Sugarcane has recently attracted increasing attention for its potential as a source of sugar and bioethanol,so increasing its yield is essential to ensure the sugar security and bioenergy production.Intergeneric hybri...Sugarcane has recently attracted increasing attention for its potential as a source of sugar and bioethanol,so increasing its yield is essential to ensure the sugar security and bioenergy production.Intergeneric hybridization is a highly efficient method to produce new genetic variants of crop plants,particularly those species with high ploidy such as sugarcane(Saccharum spp.).Tripidium arundinaceum exhibits many desirable agronomic traits,and has been widely studied to produce hybrids with improved stress tolerance and other characteristics in sugarcane breeding.However,the genetic relationship between T.arundinaceum and Saccharum species,and the individual T.arundinaceum chromosomal compositions in sugarcane hybrids are still elusive.Here we used whole-genome single-nucleotide polymorphisms(SNPs)to ascertain the phylogenetic relationships between these species and found that T.arundinaceum is more closely related to Saccharum than Sorghum,in contrast to the previous narrow genetic analyses using chloroplast DNA.Additionally,oligonucleotide(oligo)-based chromosome-specific painting derived from Saccharum officinarum was able to distinctly identify the chromosomes of T.arundinaceum.We developed the oligo-genomic in situ hybridization(GISH)system for the first time,to unveil the novel chromosome translocations and the transmission of individual T.arundinaceum chromosomes in sugarcane progeny.Notably,we discovered that the chromosomal transmission of T.arundinaceum exhibited several different inheritance modes,including n,2n,and over 2n in the BC1 progenies.Such inheritance patterns may have resulted from first division restitution(FDR)or FDR+nondisjunction of a chromosome with the sister chromatids in the second meiosis division/second division restitution(FDR+NSC/SDR)model during meiosis.These results will be of substantial benefit for the further selection of T.arundinaceum chromosomes for sugarcane genetic improvement.展开更多
Background:Pancreatic cancer is a common malignancy with poor prognosis and limited treatment.Here we aimed to investigate the role of host chromosomal instability(CIN)and tumor microbiome in the prognosis of pancreat...Background:Pancreatic cancer is a common malignancy with poor prognosis and limited treatment.Here we aimed to investigate the role of host chromosomal instability(CIN)and tumor microbiome in the prognosis of pancreatic cancer patients.Methods:One hundred formalin-fixed paraffin-embedded(FFPE)pancreatic cancer samples were collected.DNA extracted from FFPE samples were analyzed by low-coverage whole-genome sequencing(WGS)via a customized bioinformatics workflow named ultrasensitive chromosomal aneuploidy detector.Results:Samples were tested according to the procedure of ultrasensitive chromosomal aneuploidy detector(UCAD).We excluded 2 samples with failed quality control,1 patient lost to follow-up and 6 dead in the perioperative period.The final 91 patients were admitted for the following analyses.Thirteen(14.3%)patients with higher CIN score had worse overall survival(OS)than those with lower CIN score.The top 20 microbes in pancreatic cancer samples included 15 species of bacteria and 5 species of viruses.Patients with high human herpesvirus(HHV)-7 and HHV-5 DNA reads exhibited worse OS.Furthermore,we classified 91 patients into 3 subtypes.Patients with higher CIN score(n=13)had the worst prognosis(median OS 6.9 mon);patients with lower CIN score but with HHV-7/5 DNA load(n=24)had worse prognosis(median OS 10.6 mon);while patients with lower CIN score and HHV-7/5 DNA negative(n=54)had the best prognosis(median OS 21.1 mon).Conclusions:High CIN and HHV-7/5 DNA load were associated with worse survival of pancreatic cancer.The novel molecular subtypes of pancreatic cancer based on CIN and microbiome had prognostic value.展开更多
BACKGROUND Few studies have reported an association between an increased risk of acquiring cancers and survival in patients with 4q deletion syndrome.This study presents a rare association between chromosome 4q abnorm...BACKGROUND Few studies have reported an association between an increased risk of acquiring cancers and survival in patients with 4q deletion syndrome.This study presents a rare association between chromosome 4q abnormalities and fallopian tube highgrade serous carcinoma(HGSC)in a young woman.CASE SUMMARY A 35-year-old woman presented with acute dull abdominal pain and a known chromosomal abnormality involving 4q13.3 duplication and 4q23q24 deletion.Upon arrival at the emergency room,her abdomen appeared ovoid and distended with palpable shifting dullness.Ascites were identified through abdominal ultrasound,and computed tomography revealed an omentum cake and an enlarged bilateral adnexa.Blood tests showed elevated CA-125 levels.Paracentesis was conducted,and immunohistochemistry indicated that the cancer cells favored an ovarian origin,making us suspect ovarian cancer.The patient underwent debulking surgery,which led to a diagnosis of stage IIIC HGSC of the fallopian tube.Subsequently,the patient received adjuvant chemotherapy with carboplatin and paclitaxel,resulting in stable current condition.CONCLUSION This study demonstrates a rare correlation between a chromosome 4q abnormality and HGSC.UBE2D3 may affect crucial cancer-related pathways,including P53,BRCA,cyclin D,and tyrosine kinase receptors,thereby possibly contributing to cancer development.In addition,ADH1 and DDIT4 may be potential influencers of both carcinogenic and therapeutic responses.展开更多
