Distal Short Arm Of Chromosome Research Articles

Loss of function in NSD2 causes DNA methylation signature similar to that in Wolf-Hirschhorn syndrome

PurposeWolf-Hirschhorn syndrome (WHS), a contiguous gene syndrome caused by heterozygous deletions of the distal short arm of chromosome 4 that includes NSD2, reportedly causes specific DNA methylation signatures in peripheral blood cells. However, the genomic loci responsible for these signatures have not been elucidated. The present study aims to define the loci underlying WHS-related DNA methylation signatures and explore the role of NSD2 in these signatures. MethodsWe conducted genome-wide methylation analysis of individuals with WHS or NSD2 variants using an array method. We studied genome-edited knockin mice and induced pluripotent stem cells to explore the function of NSD2 variants. ResultsThree undiagnosed cases with NSD2 variants showed WHS-related DNA methylation signatures. In patient-derived induced pluripotent stem cells and genome-edited knockin mice, these variants cause NSD2 loss of function, respectively. The p.Pro905Leu variant caused decreased Nsd2 protein levels and altered histone H3-lysine 36 dimethylation levels similarly to what was observed in Nsd2 knockout mice. Nsd2 knockout and p.Pro905Leu knockin mice exhibited common DNA methylation changes. ConclusionThese results revealed that WHS-related DNA methylation signatures are dependent on NSD2 dysfunction and could be useful in identifying NSD2 variants of uncertain significance.

Hip displacement in Wolf-Hirschhorn syndrome: Report on three cases and review of associated musculoskeletal pathologies.

Wolf-Hirschhorn syndrome is a rare genetic disease caused by a chromosomal deletion of the distal short arm of Chromosome 4. It is associated with multisystem abnormalities, including delayed growth, characteristic facial features, epilepsy, and skeletal abnormalities. We report three patients who developed hip displacement, and describe the occurrence of delayed and nonunion in patients who underwent corrective proximal femoral osteotomy for hip displacement. We also performed a literature review identifying common musculoskeletal presentations associated with the condition. Patients with Wolf-Hirschhorn Syndrome are at risk of hip displacement (subluxation), and we would advocate annual hip surveillance in this patient group.

Elevated C1orf63 expression is correlated with CDK10 and predicts better outcome for advanced breast cancers: a retrospective study.

BackgroundChromosome 1 open reading frame 63 (C1orf63) is located on the distal short arm of chromosome 1, whose allelic loss has been observed in several human cancers. C1orf63 has been reported to be up-regulated in IL-2-starved T lymphocytes, which suggests it might be involved in cell cycle control, a common mechanism for carcinogenesis. Here we investigated the expression and clinical implication of C1orf63 in breast cancer.MethodsParaffin-embedded specimens, clinicopathological features and follow-up data of the breast cancer patients were collected. Publicly available microarray and RNA-seq datasets used in this study were downloaded from ArrayExpress of EBI and GEO of NCBI. KM plotter tool was also adopted. The expression of C1orf63 and CDK10, one known cell cycle-dependent tumor suppressor in breast cancer, was assessed by immunohistochemistry. Western blotting was performed to detect C1orf63 protein in human breast cancer cell lines, purchased from the Culture Collection of the Chinese Academy of Sciences, Shanghai.ResultsIn a group of 12 human breast tumors and their matched adjacent non-cancerous tissues, C1orf63 expression was observed in 7 of the 12 breast tumors, but not in the 12 adjacent non-cancerous tissues (P < 0.001). Similar results were observed of C1orf63 mRNA expression both in breast cancer and several other cancers, including lung cancer, prostate cancer and hepatocellular carcinoma. In another group of 182 breast cancer patients, C1orf63 expression in tumors was not correlated with any clinicopathological features collected in this study. Survival analyses showed that there was no significant difference of overall survival (OS) rates between the C1orf63 (+) group and the C1orf63 (−) group (P = 0.145). However, the analyses of KM plotter displayed a valid relationship between C1orf63 and RFS (relapse free survival)/OS (P < 0.001; P = 0.007). Notablely, in breast cancers with advanced TNM stages (III ~ IV) among these 182 patients, C1orf63 expression was an independent prognostic factor predicting better clinical outcome (HR: 0.41; 95 % CI: 0.17 ~ 0.97; P = 0.042). Additionally, we found that CDK10 mRNA expression was positively correlated with C1orf63, which was consistent with the relationship of protein expression between C1orf63 and CDK10 (rs = 0.391; P < 0.001).ConclusionsCompared to adjacent non-cancerous tissues, C1orf63 expression was elevated in tumor tissues. However, C1orf63 predicts better prognosis for breast cancers with advanced TNM stage, and the underlying mechanism is unknown. In addition, C1orf63 is correlated with the cell cycle related gene, CDK10.

