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Results for “Chromosomes, Human, Pair 9”

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PubMed2026

[Optical genome mapping analysis of a Chinese pedigree with a complex balanced translocation involving four chromosomes].

OBJECTIVE: To explore the genetic characteristics of a complex balanced translocation involving four non-homologous chromosomes in a Chinese pedigree using optical genomic mapping (OGM). METHODS: A woman with primary infertility and her family members who presented at the Prenatal Diagnosis Center of the Sixth Affiliated Hospital of Sun Yat-sen University in October 2021 were selected as study subjects. Comprehensive analysis and verification of chromosomal abnormalities were conducted through conventional G-band karyotyping analysis, single nucleotide polymorphism microarray (SNP array) and OGM. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: E2022210). RESULTS: G-band karyotyping analysis indicated that the proband, her father, and younger brother have all carried a complex translocation involving four chromosomes. SNP array analysis revealed a duplication of approximately 21.63 Mb in the 9p24.1-p21.1 region in the proband's younger brother, while no abnormality was detected in other family members. OGM confirmed that the complex balanced translocation has involved chromosomes 5, 8, 9, and 10. CONCLUSION: The proband has harbored a complex balanced translocation. OGM has demonstrated certain advantages in characterization of complex chromosomal structural abnormalities.

Humans↗

PubMed2026

Deletion of 9p drives B-ALL through heterozygous inactivation of Pax5 and Cd72 in preleukemic cells.

The contribution of 9p deletion to B cell acute lymphoblastic leukemia (B-ALL) has remained elusive since its discovery more than 40 years ago. Here we show that loss of CD72 is recurrent in B-ALL cases containing PAX5 deletions, and that Cd72 haploinsufficiency drives B-ALL development in Pax5+/- mice. Mechanistically, Cd72+/-;Pax5+/- precursor B cells exhibited an inflammatory transcriptional profile characterized by a decrease in Myd88 expression, a finding that aligns with our previous studies of B-ALL development in Pax5+/- mice following exposure to immune stressors. These combined genomic analyses and functional models provide compelling evidence that co-deletion of 2 contiguous genes, Pax5 and Cd72, drives B cell leukemogenesis.

Animals↗

PubMed2024

Clinical characteristics and genetic analysis of four pediatric patients with Kleefstra syndrome.

BACKGROUND: Kleefstra syndrome spectrum (KLEFS) is an autosomal dominant disorder that can lead to intellectual disability and autism spectrum disorders. KLEFS encompasses Kleefstra syndrome-1 (KLEFS1) and Kleefstra syndrome-2 (KLEFS2), with KLEFS1 accounting for more than 75%. However, limited information is available regarding KLEFS2. KLEFS1 is caused by a subtelomeric chromosomal abnormality resulting in either deletion at the end of the long arm of chromosome 9, which contains the EHMT1 gene, or by variants in the EHMT1 gene and the KMT2C gene that cause KLEFS2. METHODS: This study was a retrospective analysis of clinical data from four patients with KLEFS. Exome sequencing (ES) and Sanger sequencing techniques were used to identify and validate the candidate variants, facilitating the analysis of genotype‒phenotype correlations of the EHMT1 and KMT2C genes. Protein structure modeling was performed to evaluate the effects of the variants on the protein's three-dimensional structure. In addition, real-time quantitative reverse transcription‒polymerase chain reaction (RT‒qPCR) and western blotting were used to examine the protein and mRNA levels of the KMT2C gene. RESULTS: Two patients with KLEFS1 were identified: one with a novel variant (c.2382 + 1G > T) and the other with a previously reported variant (c.2426 C > T, p.Pro809Leu) in the EHMT1 gene. A De novo deletion at the end of the long arm of chromosome 9 was also reported. Furthermore, a patient with KLEFS2 was identified with a novel variant in the KMT2C gene (c.568 C > T, p.Arg190Ter). The RT‒qPCR and western blot results revealed that the expression of the KMT2C gene was downregulated in the KLEFS2 sample. CONCLUSION: This study contributes to the understanding of both KLEFS1 and KLEFS2 by identifying novel variants in EHMT1 and KMT2C genes, thereby expanding the variant spectrum. Additionally, we provide the first evidence of how a KMT2C variant leads to decreased gene and protein expression, enhancing our understanding of the molecular mechanisms underlying KLEFS2. Based on these findings, children exhibiting developmental delay, hypotonia, distinctive facial features, and other neurodevelopmental abnormalities should be considered for ES to ensure early intervention and treatment.