Gastric cancer(GC)is a prevalent malignant tumor within the digestive system,with over 40%of new cases and deaths related to GC globally occurring in China.Despite advancements in treatment modalities,such as surgery ...Gastric cancer(GC)is a prevalent malignant tumor within the digestive system,with over 40%of new cases and deaths related to GC globally occurring in China.Despite advancements in treatment modalities,such as surgery supplemented by adjuvant radiotherapy or chemotherapeutic agents,the prognosis for GC remains poor.New targeted therapies and immunotherapies are currently under invest-igation,but no significant breakthroughs have been achieved.Studies have indicated that GC is a heterogeneous disease,encompassing multiple subtypes with distinct biological characteristics and roles.Consequently,personalized treatment based on clinical features,pathologic typing,and molecular typing is crucial for the diagnosis and management of precancerous lesions of gastric cancer(PLGC).Current research has categorized GC into four subtypes:Epstein-Barr virus-positive,microsatellite instability,genome stability,and chromosome instability(CIN).Technologies such as multi-omics analysis and gene sequencing are being employed to identify more suitable novel testing methods in these areas.Among these,ultrasensitive chromosomal aneuploidy detection(UCAD)can detect CIN at a genome-wide level in subjects using low-depth whole genome sequencing technology,in conjunction with bioinformatics analysis,to achieve qualitative and quantitative detection of chromosomal stability.This editorial reviews recent research advancements in UCAD technology for the diagnosis and management of PLGC.展开更多
Objective:To analyze the clinical value of non-invasive prenatal testing(NIPT)in detecting chromosomal copy number variations(CNVs)and to explore the relationship between gene expression and clinical manifestations of...Objective:To analyze the clinical value of non-invasive prenatal testing(NIPT)in detecting chromosomal copy number variations(CNVs)and to explore the relationship between gene expression and clinical manifestations of chromosomal copy number variations.Methods:3551 naturally conceived singleton pregnant women who underwent NIPT were included in this study.The NIPT revealed abnormalities other than sex chromosome abnormalities and trisomy 13,18,and 21.Pregnant women with chromosome copy number variations underwent genetic counseling and prenatal ultrasound examination.Interventional prenatal diagnosis and chromosome microarray analysis(CMA)were performed.The clinical phenotypes and pregnancy outcomes of different prenatal diagnoses were analyzed.Additionally,a follow-up was conducted by telephone to track fetal development after birth,at six months,and one year post-birth.Results:A total of 53 cases among 3551 cases showed chromosomal copy number variation.Interventional prenatal diagnosis was performed in 36 cases:27 cases were negative and 8 were consistent with the NIPT test results.This indicates that NIPT’s positive predictive value(PPV)in CNVs is 22.22%.Conclusion:NIPT has certain clinical significance in screening chromosome copy number variations and is expected to become a routine screening for chromosomal microdeletions and microduplications.However,further interventional prenatal diagnosis is still needed to identify fetal CNVs.展开更多
The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli stra...The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli strain for coenzyme Q10 production. A series of integration expression vectors, pxKC3T5b and pxKT5b, were constructed for chemically inducible chromosomal evolution(multiple copy integration) and replicon-free and markerless chromosomal integration(single copy integration), respectively. A coenzyme Q10 hyper-producer Escherichia coli TBW20134 was constructed by applying chemically inducible chromosomal evolution,replicon-free and markerless chromosomal integration as well as deletion of menaquinone biosynthetic pathway.The engineered E. coli TBW20134 produced 10.7 mg per gram of dry cell mass(DCM) of coenzyme Q10 when supplemented with 0.075 g·L-1of 4-hydroxy benzoic acid; this yield is unprecedented in E. coli and close to that of the commercial producer Agrobacterium tumefaciens. With this strain, the coenzyme Q10 production capacity was very stable after 30 sequential transfers and no antibiotics were required during the fermentation process. The strategy presented may be useful as a general approach for construction of stable production strains synthesizing natural products where various copy numbers for different genes are concerned.展开更多
In this Editorial review,we would like to focus on a very recent discovery showing the global autosomal gene regulation by Y-and inactivated X-chromosomal transcription factors,zinc finger gene on the Y chromosome(ZFY...In this Editorial review,we would like to focus on a very recent discovery showing the global autosomal gene regulation by Y-and inactivated X-chromosomal transcription factors,zinc finger gene on the Y chromosome(ZFY)and zinc finger protein X-linked(ZFX).ZFX and ZFY are both zinc-finger proteins that encode general transcription factors abundant in hematopoietic and embryonic stem cells.Although both proteins are homologs,interestingly,the regulation of self-renewal by these transcriptional factors is almost exclusive to ZFX.This fact implies that there are some differential roles between ZFX and ZFY in regulating the maintenance of self-renewal activity in stem cells.Besides the maintenance of stemness,ZFX overexpression or mutations may be linked to certain cancers.Although cancers and stem cells are double-edged swords,there is no study showing the link between ZFX activity and the telomere.Thus,stemness or cancers with ZFX may be linked to other molecules,such as Oct4,Sox2,Klf4,and others.Based on very recent studies and a few lines of evidence in the past decade,it appears that the ZFX is linked to the canonical Wnt signaling,which is one possible mechanism to explain the role of ZFX in the self-renewal of stem cells.展开更多
Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain large...Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain largely undiscovered. Nevertheless, more and more genetic factors associated with infertility are being identified. This review will focus on our current understanding of the chromosomal basis of male infertility specifically: chromosomal aneuploidy, structural and numerical karyotype abnormalities and Y chromosomal microdeletions. Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans. Aneuploidy is predominantly maternal in origin, but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts. Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm. Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed, as well as the application of preimplantation genetic diagnosis (PGD) in such cases. Clinical recommendations where possible will be made, as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility.展开更多
