High-grade serous carcinoma of the fallopian tube in a young woman with chromosomal 4q abnormality:A case report

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.

Prospects in the application of ultrasensitive chromosomal aneuploidy detection in precancerous lesions of gastric cancer

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.

Relationship Between Gene-Phenotype and Clinical Manifestations of Chromosomal Copy Number Variations Indicated by Non-Invasive Prenatal Testing

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.

Maintenance of stem cell self-renewal by sex chromosomal zincfinger transcription factors

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.

Embryo quality and chromosomal abnormality in embryos from couples undergoing assisted reproductive technology using preimplantation genetic screening

Objective:To detect common chromosomal aneuploidy variations in embryos from couples undergoing assisted reproductive technology and preimplantation genetic screening and their possible associations with embryo quality.Methods:In this study,359 embryos from 62 couples were screened for chromosomes 13,21,18,X,and Y by fluorescence insitu hybridization.For biopsy of blastomere,a laser was used to remove a significantly smaller portion of the zona pellucida.One blastomere was gently biopsied by an aspiration pipette through the hole.After biopsy,the embryo was immediately returned to the embryo scope until transfer.Embryo integrity and blastocyst formation were assessed on day 5.Results:Totally,282 embryos from 62 couples were evaluated.The chromosomes were normal in 199(70.57%)embryos and abnormal in 83(29.43%)embryos.There was no significant association between the quality of embryos and numerical chromosomal abnormality(P=0.67).Conclusions:Embryo quality is not significantly correlated with its genetic status.Hence,the quality of embryos determined by morphological parameters is not an appropriate method for choosing embryos without these abnormalities.

Correlation between Reasons for Prescription and Karyotype Results in Patients Referred for Suspected Chromosomal Abnormalities

Karyotype prescription is based on clinical signs (or reasons for karyotype prescription) which are phenotypic manifestations associated with chromosomal abnormalities. The aim of this study was to establish a correspondence between karyotype indications and their results in patients. This was a retrospective study that was carried out in the Histology-Embryology-Cytogenetics laboratory of the University Hospital of Cocody-Abidjan from 2014 to 2019. 58 patient files were identified and included the indication or reason for prescribing a constitutional karyotype and the biological result obtained. An individual data sheet was used to collect the data. 17 reasons for prescription were identified and divided into 2 groups. Sexual ambiguity was the most frequent reason (29.3%). The first group (G1) represented the 10 reasons for which the karyotype results were normal. The second group (G2) corresponded of the 7 motives with normal or abnormal karyotype results. Several anomalies were listed according to these reasons: inversions, mosaics (anomalies of number and structure) and trisomy 21. The last was the most frequent chromosomal anomaly (69.24%). It was found in several reasons for karyotype prescription: malformations, neurological disorders, suspected trisomy and cardiac pathology. Several factors could explain these results, among which are the limits of the karyotype and the non-genetic causes that can induce these abnormal phenotypes. Complementary examinations to the karyotype are molecular cytogenetic techniques, notably fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (Array-CGH).

Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut

Oligo probe staining is a low-cost and efficient chromosome identification technique.In this study,oligo genomic in situ hybridization(Oligo-GISH)technology was established in peanut.Peanut A and B subgenome-specific interspersed repeat(IR)oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner.The OligoGISH kit was then used to perform staining of 15 Arachis species.The A-subgenome probe set stained the chromosomes of A-and E-genome Arachis species,the B-subgenome probe set stained those of B-,F-,K-,and E-genome species,and neither set stained those of H-genome species.These results indicate the relationships among the genomes of these Arachis species.The Oligo-GISH kit was also used for batch staining of the chromosomes of 389 seedlings from the irradiated M1generation,allowing 67 translocation and deletion lines to be identified.Subsequent Oligo-FISH karyotyping,FISH using single-copy probe libraries,and trait investigation identified seven homozygous chromosomal variants from the M3generation and suggested that there may be genes on chromosome 4B controlling seed number per pod.These findings demonstrate that the IR probe sets and method developed in this study can facilitate research on distant hybridization and genetic improvement in peanut.

Chromosomal Engineering of Escherichia coli for Efficient Production of Coenzyme Q_(10)

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.

Chromosome 5P of Agropyron cristatum induces chromosomal translocation by disturbing homologous chromosome pairing in a common wheat background

Wide hybridization is a strategy for broadening the genetic basis of wheat. Because an efficient method for inducing wheat–alien chromosome translocations will allow producing useful germplasm, it is desirable to discover new genes that induce chromosomal variation. In this study, chromosome 5P from A.cristatum was shown to induce many types of chromosomal structural variation in a common wheat background, including nonhomoeologous chromosome translocations, as revealed by genomic in situ hybridization, fluorescence in situ hybridization, and DNA marker analysis. Aberrant meiosis was associated with chromosomal structural variation, and aberrant meiotic behavior was observed in wheat–A.cristatum 5P monosomic and disomic addition lines, suggesting that the effect of chromosome 5P was independent of the number of chromosome 5P copies. Chromosome 5P disturbed homologous chromosome pairing at pachytene stage in a common wheat background, resulting in a high frequency of univalent formation and reduced crossing over. Thirteen genes involved in DNA repair or chromatin remodeling, including RAD52-like and MSH6 genes, were differentially expressed(upregulated) in wheat–A. cristatum 5P addition lines according to transcriptome analysis, implicating chromosome 5P in the process of meiotic double-strand break repair. These findings provide a new, efficient tool for inducing wheat–alien chromosome translocations and producing new germplasm.

Chromosomal disorders and male infertility

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.

Function and Chromosomal Localization of Differentially Expressed Genes Induced by Marssonina brunnea f.sp.multigermtubi in Populus deltoides

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.

Predominance of constitutional chromosomal rearrangements in human chromosomal fragile sites

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.

Chromosomal level assembly and population sequencing of the Chinese tree shrew genome

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.

Isolation and Chromosomal Mapping of a Corn B Chromosome Specific RAPDs

B染色体存在于多种动植物中 ,具有很多独特的性状。B染色体与正常染色体在DNA组成方面十分相似 ,寻找B染色体特异序列一直是B染色体研究的难点和热点。通过对含有和不含有B染色体的两种玉米 (ZeamaysL .)基因组进行了RAPD分析 ,筛选到一个B染色体特异性分子标记B480。该标记与玉米的自主复制起始序列ARS1和ARS2同源 ,特别是该序列中的 2 5bp出现在多种模式生物基因组中。FISH的结果显示 。

Metabolomic alterations and chromosomal instability status in gastric cancer

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.

Expression and Chromosomal Mapping of Mouse Gpx2 Gene Encoding the Gastrointestinal Form of Glutathione Peroxidase, 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

Antimutagenic potential of curcumin on chromosomal aberrations in Allium cepa

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.

Development of Chromosomal Segment Substitution Lines from a Backcross Recombinant Inbred Population of Interspecific Rice Cross

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.

RNA-seq reveals hormone-regulated synthesis of non-cellulose polysaccharides associated with fiber strength in a single-chromosomal-fragmentsubstituted upland cotton line

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.

Chromosomal localization of 5S rDNA in Chinese shrimp (Fenneropenaeus chinensis):a chromosome-specific marker for chromosome identification

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.