Child↗

PubMed2026

Elucidating the Role of SET as a Key Contributor to Neurodevelopmental Disability Within the 9q34.11 Deletion Syndrome Interval.

The 9q34.11 chromosomal region contains multiple neurodevelopmental genes involved in synaptic transmission, axonal structure and neuronal maturation. Pathogenic microdeletions, duplications and single nucleotide variants in numerous genes were previously linked with neurodevelopmental disorders (NDDs). Amongst them, SET has recently been implicated in a rare NDD with speech delay and facial dysmorphism. This study reports a female with a heterozygous de novo deletion impacting SET but not other NDD-associated genes at 9q34.11. The proband was initially diagnosed with atypical Rett syndrome with overlapping clinical features of SET haploinsufficiency. The deletion was confirmed using microarray and long-read sequencing. Subsequent quantitative proteomic evaluation identified a significant decrease of SET protein in patient-derived fibroblasts compared to control lines. This study provides insights into the proband's clinical course over their 28 year diagnostic odyssey, and emphasises the benefits of early speech therapy interventions. The proband had no functional speech, but regained the capacity to meaningfully communicate and articulate a limited vocabulary in adulthood, concordant with other reported non-paediatric cases of SET-NDD. This study expands current knowledge on the genotypic and phenotypic spectra of SET-NDD, and pinpoints a smaller 9q34.11 critical region excluding upstream NDD-associated genes, STXBP1 and SPTAN1, implicating SET as a significant NDD-associated gene.

Humans↗

PubMed2020

Metabolic Dysregulation of the Lysophospholipid/Autotaxin Axis in the Chromosome 9p21 Gene SNP rs10757274.

BACKGROUND: Common chromosome 9p21 single nucleotide polymorphisms (SNPs) increase coronary heart disease risk, independent of traditional lipid risk factors. However, lipids comprise large numbers of structurally related molecules not measured in traditional risk measurements, and many have inflammatory bioactivities. Here, we applied lipidomic and genomic approaches to 3 model systems to characterize lipid metabolic changes in common Chr9p21 SNPs, which confer ≈30% elevated coronary heart disease risk associated with altered expression of ANRIL, a long ncRNA. METHODS: Untargeted and targeted lipidomics was applied to plasma from NPHSII (Northwick Park Heart Study II) homozygotes for AA or GG in rs10757274, followed by correlation and network analysis. To identify candidate genes, transcriptomic data from shRNA downregulation of ANRIL in HEK-293 cells was mined. Transcriptional data from vascular smooth muscle cells differentiated from induced pluripotent stem cells of individuals with/without Chr9p21 risk, nonrisk alleles, and corresponding knockout isogenic lines were next examined. Last, an in-silico analysis of miRNAs was conducted to identify how ANRIL might control lysoPL (lysophosphospholipid)/lysoPA (lysophosphatidic acid) genes. RESULTS: Elevated risk GG correlated with reduced lysoPLs, lysoPA, and ATX (autotaxin). Five other risk SNPs did not show this phenotype. LysoPL-lysoPA interconversion was uncoupled from ATX in GG plasma, suggesting metabolic dysregulation. Significantly altered expression of several lysoPL/lysoPA metabolizing enzymes was found in HEK cells lacking ANRIL. In the vascular smooth muscle cells data set, the presence of risk alleles associated with altered expression of several lysoPL/lysoPA enzymes. Deletion of the risk locus reversed the expression of several lysoPL/lysoPA genes to nonrisk haplotype levels. Genes that were altered across both cell data sets were DGKA, MBOAT2, PLPP1, and LPL. The in-silico analysis identified 4 ANRIL-regulated miRNAs that control lysoPL genes as miR-186-3p, miR-34a-3p, miR-122-5p, and miR-34a-5p. CONCLUSIONS: A Chr9p21 risk SNP associates with complex alterations in immune-bioactive phospholipids and their metabolism. Lipid metabolites and genomic pathways associated with coronary heart disease pathogenesis in Chr9p21 and ANRIL-associated disease are demonstrated.