A total of 1,160 differentially expressed genes induced by Marssonina brunnea f. sp. muhigermtubi were identified in Populus deltoides cv. 'Lux' (1-69/55) with two-colour cDNA microarray including 2,952 cDNAs from...A total of 1,160 differentially expressed genes induced by Marssonina brunnea f. sp. muhigermtubi were identified in Populus deltoides cv. 'Lux' (1-69/55) with two-colour cDNA microarray including 2,952 cDNAs from two cDNA libraries constructed with 72 h inoculated poplar leaves. Functional analysis showed that 1,160 genes were classified into 11 functional categories that are involved in metabolism (15.9%), signal transduction (9.5%), transcription and replication (8.7%), and cell rescue and defense (7.8%). Among them, 926 genes were sporadically localized on 19 linkage groups. Chromosome 2 contained 102 (11%) differentially expressed genes, followed by chromosome 1 which contains 93 genes (10%), and chromosome 17 had the least number of differentially expressed genes. Clustering of expressed sequence tags (ESTs) in poplar genome was observed at the terminal regions of several chromosomes. The relationship between cluster of genes and plant defense response would be further studied.展开更多
Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database...Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources). We mapped fragile sites to chromosomal bands and divided the 23 chromosomes into fragile and non-fragile sites. The frequency of rearrangements at the chromosomal location of clones found to be deleted or duplicated in the array/CGH analysis, provided by DECIPHER, was compared in Chromosomal Fragile Sites vs. non-Fragile Sites of the human genome. The POSSUM Web was used to complement this study. The results indicated 1) a predominance of rearrangements in CFSs, 2) the absence of statistically significant difference between the frequency of rearrangements in common CFSs vs. rare CFSs, 3) a predominance of deletions over duplications in CFSs. These results on constitutional chromosomal rearrangements are evocative of the findings previously reported by others relatively to cancer supporting the current line of evidence and suggesting that a common mechanism can underlie the generation of constitutional and somatic rearrangements. The combination of insights obtained from our results and their interrelationships can indicate strategies by which the mechanisms can be targeted with preventive medical interventions.展开更多
Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled geno...Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://www.treeshrewdb.org) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.展开更多
AIM To explore the correlation of metabolomics profiles ofgastric cancer(GC) with its chromosomal instability(CIN) status.METHODS Nineteen GC patients were classified as CIN and nonCIN type by The Cancer Genome Atlas ...AIM To explore the correlation of metabolomics profiles ofgastric cancer(GC) with its chromosomal instability(CIN) status.METHODS Nineteen GC patients were classified as CIN and nonCIN type by The Cancer Genome Atlas Research Group system, based on 409 oncogenes and tumor suppressor genes sequenced. The aqueous metabolites of the GC tumor and its surrounding adjacent healthy tissues were identified through liquid chromatographymass spectrometry. Groups were compared by defining variable importance in projection score of > 1.2, a fold change value or its reciprocal of > 1.2, and a P value of < 0.05 as a significant difference.RESULTS In total,twelve men and seven women were enrolled, with a median age of 66 years(range, 47-87 years). The numbers of gene alterations in the CIN GC group were significantly higher than those in the non-CIN GC(32-218 vs 2-17; P < 0.0005). Compared with the adjacent healthy tissues, GC tumors demonstrated significantly higher aspartic acid, citicoline, glutamic acid, oxidized glutathione, succinyladenosine, and uridine diphosphate-Nacetylglucosamine levels, but significantly lower butyrylcarnitine, glutathione hydroxyhexanoycarnitine, inosinic acid, isovalerylcarnitine, and threonine levels(all P < 0.05). CIN tumors contained significantly higher phosphocholine and uridine 5'-monophosphate levels but significantly lower beta-citryl-L-glutamic acid levels than did non-CIN tumors(all P < 0.05). CIN GC tumors demonstrated additional altered pathways involving alanine, aspartate, and glutamate metabolism, glyoxylate and dicarboxylate metabolism, histidine metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis.CONCLUSION Metabolomic profiles of GC tumors and the adjacent healthy tissue are distinct, and the CIN status is associated with downstream metabolic alterations in GC.展开更多
GPX-GI is a cytosolic tetrameric Se-dependent glutathione peroxidase, similar in properties to GPX-1. Unlike the almost ubiquitous GPX-1, GPX-GI is mainly expressed in the epithelium of gastrointestinal tract. GPX-GI ...GPX-GI is a cytosolic tetrameric Se-dependent glutathione peroxidase, similar in properties to GPX-1. Unlike the almost ubiquitous GPX-1, GPX-GI is mainly expressed in the epithelium of gastrointestinal tract. GPX-GI contributes to at least fifty percent of GPX activity in rodent small intestmal epithelium. The total GPX activity consists of at least 70% of selenium-dependent GPX activity in this compartment.By analyzing a panel of mouse mterspecies DNA from the Jackson Laboratory's backcross resource,we mapped Gpx2 gene to mouse chromosome 12 between D12Mit4 and D12Mit5, near the Ccs1 locus which contains a colon cancer susceptibility gene. A pseudogene, Gpx2-ps is mapped to mouse chromosome 7.Comparison of Gpx2 gene expression in three pairs of C57BL/6Ha and ICR/Ha mice which are respectively resistant and sensitive to dimethylhydrazine-induced colon cancer, we found a higher Gpx2 mRNA level in C57BL/6Ha colon than ICR/Ha colon. Interestingly, a lower level of GPX activity is found in the resistant strain of mice. Because GPX-1 has three times higher specific activity than GPX GI, our data suggest that the decreased GPX activity may result from a higher level of Gpx2 gene expression in those cells co-express GPx1 gene展开更多