Prenatal Diagnosis of a Satellited Chromosome 8p Results from a de novo Cryptic Translocation between Chromosomes 8 and 22

The authors of the present study report the prenatal detection of a chromosomal abnormality with additional satellites on the distal short arm of chromosome 8. A 35-year-old woman was referred for amniocentesis because of her advanced maternal age and positive result for maternal serum screening test. Cytogenetic analysis of cultured amniocytes showed a satellite 8p chromosome. The satellite 8p chromosome was positive for nucleolus organizer region (NOR) staining. The parents karyotypes were normal. Fluorescence ’ in situ hybridization (FISH) study for metaphases of fetal amniocytes revealed a cryptic translocation of chromosomes 8p and 22p. The fetal karyotype was described as 46,XY,8ps.ish t(8;22)(p23.3;p11.2) (D8S504-;D8S504+)dn. The parents decided to continue the pregnancy and a phenotypically normal boy was born at 38 weeks of gestation. In case of de novo terminal NORs detected prenatally, more accurate cytogenetic and molecular analysis should be performed in order to rule out cryptic chromosomal rearrangement among other chromosomes.

PP-204. A new case of trisomy 9 in postnatal period

WHS is a rare genetic disease characterized by typical craniofacial features in infancy, growth delay, psychomotor retardation, and seizures, and results from the deletion of the distal short arm of chromosome 4. Early diagnosis is important, providing individuals the appropriate interventions and follow-up by a multidisciplinary team. Medical care is supportive as the underlying disorder has no known treatment.

Copy number changes of the microcephalin 1 gene (MCPH1) in patients with autism spectrum disorders

Autism spectrum disorder (ASD) represents a set of neurodevelopmental disorders with a strong genetic aetiology. Chromosomal rearrangements have been detected in 5-10% of the patients with ASD, and recent applications of array comparative genomic hybridisation (aCGH) are identifying further candidate regions and genes. In this study, we present four patients who implicate microcephalin 1 (MCPH1) in band 8p23.1 as an ASD susceptibility gene. Patient 1 was a girl with a syndromic form of autistic disorder satisfying the Autism Diagnostic Interview-Revised (ADI-R), Autism Diagnostic Observation Schedule (ADOS) and Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) criteria. Oligonucleotide aCGH (oaCGH) showed that she had a classic inv dup del(8)(qter-> p23.1::p23.1-> p21.2) containing at least three candidate genes; MCPH1 and DLGAP2 within the 6.9-Mb terminal deletion and NEF3 within the concomitant 14.1-Mb duplication. Three further patients with MCPH1 copy number changes were found using single-nucleotide polymorphism (SNP) array analysis in a cohort of 54 families with ASD patients. Our results show that ASD can be a component of the classical inv dup del(8) phenotype and identify changes in copy number of MCPH1 as a susceptibility factor for ASD in the distal short arm of chromosome 8.

Psychotic Manifestations in a Patient with Mental Retardation and a 6.2 Megabase Deletion at the Distal Short Arm of Chromosome 12

Genetic factors are known to contribute to the development of schizophrenia and related psychoses. Cytogenetic abnormalities have been occasionally found in patients with psychotic disorders and, thus, have helped identify candidate gene contributors for these conditions. The individual described here first presented with mental retardation and anxiety disorder in his mid-childhood. In his early 20s, the patient started exhibiting various psychotic manifestations, including delusions and hallucinations. His psychotic symptoms were difficult to control with psychotropic medications. The family history was negative for psychiatric disorders. This patient was found to have a 6.2 megabase deletion of the terminal portion of the short arm of chromosome 12 that was characterized using fluorescence in situ hybridization and microarray comparative genomic hybridization analysis. The maternal chromosomes were normal, but the paternal chromosomes could not be tested. To-date such a chromosomal abnormality has not been described in association with schizophrenia/psychosis. This case suggests that psychosis-associated gene(s) may be located in the terminal region of the short arm of chromosome 12.

