Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring.

The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.

Genotype-phenotype correlation of deletions and duplications of 4p: case reports and literature review.

Structural rearrangements of chromosome 4p gives rise to a group of rare genomic disorders that mainly result in two different clinical entities: Wolf-Hirschhorn syndrome (WHS) and partial 4p trisomy. The severity of the phenotype depends on the size of the deletion or locus duplication. Here, we present two unrelated individuals with a copy number variation of chromosome 4p. Inverted duplication deletions (inv dup-del) in 4p are particularly rare. Case 1 describes a 15-year-old girl with a 1.055 Mb deletion of terminal 4p, distal to the recognized critical region of WHS, and a large duplication of 9.6 Mb in size from 4p16.3 to p16.1. She had postnatal development delay, intellectual disability (especially pronounced in speech), seizure/electroencephalogram anomalies, and facial dysmorphic features. This unusual chromosomal imbalance resulted in the WHS phenotype rather than the 4p trisomy syndrome phenotype. Case 2 describes a 21-month-old boy with a 1.386 Mb terminal 4p deletion who presented with slight developmental delay, borderline intellectual disability, and seizures. Combined with previous reported cases of 4 pter del-dup or pure 4p terminal deletions, our observations suggest that terminal chromosome 4p deletion is more pathogenic than the concomitant partial 4p duplication, and some regions of the 4p terminal may have regulatory effects on the remaining region of 4p. About nine cases have been reported thus far to date, and our study delineates further genotype-phenotype correlations about terminal 4p duplication-deletions for predicting disease prognosis and patient counseling.

Familial 4p Interstitial Deletion Provides New Insights and Candidate Genes Underlying This Rare Condition.

Chromosome 4p deletions can lead to two distinct phenotypic outcomes: Wolf--Hirschhorn syndrome (a terminal deletion at 4p16.3) and less frequently reported proximal interstitial deletions (4p11-p16). Proximal 4p interstitial deletions can result in mild to moderate intellectual disability, facial dysmorphisms, and a tall thin body habitus. To date, only 35 cases of proximal 4p interstitial deletions have been reported, and only two of these cases have been familial. The critical region for this syndrome has been narrowed down to 4p15.33-15.2, but the underlying causative genes remain unclear. In this study, we report the case of a 3-year-old female with failure to thrive, developmental and motor delays, and morphological features. The mother also had a 4p15.2-p14 deletion, and the proband was found to have a 13.4-Mb 4p15.2-p14 deletion by chromosome microarray analysis. The deleted region encompasses 16 genes, five of which have a high likelihood of contributing to the phenotype: PPARGC1A, DHX15, RBPJ, STIM2, and PCDH7. These findings suggest that multiple genes are involved in this rare proximal 4p interstitial deletion syndrome. This case highlights the need for healthcare providers to be aware of proximal 4p interstitial deletions and the potential phenotypic manifestations.

De novo c.2455C>T mutation of NPR2 gene in a fetus with shortened long bones and a ventricular septal defect conceived by a mother with a fragile site at 16q22.1 and a father with a rare heterochromatic variant of chromosome 4 from Vietnam.

BACKGROUND: A heterozygous natriuretic peptide receptor 2 (NPR2) gene c.2455C>T mutation was identified as a cause of familial idiopathic short stature (ISS). Only two cases with this mutation were reported previously, and the probands with ISS had no organ system defects. METHODS: Next-generation sequencing (NGS) was performed on an amniotic fluid DNA sample of a fetus with shortened long bones and a small ventricular septal defect detected by an obstetric ultrasound examination. The pathogenic variant of the fetus was confirmed by Sanger sequencing. Sanger sequencing, G-banded, and C-banded karyotyping of the fetus's parents were subsequently performed. RESULTS: A de novo NPR2 gene c.2455C>T, p.(Arg819Cys) mutation was identified in the fetus. No microdeletion or microduplication was identified in the fetus by copy number variation sequencing with a maximum resolution of 400 kb. The two previous miscarriages experienced by the fetus's parents were interpreted as a result of chromosomal aberrations, including a maternal fragile site at 16q22.1 and a rare paternal variant involving in a large G-band-positive and C-band-positive block of paracentric heterochromatin of chromosome 4p. CONCLUSION: This report provides clinical signs of a de novo heterozygous NPR2 gene c.2455C>T mutation in the fetus and shows paternal chromosomal aberrations causing repeated pregnancy loss.