Turmeric has long been used as a spice and food colouring agent in Asia. In the present investigation, the antimutagenic potential of curcumin was evaluated in Allium cepa root meristem cells. So far there is no repor...Turmeric has long been used as a spice and food colouring agent in Asia. In the present investigation, the antimutagenic potential of curcumin was evaluated in Allium cepa root meristem cells. So far there is no report on the biological properties of curcumin in plant test systems. The root tip cells were treated with sodium azide at 200 and 300 μg/ml for 3 h and curcumin was given at 5, 10 and 20 μg/ml for 16 h, prior to sodium azide treatment. The tips were squashed after colchicine treatment and the cells were analyzed for chromosome aberration and mitotic index. Curcumin induces chromosomal aberration in Allium cepa root tip cells in an insignificant manner, when compared with untreated control. Sodium azide alone induces chromosomal aberrations significantly with increasing concentrations. The total number of aberrations was significantly reduced in root tip cells pretreated with curcumin. The study reveals that curcumin has antimutagenic potential against sodium azide induced chromosomal aberrations in Allium cepa root meristem cells. In addition, it showed mild cytotoxicity by reducing the percentage of mitotic index in all curcumin treated groups, but the mechanism of action remains unknown. The antimutagenic potential of curcumin is effective at 5 μg/ml in Allium cepa root meristem cells.展开更多
A backcross recombinant inbred line population consisting of 202 lines was developed from Xieqingzao B//Xieqingzao B / Dongxiang wild rice. The population was assayed with DNA markers and phenotyped on planthopper res...A backcross recombinant inbred line population consisting of 202 lines was developed from Xieqingzao B//Xieqingzao B / Dongxiang wild rice. The population was assayed with DNA markers and phenotyped on planthopper resistance and yield traits. A linkage map consisting of 119 DNA markers and spanned for 1188 cM over the 12 rice chromosomes was constructed. Thirty-two chromosomal segment substitution lines were selected based on the percentage of Xieqingzao B allele at marker loci. These lines are of great potential for gene mapping and alien gene introgression.展开更多
Cotton fibers are the main raw materials of the textile industry.Exogenous superior fiber genes have been introduced into upland cotton to develop high-yield cultivars with excellent fiber quality.We used a single chr...Cotton fibers are the main raw materials of the textile industry.Exogenous superior fiber genes have been introduced into upland cotton to develop high-yield cultivars with excellent fiber quality.We used a single chromosomal segment on the chromosome A07 substitution line SL7,with high fiber strength,to investigate the molecular mechanism underlying its fiber quality.RNA-seq and KEGG analysis showed that 70 differentially expressed genes were enriched in plant hormone transduction pathways,including auxin,ethylene and abscisic acid,in fibers at 10 days post-anthesis(DPA).Among these,fiberdevelopment related transcription factors MYB and NAC,including Gh_A11G0981(MYB108),Gh_A03G0887(NAC029),and Gh_A08G1691(NAC021),were significantly upregulated in SL7,as were numerous cellulose synthase-like(CSL)genes involved in non-cellulose polysaccharide and cell wall synthesis.The hemicellulose content of SL7 was significantly higher than that of L22,an upland cotton cultivar.These results suggest that key genes in the introgressed chromosomal segment of SL7 regulate the expression of transcription-factor genes via hormone-transduction pathways,thereby inducing the expression of genes involved in secondary wall synthesis and ultimately improving fiber quality.This study has shed light on the molecular mechanism of fiber development and will contribute to the improvement of fiber quality of upland cotton by molecular breeding.展开更多
Chinese shrimp (Fenneropenaeus chinensis) is an economically important aquaculture species in China. However, cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to i...Chinese shrimp (Fenneropenaeus chinensis) is an economically important aquaculture species in China. However, cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to isolate and analyze. In this study, fluorescence in-situ hybridization (FISH) was used to identify the chromosomes of F. chinensis. The 5S ribosomal RNA gene (rDNA) of F. chinensis was isolated, cloned and then used as a hybridization probe. The results show that the 5S rDNA was located on one pair of homologous chromosomes in F chinensis. In addition, triploid shrimp were used to evaluate the feasibility of chromosome identification using FISH and to validate the method. It was confirmed that 5S rDNA can be used as a chromosome-specific probe for chromosome identification in E chinensis. The successful application ofFISH in E chinensis shows that chromosome-specific probes can be developed and this finding will facilitate further research on the chromosomes ofpenaeid shrimps.展开更多
One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-
Objective:Chromosomal instability(CIN)is a hallmark of cancer characterized by cell-to-cell variability in the number or structure of chromosomes,frequently observed in cancer cell populations and is associated with p...Objective:Chromosomal instability(CIN)is a hallmark of cancer characterized by cell-to-cell variability in the number or structure of chromosomes,frequently observed in cancer cell populations and is associated with poor prognosis,metastasis,and therapeutic resistance.Breast cancer(BC)is characterized by unstable karyotypes and recent reports have indicated that CIN may influence the response of BC to chemotherapy regimens.However,paradoxical associations between extreme CIN and improved outcome have been observed.Methods:This study aimed to 1)evaluate CIN levels and clonal heterogeneity(CH)in MCF7,ZR-751,MDA-MB468,BT474,and KPL4 BC cells treated with low doses of tamoxifen(TAM),docetaxel(DOC),doxorubicin(DOX),Herceptin(HT),and combined treatments(TAM/DOC,TAM/DOX,TAM/HT,HT/DOC,and HT/DOX)by using fluorescence in situ hybridization(FISH),and 2)examine the association with response to treatments by comparing FISH results with cell proliferation.Results:Intermediate CIN was linked to drug sensitivity according to three characteristics:estrogen receptorα(ERα)and HER2 status,pre-existing CIN level in cancer cells,and the CIN induced by the treatments.ERα+/HER2-cells with intermediate CIN were sensitive to treatment with taxanes(DOC)and anthracyclines(DOX),while ERα-/HER2-,ERα+/HER2+,and ERα-/HER2+cells with intermediate CIN were resistant to these treatments.Conclusions:A greater understanding of CIN and CH in BC could assist in the optimization of existing therapeutic regimens and/or in supporting new strategies to improve cancer outcomes.展开更多