A patient with duplication (7)(p22.1pter) characterized by array‐CGH

Approximately 40 patients with terminal duplication of the distal short arm of chromosome 7 have been reported, the smallest being dup(7)(p21). We report here on a patient with a smaller duplication, dup(7)(p22.1), detected on G-banding and characterized by array-CGH. We establish phenotype-karyotype correlations with the reported patients with other 7p duplications.

A new genomic mechanism leading to cri‐du‐chat syndrome

Using standard banding techniques, a within-arm intrachromosomal insertion can be mistakenly interpreted as a paracentric inversion. The need to correctly distinguish between these two types of chromosome rearrangements is emphasized by their different reproductive risks. For carriers of an intrachromosomal insertion, the empiric risk of having a liveborn child with a recombinant chromosome leading to a genetic imbalance is at least 15%, whereas the risk for a carrier of a paracentric inversion having a liveborn child with a recombinant chromosome leading to a genetic imbalance is thought to be practically negligible. We report a unique observation in which a paracentric inversion in the short arm of chromosome 5, 46,XX,inv(5)(p13.3p15.3), was identified in a women who had a daughter with an apparently terminal deletion in the distal short arm of chromosome 5, 46,XX,del(5)(p14.3), and the clinical diagnosis of cri-du-chat syndrome. We further characterized the rearrangement, and fluorescence in situ hybridization (FISH) and microsatellite analyses confirmed the paracentric inversion in the mother and showed the deletion in the daughter was maternal in origin. Therefore, this represents a case in which a confirmed paracentric inversion likely resulted in a viable terminal deletion. We propose a mechanism involving dicentric chromosome formation with subsequent breakage and telomere healing during meiosis. This illustrates a new genomic mechanism of chromosome rearrangement leading to cri-du-chat syndrome and should provide significant information for the medical management of patients with other terminal deletion syndromes.

ATR-16 Due to a De Novo Complex Rearrangement of Chromosome 16

We describe a child with ATR-16 [α-thalassemia (thal)/mental retardation], who was referred forgenetic evaluation because of minor anomalies and developmental delay. Cytogenetic analysisdemonstrated a de novo complex rearrangement of chromosome 16. Fluorescence in situ hybridization(FISH) analysis, using chromosome 16 subtelomeric probes, showed that this patient had a deletion ofthe distal short arm of chromosome 16 that contains the α-globin genes and a duplication of 16q.Analysis of the α-globin locus by Southern blot showed a half normal dose of the α-globin gene.Microsatellite marker studies revealed that the duplicated 16q region was maternal in origin.Hematological studies revealed anemia, hypochromia and occasional cells with Hb H inclusion bodies. Ahematological screening for α-thal should be considered in patients with mild developmental delay and asuggestive phenotype of ATR-16 with microcytic hypochromic anemia and normal iron status. The stellatepattern of the iris, a new finding in our patient, may contribute to a better clinical delineation ofboth syndromes, ATR-16 and/or duplication of 16qter.

Biallelic inactivation of the RIZ1 gene in human gastric cancer.

The distal short arm of chromosome 1 is commonly deleted in a variety of human neoplasms including gastrointestinal cancer. Genetic alterations of the retinoblastoma protein-interacting zing-finger gene (RIZ)1 including loss of heterozygosity (LOH) at 1p36, frameshift mutations, and promoter hypermethylation were reported previously in several cancers. In this study, we evaluated RIZ1 in 30 primary gastric cancers and found frameshift mutations in two cases (6.7%). Moreover, using real-time quantitative methylation-specific PCR, methylation of the RIZ1 promoter was detected in 11 (37%) cases. In all 11 cases with methylation, inactivation of the second allele occurred through frameshift mutation, LOH or promoter methylation. Our results suggest that RIZ1 is a specific target of inactivation in human gastric cancer.