Wolf-Hirschhorn (4p-) Syndrome Presenting with Status Epilepticus

Wolf-Hirschhorn syndrome is a well-recognized malformation syndrome with multiple congenital anomalies, resulting from partial deletion of the short arm of chromosome 4 (4p-). All affected individuals have intrauterine and postnatal growth retardation with marked feeding difficulties, developmental delay, and intellectual disability. Additionally, most of patients have seizures from early infancy. Although seizures are common with this syndrome, presenting with status epilepticus (SE) is rare. We report two cases of Wolf-Hirschhorn syndrome presenting with SE.

Wolf-Hirschhorn (4p-) Syndrome Presenting with Status Epilepticus / 대한간질학회지

Wolf-Hirschhorn syndrome is a well-recognized malformation syndrome with multiple congenital anomalies, resulting from partial deletion of the short arm of chromosome 4 (4p-). All affected individuals have intrauterine and postnatal growth retardation with marked feeding difficulties, developmental delay, and intellectual disability. Additionally, most of patients have seizures from early infancy. Although seizures are common with this syndrome, presenting with status epilepticus (SE) is rare. We report two cases of Wolf-Hirschhorn syndrome presenting with SE.

A Case of Wolf-Hirschhorn Syndrome with Long Term Survival Diagnosed by Fluorescent In-situ Hybridization (FISH)

Wolf-Hirschhorn syndrome is a multiple malformation syndrome associated with mental and developmental retardation, resulting from a deletion at the short arm of chromosome 4 (4p16.3). We report a 11-year-old girl with Wolf-Hirschhorn syndrome, who was presented with severe growth and mental retardation along with characteristic features-frontal bossing, hypertelorism, downslanting of the palpebral fissures and fishlike lips. The diagnosis was confirmed by fluorescent in-situ hybridization (FISH).

A Case of Wolf-Hirschhorn Syndrome with Long Term Survival Diagnosed by Fluorescent In-situ Hybridization (FISH)

Wolf-Hirschhorn syndrome is a multiple malformation syndrome associated with mental and developmental retardation, resulting from a deletion at the short arm of chromosome 4 (4p16.3). We report a 11-year-old girl with Wolf-Hirschhorn syndrome, who was presented with severe growth and mental retardation along with characteristic features-frontal bossing, hypertelorism, downslanting of the palpebral fissures and fishlike lips. The diagnosis was confirmed by fluorescent in-situ hybridization (FISH).

Prenatal Diagnosis of the Wolf-Hirschhorn Syndrome

Wolf-Hirschhorn syndrome (WHS) is caused by a deletion of the short arm on chromosome 4 and is characterized by multiple congenital abnormalities, growth and mental retardation. In this case report, we performed amniocentesis for the chromosome analysis on a 25-year-old pregnant woman at 16 weeks of gestation whom we suspected of Edward's syndrome by the triple test of maternal serum and ultrasonography. The result of analysis revealed a karyotype of the fetus with 46,XY,del(4)(p15) by trypsin Giemsa's banding technique. With the result, we were able to diagnose the fetus as having WHS. As such, after therapeutic termination of the pregnancy, we confirmed WHS through the sampling of tissue by both trypsin Giemsa's banding and fluorescence in situ hybridization (FISH) method. To determine the origin of the WHS, we further tested the karyotypes of the parents. As parental karyotypes were found to be normal, we determined the case of the fetal WHS to be de novo.