基金funded by the Central Government and Local Science and Technology Development Special Project,China(2022L3086)the Sugarcane Research Foundation of Guangxi University,China(2022GZB006)+3 种基金supported by the National Natural Science Foundation of China(31771863)the Academy of Sugarcane and Sugar Industry,Guangxi University,China(ASSI-2023009)an independent fund of Guangxi Key Laboratory of Sugarcane Biology,China(GXKLSCB-20190201)the China Agriculture Research System of MOF and MARA(CARS-20-1-5)。
文摘Sugarcane has recently attracted increasing attention for its potential as a source of sugar and bioethanol,so increasing its yield is essential to ensure the sugar security and bioenergy production.Intergeneric hybridization is a highly efficient method to produce new genetic variants of crop plants,particularly those species with high ploidy such as sugarcane(Saccharum spp.).Tripidium arundinaceum exhibits many desirable agronomic traits,and has been widely studied to produce hybrids with improved stress tolerance and other characteristics in sugarcane breeding.However,the genetic relationship between T.arundinaceum and Saccharum species,and the individual T.arundinaceum chromosomal compositions in sugarcane hybrids are still elusive.Here we used whole-genome single-nucleotide polymorphisms(SNPs)to ascertain the phylogenetic relationships between these species and found that T.arundinaceum is more closely related to Saccharum than Sorghum,in contrast to the previous narrow genetic analyses using chloroplast DNA.Additionally,oligonucleotide(oligo)-based chromosome-specific painting derived from Saccharum officinarum was able to distinctly identify the chromosomes of T.arundinaceum.We developed the oligo-genomic in situ hybridization(GISH)system for the first time,to unveil the novel chromosome translocations and the transmission of individual T.arundinaceum chromosomes in sugarcane progeny.Notably,we discovered that the chromosomal transmission of T.arundinaceum exhibited several different inheritance modes,including n,2n,and over 2n in the BC1 progenies.Such inheritance patterns may have resulted from first division restitution(FDR)or FDR+nondisjunction of a chromosome with the sister chromatids in the second meiosis division/second division restitution(FDR+NSC/SDR)model during meiosis.These results will be of substantial benefit for the further selection of T.arundinaceum chromosomes for sugarcane genetic improvement.
基金supported by grants from the National Natural Science Foundation of China(82171757)the Zhejiang Provincial Natural Science Foundation of China(LZ22H030004 and LQ20H160048).
文摘Background:Pancreatic cancer is a common malignancy with poor prognosis and limited treatment.Here we aimed to investigate the role of host chromosomal instability(CIN)and tumor microbiome in the prognosis of pancreatic cancer patients.Methods:One hundred formalin-fixed paraffin-embedded(FFPE)pancreatic cancer samples were collected.DNA extracted from FFPE samples were analyzed by low-coverage whole-genome sequencing(WGS)via a customized bioinformatics workflow named ultrasensitive chromosomal aneuploidy detector.Results:Samples were tested according to the procedure of ultrasensitive chromosomal aneuploidy detector(UCAD).We excluded 2 samples with failed quality control,1 patient lost to follow-up and 6 dead in the perioperative period.The final 91 patients were admitted for the following analyses.Thirteen(14.3%)patients with higher CIN score had worse overall survival(OS)than those with lower CIN score.The top 20 microbes in pancreatic cancer samples included 15 species of bacteria and 5 species of viruses.Patients with high human herpesvirus(HHV)-7 and HHV-5 DNA reads exhibited worse OS.Furthermore,we classified 91 patients into 3 subtypes.Patients with higher CIN score(n=13)had the worst prognosis(median OS 6.9 mon);patients with lower CIN score but with HHV-7/5 DNA load(n=24)had worse prognosis(median OS 10.6 mon);while patients with lower CIN score and HHV-7/5 DNA negative(n=54)had the best prognosis(median OS 21.1 mon).Conclusions:High CIN and HHV-7/5 DNA load were associated with worse survival of pancreatic cancer.The novel molecular subtypes of pancreatic cancer based on CIN and microbiome had prognostic value.
文摘BACKGROUND Few studies have reported an association between an increased risk of acquiring cancers and survival in patients with 4q deletion syndrome.This study presents a rare association between chromosome 4q abnormalities and fallopian tube highgrade serous carcinoma(HGSC)in a young woman.CASE SUMMARY A 35-year-old woman presented with acute dull abdominal pain and a known chromosomal abnormality involving 4q13.3 duplication and 4q23q24 deletion.Upon arrival at the emergency room,her abdomen appeared ovoid and distended with palpable shifting dullness.Ascites were identified through abdominal ultrasound,and computed tomography revealed an omentum cake and an enlarged bilateral adnexa.Blood tests showed elevated CA-125 levels.Paracentesis was conducted,and immunohistochemistry indicated that the cancer cells favored an ovarian origin,making us suspect ovarian cancer.The patient underwent debulking surgery,which led to a diagnosis of stage IIIC HGSC of the fallopian tube.Subsequently,the patient received adjuvant chemotherapy with carboplatin and paclitaxel,resulting in stable current condition.CONCLUSION This study demonstrates a rare correlation between a chromosome 4q abnormality and HGSC.UBE2D3 may affect crucial cancer-related pathways,including P53,BRCA,cyclin D,and tyrosine kinase receptors,thereby possibly contributing to cancer development.In addition,ADH1 and DDIT4 may be potential influencers of both carcinogenic and therapeutic responses.