A Genetic Locus for Adolescent Idiopathic Scoliosis Linked to Chromosome 19p13.3

Adolescent idiopathic scoliosis (AIS) is one of the most common orthopedic disorders, affecting up to 4% of schoolchildren worldwide. We studied seven unrelated multiplex families of southern Chinese descent with AIS, consisting of 25 affected members. A genomewide scan with >400 fluorescent microsatellite markers was performed. Multipoint linkage analysis by GENEHUNTER revealed significant linkage of the abnormal phenotype to the distal short arm of chromosome 19, with both a maximum multipoint LOD score and a nonparametric LOD score of 4.93. Two-point linkage analysis by MLINK gave a LOD score of 3.63 (recombination fraction theta[m=f]=0.00) at D19S216. Further high-density mapping and informative recombinations defined the AIS critical region in the vicinity of D19S216, flanked by D19S894 and D19S1034, spanning 5.2 cM on the sex-averaged genetic map on chromosome 19p13.3.

American College of Medical Genetics Statement on Diagnostic Testing for Uniparental Disomy

American College of Medical Genetics Statement on Diagnostic Testing for Uniparental Disomy

Analysis of genomic imprinting at 1p35-36 in neuroblastoma.

Deletion of the distal short arm of chromosome 1 occurs in 25-35% of primary neuroblastomas, and a putative tumor suppressor gene has been mapped to a consensus region of deletion at 1p36.2-36.3. Indirect evidence suggests the presence of an imprinted neuroblastoma suppressor gene within this region, as well as an additional nonimprinted, proximal suppressor gene, inactivation of which correlates with MYCN amplification. To test this hypothesis, we performed 1p loss of heterozygosity (LOH) studies on a series of neuroblastomas for which parental DNA had been collected. PCR-formatted polymorphic markers were used to determine the size of the 1p deletion and the parental origin of the deleted 1p homologue. Twenty-six neuroblastomas with 1p LOH were evaluated. Twenty-four had MYCN amplification, and of these, 15 demonstrated loss of the paternally inherited 1p. Two neuroblastomas with a single copy of MYCN were evaluated and both had deletion of the paternally inherited 1p, with one case exhibiting a small terminal deletion. In addition, we have reviewed 49 previously reported neuroblastomas where 1p LOH data and the parental origin of the deleted lp homologue were available. Analyzed together, these 75 neuroblastomas demonstrate random deletion of parental 1p homologues (P = 0.30). Further, tumors with smaller deletions (breakpoints distal to D1S201 or D1S7) showed a random loss of the parental 1p homologues (P = 0.59), contrary to the expected preferential maternal 1p deletion if an imprinted suppressor gene mapped to this region. However, 19 tumors with 1p LOH and single copy MYCN had deletion of the maternal 1p homologue preferentially (P = 0.02), which does not exclude the possibility that loss of an imprinted suppressor gene plays a role in this subset.

Molecular and clinical characterization of a patient with a chromosome 4p deletion, Wolf-Hirschhorn syndrome, and congenital glaucoma

Wolf-Hirschhorn syndrome is a developmental disorder associated with hemizygous deletion of the distal short arm of chromosome 4. We have identified a patient affected with Wolf-Hirschhorn syndrome and early onset glaucoma. Five other patients with Wolf-Hirschhorn syndrome and early onset glaucoma or ocular anomalies associated with early onset glaucoma have been previously described, suggesting that the association with Wolf-Hirschhorn syndrome is not coincidental. The infrequent association of early onset glaucoma suggests that the chromosomal region commonly deleted in Wolf-Hirschhorn patients does not contain genes responsible for early onset glaucoma. In this study, we performed a molecular characterization of the deleted chromosome 4 to determine the extent of the deletion in an attempt to begin to identify the chromosomal region responsible for the associated glaucoma. Using microsatellite repeat markers located on 4p, we determined that the deletion spanned a 60-cM region including the minimal Wolf-Hirschhorn region. The proximal breakpoint occurred between markers D4S3045 and D4S2974. These results support the hypothesis that patients with Wolf-Hirschhorn syndrome and early onset glaucoma may have large deletions of 4p that include a gene(s) that may be responsible for a dominant form of congenital glaucoma.

