis （IM）/EBV-associated hemophagocytic Iymphohistiocytosis （EBV-HLH）. The polymorphisms of KIR genes were detected by polymerase chain reaction with sequence-specific primers （PCR-SSP）. The results would contribute to clarify the association of KIRs with EBV induced diseases, and provide new insights into the role of NK cells and innate immune response against viral infections and/or subsequent progression.

A novel nonsense mutation of GPR143 gene in a Korean kindred with X-linked congenital nystagmus

Dear Editor,I am Dr.Ungsoo Samuel Kim.from Kim＇s Eye Hospital,Konyang University,Seoul,Korea.I write to present a novel mutation of GPR143 in Korean patients with X-linked congenital nystagmus by using exome sequencing.Congenital nystagmus is an inherited ocular disorder that can occur as an X-linked condition.

Characterization of the 19 Novel Cotton FLA Genes and Their Expression Profiling in Fiber Development and in Response to Phytohormones and Salt Stress

Fasciclin-like arabinogalactan proteins(FLAs),a subclass of arabinogalactan proteins(AGPs),are usually involved in cell development in plants.To investigate the expression profiling as well

Microarray-Based Differential Expression Monitoring of 79 Novel Genes in Human Fetal Tissues

ESTs fragments which represents corresponding novel genes were obtained by sequencing and bioinformatics analysis of human fet al kidney cDNA library. Microarray was prepared by using these novel EST fragmen ts by automatic spotting. Expression patters of 79 ESTs of novel genes from huma n fetal kidney were analyzed in fetal brain and fetal heart tissues of 20\|week\ | and 26\|week\|age fetus by performing of cDNA chip hybridization. This provide s clues for studying exact functions of the novel genes. 8 genes were obtained w hich were expressed differentially in the fetal brain and heart of 20\|week\| an d 26\|week\|age respectively. Then differentially expressed genes were identifie d by Northern analysis. The more exact function of the novel genes is under stud y.

Expression and subcellular localization of a novel gene <i>Bm-X</i>of the silkworm, <i>Bombyx mori</i>

According to the large-scale sequencing of cDNA library from silkworm pupae, the cDNA of a novel gene with blank research background was identified and temporarily named Bm-X. The length of this cDNA is 778 bp. We obtained its ORF for further study by bioinformatics analysis. It is 444 bp and encodes 147 amino acid residues, with a predicted molecular weight (MW) of 16.4 kD and an isoelectric point (pI) of 3.69. In this study, we successfully constructed a recombinant plasmid pET-28a(+)-Bm-X and expressed it in Escherichia coli. We used the fusion protein rBm-X which purified by Niaffinity chromatography to produce polyclonal antibodies against Bm-X for Western blot analysis. The analysis revealed that Bm-X was expressed in the larval midgut, the epidermis and the silk gland. In addition, the subcellular localization analysis of silkworm ovary epithelial cells (BmN cells) showed that Bm-X protein was located both in cytoplasm and nucleus, and the signal was stronger in cytoplasm than in nucleus. Our findings indicate that Bm-X gene is a novel species-specificity gene and its expression product can be detected in tissues of the fifth silkworm instar larvae and BmN cells.

Cloning and genetic transformation of a novel rice gene OsAPT2

A novel rice gene OsAPT2,which encodes a putative adenine phosphoribosyl transferase(APRT),was cloned.Its full-length cDNA is 1125bp,composing an ORF encoding 212 amino acid residues and a stop cordon,a 5' UTR of 123 bp and a 3' UTR of 363 bp.The sequence data have been submitted to the DDBJ/EMBL/GenBank databases(accession number:AY238894).The deduced amino acid sequence of OsAPT2 is highly homologous to those of previously reported APRTs.The genomic OsAPT2 gene contains 7 exons and 6 introns.Its total length is 4758 bp.Then,an antisense expression vector of the full-length OsAPT2 cDNA was constructed and transformed into rice variety Taibei309 by Agrobacterium tumefaciens mediated transformation method.In total,650 T0 transgenic plants were obtained based on both antibiotic screening and specific PCR identification.One hundred individuals of them were selected and planted in Hainan Island.From those 11 male sterile lines with seed-setting rate lower than 3% in bagged spike were obtained.Results suggest that OsAPT2 is involved in male sterility.Nine of the 11 male sterile lines were constitutive sterile lines;two of the 11 male sterile lines were thermo-sensitive genic male sterile lines,which may be useful in hybride rice breeding.

Cloning and characterization of a novel barley gene,HvORG4,induced by Fusarium graminearum infection

Barley Fusarium head blight(FHB),caused by species of the Fusarium fungus,is a devastating disease that is reemerging worldwide in recent years.In this study,a novel gene,HvORG4,was cloned from barley by using cDNA library and suppression subtractive hybridization(SSH) library strategies.The SSH library and cDNA library were constructed from the Chinese barley cultivar Jing02-461(resistance to FHB) infected by Fusarium graminearum isolate Huanggang-1.For the SSH analysis,more than 120 differentially expressed cDNAs were identified and sequenced.One of them showed high homology to the AtORG4 gene and was used as a probe to screen the cDNA library of Jing02-461.Six positive clones were identified and one of them contained a full-length cDNA,which was named HvORG4.Sequence analysis showed that HvORG4 encoded a deduced basic protein of 197 amino acids.Northern blotting analysis showed that HvORG4 was constitutively expressed in root and stalk,not in leaf or spike,and strongly induced in barley spikelets in response to infection with F.graminearum isolate Huanggang-1.Its homology and expression profile suggest that the HvORG4 might function as a transcription factor,playing an important role in signal transduction pathway for defense against FHB in barley.