文摘Gastric cancer(GC)is a prevalent malignant tumor within the digestive system,with over 40%of new cases and deaths related to GC globally occurring in China.Despite advancements in treatment modalities,such as surgery supplemented by adjuvant radiotherapy or chemotherapeutic agents,the prognosis for GC remains poor.New targeted therapies and immunotherapies are currently under invest-igation,but no significant breakthroughs have been achieved.Studies have indicated that GC is a heterogeneous disease,encompassing multiple subtypes with distinct biological characteristics and roles.Consequently,personalized treatment based on clinical features,pathologic typing,and molecular typing is crucial for the diagnosis and management of precancerous lesions of gastric cancer(PLGC).Current research has categorized GC into four subtypes:Epstein-Barr virus-positive,microsatellite instability,genome stability,and chromosome instability(CIN).Technologies such as multi-omics analysis and gene sequencing are being employed to identify more suitable novel testing methods in these areas.Among these,ultrasensitive chromosomal aneuploidy detection(UCAD)can detect CIN at a genome-wide level in subjects using low-depth whole genome sequencing technology,in conjunction with bioinformatics analysis,to achieve qualitative and quantitative detection of chromosomal stability.This editorial reviews recent research advancements in UCAD technology for the diagnosis and management of PLGC.
基金Dongguan City Social Development Project(Project number:20161081101023)。
文摘Objective:To analyze the clinical value of non-invasive prenatal testing(NIPT)in detecting chromosomal copy number variations(CNVs)and to explore the relationship between gene expression and clinical manifestations of chromosomal copy number variations.Methods:3551 naturally conceived singleton pregnant women who underwent NIPT were included in this study.The NIPT revealed abnormalities other than sex chromosome abnormalities and trisomy 13,18,and 21.Pregnant women with chromosome copy number variations underwent genetic counseling and prenatal ultrasound examination.Interventional prenatal diagnosis and chromosome microarray analysis(CMA)were performed.The clinical phenotypes and pregnancy outcomes of different prenatal diagnoses were analyzed.Additionally,a follow-up was conducted by telephone to track fetal development after birth,at six months,and one year post-birth.Results:A total of 53 cases among 3551 cases showed chromosomal copy number variation.Interventional prenatal diagnosis was performed in 36 cases:27 cases were negative and 8 were consistent with the NIPT test results.This indicates that NIPT’s positive predictive value(PPV)in CNVs is 22.22%.Conclusion:NIPT has certain clinical significance in screening chromosome copy number variations and is expected to become a routine screening for chromosomal microdeletions and microduplications.However,further interventional prenatal diagnosis is still needed to identify fetal CNVs.
基金Supported by the National Natural Science Foundation of China(30970089,20876181,21276289)the Natural Science Foundation of Guangdong Province(9351027501000003,S2011010001396)
文摘The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli strain for coenzyme Q10 production. A series of integration expression vectors, pxKC3T5b and pxKT5b, were constructed for chemically inducible chromosomal evolution(multiple copy integration) and replicon-free and markerless chromosomal integration(single copy integration), respectively. A coenzyme Q10 hyper-producer Escherichia coli TBW20134 was constructed by applying chemically inducible chromosomal evolution,replicon-free and markerless chromosomal integration as well as deletion of menaquinone biosynthetic pathway.The engineered E. coli TBW20134 produced 10.7 mg per gram of dry cell mass(DCM) of coenzyme Q10 when supplemented with 0.075 g·L-1of 4-hydroxy benzoic acid; this yield is unprecedented in E. coli and close to that of the commercial producer Agrobacterium tumefaciens. With this strain, the coenzyme Q10 production capacity was very stable after 30 sequential transfers and no antibiotics were required during the fermentation process. The strategy presented may be useful as a general approach for construction of stable production strains synthesizing natural products where various copy numbers for different genes are concerned.
文摘In this Editorial review,we would like to focus on a very recent discovery showing the global autosomal gene regulation by Y-and inactivated X-chromosomal transcription factors,zinc finger gene on the Y chromosome(ZFY)and zinc finger protein X-linked(ZFX).ZFX and ZFY are both zinc-finger proteins that encode general transcription factors abundant in hematopoietic and embryonic stem cells.Although both proteins are homologs,interestingly,the regulation of self-renewal by these transcriptional factors is almost exclusive to ZFX.This fact implies that there are some differential roles between ZFX and ZFY in regulating the maintenance of self-renewal activity in stem cells.Besides the maintenance of stemness,ZFX overexpression or mutations may be linked to certain cancers.Although cancers and stem cells are double-edged swords,there is no study showing the link between ZFX activity and the telomere.Thus,stemness or cancers with ZFX may be linked to other molecules,such as Oct4,Sox2,Klf4,and others.Based on very recent studies and a few lines of evidence in the past decade,it appears that the ZFX is linked to the canonical Wnt signaling,which is one possible mechanism to explain the role of ZFX in the self-renewal of stem cells.
文摘Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain largely undiscovered. Nevertheless, more and more genetic factors associated with infertility are being identified. This review will focus on our current understanding of the chromosomal basis of male infertility specifically: chromosomal aneuploidy, structural and numerical karyotype abnormalities and Y chromosomal microdeletions. Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans. Aneuploidy is predominantly maternal in origin, but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts. Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm. Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed, as well as the application of preimplantation genetic diagnosis (PGD) in such cases. Clinical recommendations where possible will be made, as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility.
基金National Natural Science Foundation of China (No. 30230300).