Inverted duplication of the distal short arm of chromosome 3 associated with lobar holoprosencephaly and lumbosacral meningomyelocele

Inverted duplication of the distal short arm of chromosome 3 associated with lobar holoprosencephaly and lumbosacral meningomyelocele

Inverted duplication of the distal short arm of chromosome 3 associated with lobar holoprosencephaly and lumbosacral meningomyelocele

A fetus with lobar holoprosencephaly and lumbosacral meningomyelocele associated with duplication of the short arm of chromosome 3 is reported. The anomalies were detected on fetal ultrasound at 20 weeks' gestation and the autopsy findings correlated well with the prenatal findings. The fetal karyotype was 46,XY,der(3)del(3)(p26) dup(3)(p26p21.3). The association of holoprosencephaly with duplication 3p is well known, but to the best of our knowledge this is the first reported association of meningomyelocele with 3p duplication. These findings suggest that a gene or genes with a crucial role in central nervous system development are located on the short arm of chromosome 3.

Identification of a 1-megabase consensus region of deletion at 1p36.3 in primary neuroblastomas.

Deletion of the distal short arm of chromosome 1 occurs frequently in neuroblastoma. In addition, neuroblastoma has been described in children with constitutional deletions within 1p36, supporting the existence of one or more neuroblastoma suppressor genes within this region. We have pursued a 1p36 tumor suppressor gene identification strategy that has included deletion mapping of 566 primary neuroblastomas and 46 neuroblastoma-derived cell lines, and have determined the parental origin of the deleted 1p homologue in 44 cases to determine whether there is evidence for genomic imprinting within this region. We have identified a 1-Mb consensus region of deletion within 1p36.3 defined by primary tumor deletions, constructed a physical map of the region that is being sequenced to completion, and have identified and prioritized candidate genes within this region for further analyses.

Deletion of the Dm-Domain Gene Cluster in a Fetus with Ring Chromosome 9 and Sex Reversal

Deletions of the distal short arm of chromosome 9 have been reported in association with gonadal dysgenesis and XY sex reversal. These findings suggest that this region harbors at least one gene that might be involved in sexual development. Recent studies narrowed the deletion interval to the subtelomeric region 9p24.3. This region contains three genes DMRT1, DMRT3, and DMRT2 characterized by a DM-domain that seems essential for sexual development in Nematoda and Arthropoda. We have investigated the possible role of this gene cluster in a fetus with ring chromosome 9 and male-to-female sex reversal. We could demonstrate by FISH analysis a very small deletion of the terminal short arm of chromosome 9 including the DM-domain gene cluster. This finding gives further evidence that hemiZygosity of this region can be the cause for male-to-female sex reversal.

A region of human chromosome 9p required for testis development contains two genes related to known sexual regulators.

Deletion of the distal short arm of chromosome 9 (9p) has been reported in a number of cases to be associated with gonadal dysgenesis and XY sex reversal, suggesting that this region contains one or more genes required in two copies for normal testis development. Recent studies have greatly narrowed the interval containing this putative autosomal testis-determining gene(s) to the distal portion of 9p24.3. We previously identified DMRT1, a human gene with sequence similarity to genes that regulate the sexual development of nematodes and insects. These genes contain a novel DNA-binding domain, which we named the DM domain. DMRT1 maps to 9p24. 3 and in adults is expressed specifically in the testis. We have investigated the possible role of DM domain genes in 9p sex reversal. We identified a second DM domain gene, DMRT2, which also maps to 9p24.3. We found that point mutations in the coding region of DMRT1 and the DM domain of DMRT2 are not frequent in XY females. We showed by fluorescence in situ hybridization analysis that both genes are deleted in the smallest reported sex-reversing 9p deletion, suggesting that gonadal dysgenesis in 9p-deleted individuals might be due to combined hemizygosity of DMRT1 and DMRT2.