Novel hydroxymethylbilane synthase gene mutation identified and confirmed in a woman with acute intermittent porphyria:A case report

BACKGROUND Acute intermittent porphyria(AIP)is a rare autosomal dominant porphyrin metabolic disease caused by a mutation in the hydroxymethylbilane synthase(HMBS)gene.This study aimed to explore the clinical manifestations of a patient with AIP,to identify a novel HMBS gene mutation in the proband and some of her family members,and to confirm the pathogenicity of the variant.CASE SUMMARY A 22-year-old Chinese woman developed severe abdominal pain,lumbago,sinus tachycardia,epileptic seizure,hypertension,and weakness in lower limbs in March,2018.Biochemical examinations indicated hypohepatia and hyponatremia.Her last menstrual period was 45 d prior to admission,and she was unaware of the pregnancy,which was confirmed by a pregnancy test after admission.Sunlight exposure of her urine sample for 1 h turned it from yellow to wine red.Urinary porphyrin test result was positive.Based on these clinical manifestations,AIP was diagnosed.After increasing her daily glucose intake(250–300 g/d),abdominal pain was partially relieved.Three days after hospitalization,spontaneous vaginal bleeding occurred,which was confirmed as spontaneous abortion;thereafter,her clinical symptoms completely resolved.Genetic testing revealed a novel heterozygous splicing variant of the HMBS gene in exon 10(c.648_651+1delCCAGG)in the proband and four other family members.The pathogenicity of the variant was verified through bioinformatic methods and a minigene assay.CONCLUSION We identified a novel HMBS gene mutation in a Chinese patient with AIP and confirmed its pathogenicity.

Cloning and Expression of HBV Infection Related Novel Gene C12orf49

To clone,express and purify C12orf49 recombinant protein.To prepare rabbit anti-C12orf49 protein polyclonal antibody and further elucidate its biological function.Methods PCR was applied to amplify the gene C12orf49 in vitro.pET-32a(+)-C12orf49,the recombinant protein prokaryotic expression vector,was transformed into E.coli.IPTG was used as an inductive agent to obtain C12orf49 recombinant protein,then the recombinant protein was analyzed with sodium dodecyl sulfatepolyacrylamide gel electrophoresis(SDS-PAGE)and Western blot.Specific polyclonal antibody was derived from rabbits that was immunized by recombinant protein.ELISA and Western blot were used to detect its titer and specificity,respectively.MTT cell proliferation experiment was carried out to observe the effect of protein on proliferation of HepG2 cells.Results The C12orf49 recombinant protein was expressed in a large quantity.Data of ELISA indicated that the titer of polyclonal antibody was higher than 1:1 280 000.And a good specificity of the antibody was confirmed by Western blot.C12orf49 recombinant protein might have an advanced effect on the proliferation of HepG2 cells.Conclusions Using C12orf49 recombinant protein,we can obtain the polyclonal antibody with great titer and good specificity.Human novel gene C12orf49 encoded protein could promote the proliferation of HepG2 cells.

Agrobacterium-meditated Genetic Transformation of an Upland Cotton(Gossypium hirsutum cv Coker 310) Using a Novel Bt Gene Cry2Ac

The development of transgenic cotton varieties resistant to bollworms has been a major success of applying plant genetic engineering technology to agriculture,evidenced by phenomenal increase in

Introgression of Bt Genes in Novel Germplasm and Contribution to Indian Cotton Economy

Emergence of transgenic Bt-cotton technology has opened up a new chapter in Indian cotton production in 21st century.The cry1Ac gene of Monsanto derived from American Upland Coker-312 background was not directly suitable for varied cotton growing situations in India.Delivery of

Novel treatments and genetics of age-related macular degeneration-a narrative review

Age-related macular degeneration(AMD)remains a leading cause of severe visual impairment in developing countries.Although dry-type AMD and geographic atrophy(GA)are progressive conditions with the associated decrease of visual functions,no well-established treatment regimen was proposed for the disease.Wet-type AMD is effectively treated with intravitreal anti-angiogenic agents,but frequent injections are a major issue for the affected patients.Recent advances in AMD genetics have provided new insights into the pathogenesis and novel therapeutic targets of AMD,but the benefits of using genetic testing and genotype-based risk models for AMD development and progression still lacks evidence.Novel AMD treatments aim to increase the interval among intravitreal injections through new therapeutic agents and modern delivery devices.Simultaneously,gene therapy for dry and wet AMD is widely studied.Although gene therapy possesses a major superiority over other novel treatments regarding a persistent cure of disease,many challenges exist in the way of its broad impact on the ocular health of AMD patients.