文摘A total of 1,160 differentially expressed genes induced by Marssonina brunnea f. sp. muhigermtubi were identified in Populus deltoides cv. 'Lux' (1-69/55) with two-colour cDNA microarray including 2,952 cDNAs from two cDNA libraries constructed with 72 h inoculated poplar leaves. Functional analysis showed that 1,160 genes were classified into 11 functional categories that are involved in metabolism (15.9%), signal transduction (9.5%), transcription and replication (8.7%), and cell rescue and defense (7.8%). Among them, 926 genes were sporadically localized on 19 linkage groups. Chromosome 2 contained 102 (11%) differentially expressed genes, followed by chromosome 1 which contains 93 genes (10%), and chromosome 17 had the least number of differentially expressed genes. Clustering of expressed sequence tags (ESTs) in poplar genome was observed at the terminal regions of several chromosomes. The relationship between cluster of genes and plant defense response would be further studied.
基金partially supported by CIGMH/FCM/UNL,under the project PEST-OE/SAU/UI0009/2011CMA/FCT/UNL,under the project PEst-OE/MAT/UI0297/2011.
文摘Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources). We mapped fragile sites to chromosomal bands and divided the 23 chromosomes into fragile and non-fragile sites. The frequency of rearrangements at the chromosomal location of clones found to be deleted or duplicated in the array/CGH analysis, provided by DECIPHER, was compared in Chromosomal Fragile Sites vs. non-Fragile Sites of the human genome. The POSSUM Web was used to complement this study. The results indicated 1) a predominance of rearrangements in CFSs, 2) the absence of statistically significant difference between the frequency of rearrangements in common CFSs vs. rare CFSs, 3) a predominance of deletions over duplications in CFSs. These results on constitutional chromosomal rearrangements are evocative of the findings previously reported by others relatively to cancer supporting the current line of evidence and suggesting that a common mechanism can underlie the generation of constitutional and somatic rearrangements. The combination of insights obtained from our results and their interrelationships can indicate strategies by which the mechanisms can be targeted with preventive medical interventions.
基金supported by the National Natural Science Foundation of China(U1402224,31601010,81571998,and U1702284)Yunnan Province(2015HA038 and 2018FB054)Chinese Academy of Sciences(CAS zsys-02)
文摘Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://www.treeshrewdb.org) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.
基金Supported by the Ministry of Science and Technology Taiwan grant,No.MOST 106-2314-B-182A-019-MY3the Chang Gung Foundation,No.CMRPG3E1321-2,No.IRB201601916B0,and No.IRB103-7448B
文摘AIM To explore the correlation of metabolomics profiles ofgastric cancer(GC) with its chromosomal instability(CIN) status.METHODS Nineteen GC patients were classified as CIN and nonCIN type by The Cancer Genome Atlas Research Group system, based on 409 oncogenes and tumor suppressor genes sequenced. The aqueous metabolites of the GC tumor and its surrounding adjacent healthy tissues were identified through liquid chromatographymass spectrometry. Groups were compared by defining variable importance in projection score of > 1.2, a fold change value or its reciprocal of > 1.2, and a P value of < 0.05 as a significant difference.RESULTS In total,twelve men and seven women were enrolled, with a median age of 66 years(range, 47-87 years). The numbers of gene alterations in the CIN GC group were significantly higher than those in the non-CIN GC(32-218 vs 2-17; P < 0.0005). Compared with the adjacent healthy tissues, GC tumors demonstrated significantly higher aspartic acid, citicoline, glutamic acid, oxidized glutathione, succinyladenosine, and uridine diphosphate-Nacetylglucosamine levels, but significantly lower butyrylcarnitine, glutathione hydroxyhexanoycarnitine, inosinic acid, isovalerylcarnitine, and threonine levels(all P < 0.05). CIN tumors contained significantly higher phosphocholine and uridine 5'-monophosphate levels but significantly lower beta-citryl-L-glutamic acid levels than did non-CIN tumors(all P < 0.05). CIN GC tumors demonstrated additional altered pathways involving alanine, aspartate, and glutamate metabolism, glyoxylate and dicarboxylate metabolism, histidine metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis.CONCLUSION Metabolomic profiles of GC tumors and the adjacent healthy tissue are distinct, and the CIN status is associated with downstream metabolic alterations in GC.
文摘GPX-GI is a cytosolic tetrameric Se-dependent glutathione peroxidase, similar in properties to GPX-1. Unlike the almost ubiquitous GPX-1, GPX-GI is mainly expressed in the epithelium of gastrointestinal tract. GPX-GI contributes to at least fifty percent of GPX activity in rodent small intestmal epithelium. The total GPX activity consists of at least 70% of selenium-dependent GPX activity in this compartment.By analyzing a panel of mouse mterspecies DNA from the Jackson Laboratory's backcross resource,we mapped Gpx2 gene to mouse chromosome 12 between D12Mit4 and D12Mit5, near the Ccs1 locus which contains a colon cancer susceptibility gene. A pseudogene, Gpx2-ps is mapped to mouse chromosome 7.Comparison of Gpx2 gene expression in three pairs of C57BL/6Ha and ICR/Ha mice which are respectively resistant and sensitive to dimethylhydrazine-induced colon cancer, we found a higher Gpx2 mRNA level in C57BL/6Ha colon than ICR/Ha colon. Interestingly, a lower level of GPX activity is found in the resistant strain of mice. Because GPX-1 has three times higher specific activity than GPX GI, our data suggest that the decreased GPX activity may result from a higher level of Gpx2 gene expression in those cells co-express GPx1 gene
基金Project (No. SP/SO/HS-21/2002) supported by the Department of Science and Technology, Government of India, New Delhi
文摘Turmeric has long been used as a spice and food colouring agent in Asia. In the present investigation, the antimutagenic potential of curcumin was evaluated in Allium cepa root meristem cells. So far there is no report on the biological properties of curcumin in plant test systems. The root tip cells were treated with sodium azide at 200 and 300 μg/ml for 3 h and curcumin was given at 5, 10 and 20 μg/ml for 16 h, prior to sodium azide treatment. The tips were squashed after colchicine treatment and the cells were analyzed for chromosome aberration and mitotic index. Curcumin induces chromosomal aberration in Allium cepa root tip cells in an insignificant manner, when compared with untreated control. Sodium azide alone induces chromosomal aberrations significantly with increasing concentrations. The total number of aberrations was significantly reduced in root tip cells pretreated with curcumin. The study reveals that curcumin has antimutagenic potential against sodium azide induced chromosomal aberrations in Allium cepa root meristem cells. In addition, it showed mild cytotoxicity by reducing the percentage of mitotic index in all curcumin treated groups, but the mechanism of action remains unknown. The antimutagenic potential of curcumin is effective at 5 μg/ml in Allium cepa root meristem cells.