Chromosomes, Human, Pair 9↗

PubMed1978

Lateral asymmetry in human constitutive heterochromatin: frequency and inheritance.

The relative frequencies and types of lateral asymmetry found in chromosomes 1, 9, 15, 16, and the Y were determined. The pattern of asymmetry is simple in chromosomes 15, 16, and the Y but compound in 1 and possibly also 9. The pattern of compound lateral asymmetry is a stable heteromorphism inherited in a simple Mendelian way and is an efficient morphological discriminator between the members of the no. 1 chromosome pair.

Chromosomes, Human↗

PubMed1979

The quantitative analysis of polymorphism on human chromosomes 1, 9, 16, and Y. III. Study of relationships of C segments' lengths in individual karyotypes.

The correlation relationship of the lengths of C segments on chromosomes 1, 9, 16, and Y was studied in a group of normal boys and girls (50 boys and 50 girls). No correlation was found between the C segment lengths, either on homologs or on chromosomes of various pairs. This confirms the idea of random combinations of the said chromosomes with C segments of different lengths in an individual karyotype.

Adolescent↗

PubMed1977

Quantitative analysis of C-bands based on optical density profiles in human chromosomes.

A method of quantitative analysis of C segments in human chromosomes 1, 9, and 16 based on longitudinal densitometry has been developed. The way of fitting apparatus data to visual estimates is represented. Density curve parameters not dependent on stain intensity were used. The general C band length error is approx. 0.05 micrometer. Heteromorphic chromosome 16 pairs have been investigated with this method. A significant difference (about 0.18 micrometer) between C bands of the homologues has been detected in chromosome 16. It has been calculated that C bands can be distinquished if the mean difference between the length of the homologues is more than 15%.

Chromosomes, Human↗

PubMed1977

Chromosomal analysis of the pygmy chimpanzee (Pan paniscus) with a comparison to man.

The karyotype of Pan paniscus is reexamined by G-banding and examined for the first time by C-banding. In addition, examination of the chromosomes by the use of the fluorochromes adreamycine and 33258 Hoechst is undertaken. C-banding showed a surprising pattern with numerous terminal C-bands, as interstitial C-band, and several chromosomes lacking C-bands. Polymorphic conditions for C-bands are also identified involving several pairs. In a comparison to the chromosomes of man, G-banding revealed two pericentric inversions not previously observed. Only chromosome pairs No. 9,11,12 and the X are similar to man's by all techniques employed.

Animals↗

PubMed1979

Chromosome studies on a human liposarcoma cell line.

Numerical and structural chromosome analysis of a human retroperitoneal liposarcoma cell line maintained under standard cell culture conditions revealed a very stable hypodiploid mode. If the cells were not trypsinized for several generations, a near-triploid stemline, which was generally a duplication of the hypodiploid mode, emerged. Some chromosomes appeared to be relatively stable pairs (1, 2, 7, 9, and 12), but most had "lost" one homolog or both (4 and 21) or were rearranged into "new" marker chromosomes. Quantitation of the genetic material showed a loss of 12.0 +/- 3.7% per spread. Only one characteristically long marker chromosome, which is present in every cell, could be identified with certainty as a translocation between chromosomes 4 and 11. Several of the marker chromosomes showed interstitial negatively staining regions with the trypsin-Giemsa method.

Cell Line↗

PubMed1979

The quantitative analysis of polymorphism on human chromosomes 1, 9, 16, and Y. I. Description of individual karyotypes.

This study was made to establish a stable quantitative characteristic of C segments on chromosomes 1, 9, 16, and Y in an individual karyotype that was reproducible in successive experiments. The C segment of these chromosomes were measured in successive cultures of cells from three males and the C segments of chromosomes 1, 9, and 16 in cells from three pairs of female monozygotic twins were measured. The results show that the absolute lengths of C segments tend to vary considerably with the cell samples analyzed, while the relative length, i.e., the length of a single C segment as a percentage of the total length of all C segments of the chromosomes being studied, is more stable and can be used for individual characteristics.

Chromosomes, Human, 1-3↗

PubMed1977

The nucleolar cycle in man.

Tissue cultures of human embryonal kidney and ovary were examined. In the nuclei of both tissues, one to ten nucleoli have been found. The maximum number of nucleoli is connected with the gene expression of rDNA of the 10 nucleolus organizers of chromosome pairs Nos. 13, 14, 15, 21 and 22, which have secondary constrictions and are the satellite chromosomes in man. The small percentage of cells with 10, 9 and 8 nucleoli is attributed to the rapid association of 3 of the homologous acrocentrics (perhaps of group D). Two of the satellite (SAT) pairs probably associate later after mitosis. The process of fusion is dynamic, resulting in one interphase nucleous--a manifestation of the association of all SAT chromosomes. Dissociation of the nucleolus occurs upon entering prophase, due to the condensation of the chromosomes and retreat of rDNA to the respective secondary constrictions. As a result, the nucleolar number increases again. The pattern of the nucleolar kinetics within the course of one mitotic division is described.

Cell Nucleolus↗

PubMed1978

C-bands in chromosomes 1,9, and 16 of twins.

Thirty-two pairs of Caucasoid twins, 16 monozygotic (MZ) and 16 dizygotic (DZ) of the same sex, were studied in relation to the C-bands of chromosomes 1, 9, and 16. Concordance was not absolute among MZ, the best evaluation of the degree of genetic determination for these traits being 0.40 for chromosome 16, 0.64 for chromosome 1, and 0.73 for chromosome 9. Possible explanations for the failure to obtain 100% concordance are methodologic shortcomings, intercell variations in chromosome contraction, and unequal mitotic crossing over.

Adolescent↗

PubMed2026

Upper airway microbiome interacts with GSDMB and ORMDL3 asthma risk SNPs to influence early-life wheeze risk.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) in the chromosome 17q12-q21 region and, independently, early-life nasal microbiota dominated by Moraxella, Streptococcus, or Haemophilus (MSH) increase risk of chronic wheeze and asthma development. OBJECTIVE: We sought to determine whether 17q12-q21 risk SNPs and nasal microbiota interact to modulate childhood wheeze risk. METHODS: Nasal wash samples from 12-month-old infants in 2 birth cohorts, COAST (Childhood Origins of Asthma; n = 180) and URECA (Urban Environment and Childhood Asthma; n = 139), underwent 16S ribosomal RNA variable region 4 sequencing. Nasal microbiota dominated by MSH or Corynebacterium, Dolosigranulum, Staphylococcus, or Bacillus (CDSB) were assessed. Paired blood was genotyped for 9 17q12-q21 risk SNPs. Logistic regression tested interactions between 17q12-q21 SNPs and MSH or CDSB on wheeze risk in the first 3 years of life. A549 lung epithelial cells, CRISPR-edited to encode the rs7216389 risk genotype (rs7216389TT) were compared to the heterozygous (rs7216389CT) line using bulk RNA sequencing. RESULTS: SNPs, particularly those in the ORMDL3 (rs8076131; odds ratio [OR]: 1.72; 95% CI: 1.09-2.71; Pint = .031) and GSDMB (rs2305480; OR: 1.72; 95% CI: 1.09-2.71; Pint = 0.042; and rs7216389; OR: 1.73; 95% CI: 1.09-2.70; Pint = .047) genes, interact with MSH microbiota to increase early-life wheeze risk (false discovery rate Pint = .016 for all), while interactions with CDSB reduce risk. A549 airway epithelial cells homozygous for rs7216389TT exhibited decreased expression of genes involved in antimicrobial responses and neutrophil recruitment and evidence increased microbial adherence compared with the heterozygous cell line. CONCLUSION: Airway microbiota interact with SNPs at the 17q12-q21 locus in genes involved in sphingolipid metabolism and intracellular antimicrobial responses, to modulate wheeze risk.