文摘A backcross recombinant inbred line population consisting of 202 lines was developed from Xieqingzao B//Xieqingzao B / Dongxiang wild rice. The population was assayed with DNA markers and phenotyped on planthopper resistance and yield traits. A linkage map consisting of 119 DNA markers and spanned for 1188 cM over the 12 rice chromosomes was constructed. Thirty-two chromosomal segment substitution lines were selected based on the percentage of Xieqingzao B allele at marker loci. These lines are of great potential for gene mapping and alien gene introgression.
基金the National Natural Science Foundation of China(31601345 and 31671742)the Earmarked Fund for China Agriculture Research System(CARS-15-05)+1 种基金the Taishan Scholar Project of Shandong Province(ts201511070)the Innovation Project in Shandong Academy of Agricultural Sciences(CXGC2016A01).
文摘Cotton fibers are the main raw materials of the textile industry.Exogenous superior fiber genes have been introduced into upland cotton to develop high-yield cultivars with excellent fiber quality.We used a single chromosomal segment on the chromosome A07 substitution line SL7,with high fiber strength,to investigate the molecular mechanism underlying its fiber quality.RNA-seq and KEGG analysis showed that 70 differentially expressed genes were enriched in plant hormone transduction pathways,including auxin,ethylene and abscisic acid,in fibers at 10 days post-anthesis(DPA).Among these,fiberdevelopment related transcription factors MYB and NAC,including Gh_A11G0981(MYB108),Gh_A03G0887(NAC029),and Gh_A08G1691(NAC021),were significantly upregulated in SL7,as were numerous cellulose synthase-like(CSL)genes involved in non-cellulose polysaccharide and cell wall synthesis.The hemicellulose content of SL7 was significantly higher than that of L22,an upland cotton cultivar.These results suggest that key genes in the introgressed chromosomal segment of SL7 regulate the expression of transcription-factor genes via hormone-transduction pathways,thereby inducing the expression of genes involved in secondary wall synthesis and ultimately improving fiber quality.This study has shed light on the molecular mechanism of fiber development and will contribute to the improvement of fiber quality of upland cotton by molecular breeding.
基金Supported by the Key Program of the National Natural ScienceFoundation of China(No.30730071)the National High-Tech Researchand Development Program of China(863 program)(No.2007AA09Z430)the General Program of National Natural Science Foundation of China(Nos.30471347&40706048)
文摘Chinese shrimp (Fenneropenaeus chinensis) is an economically important aquaculture species in China. However, cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to isolate and analyze. In this study, fluorescence in-situ hybridization (FISH) was used to identify the chromosomes of F. chinensis. The 5S ribosomal RNA gene (rDNA) of F. chinensis was isolated, cloned and then used as a hybridization probe. The results show that the 5S rDNA was located on one pair of homologous chromosomes in F chinensis. In addition, triploid shrimp were used to evaluate the feasibility of chromosome identification using FISH and to validate the method. It was confirmed that 5S rDNA can be used as a chromosome-specific probe for chromosome identification in E chinensis. The successful application ofFISH in E chinensis shows that chromosome-specific probes can be developed and this finding will facilitate further research on the chromosomes ofpenaeid shrimps.
文摘One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-
基金funded by Universidad Pedagogica y Tecnologica de Colombia(Grant No.DIN 14-2017)。
文摘Objective:Chromosomal instability(CIN)is a hallmark of cancer characterized by cell-to-cell variability in the number or structure of chromosomes,frequently observed in cancer cell populations and is associated with poor prognosis,metastasis,and therapeutic resistance.Breast cancer(BC)is characterized by unstable karyotypes and recent reports have indicated that CIN may influence the response of BC to chemotherapy regimens.However,paradoxical associations between extreme CIN and improved outcome have been observed.Methods:This study aimed to 1)evaluate CIN levels and clonal heterogeneity(CH)in MCF7,ZR-751,MDA-MB468,BT474,and KPL4 BC cells treated with low doses of tamoxifen(TAM),docetaxel(DOC),doxorubicin(DOX),Herceptin(HT),and combined treatments(TAM/DOC,TAM/DOX,TAM/HT,HT/DOC,and HT/DOX)by using fluorescence in situ hybridization(FISH),and 2)examine the association with response to treatments by comparing FISH results with cell proliferation.Results:Intermediate CIN was linked to drug sensitivity according to three characteristics:estrogen receptorα(ERα)and HER2 status,pre-existing CIN level in cancer cells,and the CIN induced by the treatments.ERα+/HER2-cells with intermediate CIN were sensitive to treatment with taxanes(DOC)and anthracyclines(DOX),while ERα-/HER2-,ERα+/HER2+,and ERα-/HER2+cells with intermediate CIN were resistant to these treatments.Conclusions:A greater understanding of CIN and CH in BC could assist in the optimization of existing therapeutic regimens and/or in supporting new strategies to improve cancer outcomes.