Humans↗

PubMed1978

Genetics of SV40 T-antigen expression: studies of twins, heritable syndromes and cancer families.

Susceptibility of human skin fibroblasts to SV40 virus infection has been suggested as a marker of cancer risk. To evaluate the role of heritable factors in the regulation of SV40 T-antigen, fibroblasts from 9 pairs of identical twins and 129 members of cancer-prone families, including 16 with cancer, were tested in a 3-day immunofluorescence assay. In the twin study, the variance of T-antigen values was significantly less in identical than in fraternal or non-twin sibs, suggesting a heritable component in the regulation of SV40 infection. In the families, T-antigen values of parents and children were compared to models of Mendelian inheritance. At least three modes of inheritance--autosomal dominant, recessive, and X-linker--were observed. The distribution of offspring values compared to those of their parents suggested that interaction of multiple genetic factors influences the T-antigen value in individual patients. With the exception of Fanconi's anemia, the values for patients with cancer or predisposing syndromes were not uniformly elevated. The utility of this assay as a marker of cancer risk appears limited because of the complexity of factors that influence T-antigen expression in individual cases.

Animals↗

PubMed1979

[Incorporation of H3-uridine in vitro into normal lymphocytes and those in cases of aberration of acrocentric chromosomes].

Literature data indicate that the formation of ribosomes is a basic function of the nucleolus. The formation of the nucleolus depends upon the function of the nucleolus organizing region (NOR). It was shown that in man the NOR locus is situated in secondary constrictions and adjacent segments of the short arms of acrocentric chromosomes of the D and G group. The presence of DNA sequences coding for 18 S and 28 S RNA i.e. ribosomal RNA (r-RNA), was demonstrated in the secondary constriction of acrocentric chromosomes using the RNA-DNA hybridization in situ method. The genes coding for 5 S RNA which is also a component of ribosomes, are located on other chromosomes. Therefore ribosome production should be considered a polygenic process, the genes situated in the NOR locus playing a basic role in its initiation. In cases of acrocentric chromosome aberration NOR "dosage" changes; in cases of regular trisomy there are 11 NOR "doses" instead of the normal 10, occurring in 5 pairs of group D and G chromosomes, in cases of translocation trisomy there are 9 such "doses" and in cases of balanced translocation carriers there are 8 "doses". Hence the following question: do changes in the NOR "dose" cause changes in ribosome production? Eventual changes should influence the intensity and/or the time course of r-RNA synthesis in cells stimulated to growth and differentiation . An approximate index for the study of this phenomenon is the 3H-uridine incorporation in an adequate experimental system. It seems that the most convenient model to study this phenomenon is the blastic transformation of lymphocytes induced by phytohaemagglutinin. This process has already been investigated in depth and is well known, the material being easily accessible. Venous blood was taken from 10 patients with 21 regular trisomy, 2 cases of 21 translocation trisomy and from 21 carriers of balanced translocations. Lymphocytes from 12 healthy persons with a normal karyotype served as controls. Lymphocytes in plasma were separated from whole blood and a routine macroculture was set up adding phaseoline of standardized mitogenic activity in the quantity 0.02 ml/ml of medium. The cells were incubated for 3, 6, 12, 24 and 48 hours. One hour before termination of the incubation period 1 microCi/ml 3H-uridine was added to the medium.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