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Sister chromatid exchanges in Bloom's syndrome.

The importance of chromosome instability in Bloom's syndrome is reviewed, and the recently developed technique for demonstrating sister chromatid exchanges (SCE) is described. In Bloom's syndrome, but not in other heritable syndromes associated with chromosome instability, there is a nine- to ten-fold increase in the frequency of spontaneous SCE. We present a case of Bloom's syndrome in which this test facilitated the diagnosis. In four obligate heterozygotes (the parents of children with Bloom's syndrome), however, an increase in the frequency of spontaneous SCE was not observed.

Abnormalities, Multiple

Ataxia telangiectasia: chromosomal stability in continuous lymphoblastoid cell lines.

Chromosomal breakage in peripheral lymphocytes, cultured fibroblasts and long-term lymphoblastoid cell lines was investigated in five hitherto undescribed patients with ataxia telangiectasia (AT). Increased chromosomal instability was observed in lymphocytes and fibroblasts, and clones possessing a Dq+ marker were observed. Breakage rates were significantly higher in the fibroblasts than in the lymphocytes of AT patients or in similar tissues from patients with Bloom syndrome or Fanconi anemia. However, chromosome breakage in lymphoblastoid lines established from these five AT patients and six others did not differ from controls. These observations suggests that selection pressures, in vivo or in vitro, or both, act differently on the expression of chromosomal instability in these various cell types.

Abnormalities, Multiple

Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation.

Centromere identity is specified by CENP-A, a histone H3 variant that epigenetically defines centromere position. How CENP-A is maintained at one location in rapidly evolving centromeric DNA is unknown. Using single-cell-derived clones of human cell lines, we demonstrate heterogeneity in CENP-A position within cell populations at neocentromeres and a native centromere. CENP-A heterogeneity is accompanied by heterogeneous DNA methylation patterns, with DNA methylation shifting according to CENP-A position. We demonstrate centromere epigenetic plasticity over extended proliferation, with native centromeres maintaining stable DNA methylation boundaries, but neocentromeres exhibiting DNA methylation instability, boundary loss, and increased missegregation. Finally, we show that neocentromeres are more sensitive to DNA methylation inhibition than native centromeres, and that this inhibition is accompanied by expanded CENP-A-enriched domains and increased missegregation. This study supports a role for DNA methylation boundaries in maintaining centromere position, stability, and function and highlights the intrinsic instability of DNA methylation at neocentromeres.

CENP-A

Transposable genetic elements as agents of gene instability and chromosomal rearrangements.

Transposable genetic elements in prokaryotes and eukaryotes, when inserted at a given locus, can control expression of the locus and cause large scale rearrangements of adjacent DNA sequences. Striking similarities in genetic behaviour between the two groups of elements have led to the proposal of a molecular model of eukaryotic controlling elements, and to suggestions about the part such elements may play in evolution and differentiation.

Base Sequence

Genomic instability, postoperative recurrence and therapeutic vulnerabilities in resectable non‑small cell lung cancer (Review).

Resectable non‑small cell lung cancer (NSCLC) is managed largely according to anatomical stage, pathological risk and actionable driver alterations, yet these factors do not fully explain postoperative recurrence. Genomic instability may contribute to recurrence by promoting clonal diversification, intratumoral heterogeneity, occult dissemination, persistence of residual tumor cells, and immune escape. In the present review, chromosomal instability (CIN), copy‑number complexity, whole‑genome doubling, DNA repair defects, replication stress, and extrachromosomal DNA (ecDNA) were critically evaluated using a three‑axis translational framework encompassing biological consequences, potential clinical roles, and strength of evidence. Current evidence suggests that clonal diversity and copy‑number complexity have the clearest near‑term prognostic rationale. By contrast, CIN and whole‑genome doubling are supported more strongly by evolutionary and mechanistic rather than prospective clinical evidence. Defects in DNA repair, replication stress, and ecDNA represent potential therapeutic vulnerabilities, but their clinical relevance remains to be established. To date, no treatment‑predictive biomarkers based on genomic instability have been identified for resectable NSCLC. Direct clinical evidence linking any specific genomic instability feature to the presence or longitudinal dynamics of postoperative molecular residual disease (MRD) remains limited. Postoperative circulating tumor DNA‑defined MRD provides prognostic information more directly related to residual disease but remains assay‑dependent and should not be considered a genomic‑instability phenotype. Therefore, features of genomic instability should remain investigational and should not replace established clinical, pathological, or molecular decision‑making. Their near‑term value lies in refining biological risk models and generating testable hypotheses for biomarker‑defined perioperative trials.

Humans

Chromatin remodeling activity of EP400 safeguards chromosomal stability by preventing CENP-A mislocalization.

The mislocalization of CENP-A to non-centromeric regions contributes to chromosomal instability (CIN). The NuA4 histone acetyltransferase complex members EP400 and KAT5 regulate histone H2A.Z-H2B exchange and acetylation of histones, respectively. Overexpression of CENP-A and mutations in NuA4 components are observed in cancers. Here, we define a role for the chromatin remodeling activity of EP400, a top hit in RNAi screens for increased nuclear levels of CENP-A, in preventing CENP-A mislocalization and CIN. Mechanistically, we demonstrate a defect in the extraction of CENP-A from chromatin in cells expressing the EP400K1085G mutant, which lacks ATPase activity for histone exchange. Consistent with these results, EP400K1085G cells show increased CENP-A enrichment in chromatin and mislocalization to non-centromeric regions. Importantly, EP400K1085G cells exhibit CIN phenotypes in stable, near-diploid RPE1 cells with wild-type p53. In summary, our findings expand the role of EP400 from nucleosome destabilization for histone exchange to preventing the stable association of CENP-A with non-centromeric regions and CIN.

Humans

The curious case of sporadic nematode susceptibility in "Tifguard" peanut (Arachis hypogaea): seed mixture or genetic instability?

The Runner-type peanut (Arachis hypogaea L.) cultivar "Tifguard" carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of "Tifguard" plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1% to 5%); suggesting that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant "Tifguard" but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.

Arachis

KIF18A promotes chromosome congression in cooperation with CENP-E downstream of CENP-C.

Chromosome congression is a key process that acts to align chromosomes at the spindle equator via kinetochore-microtubule interactions, with defects in chromosome alignment leading to chromosomal instability. However, defining the mechanisms that underlie chromosome congression is limited due to the multiple factors that act in parallel to regulate chromosome movement. Here, we conducted a genome-wide Cas9-based functional genetics screen using a hypomorphic CENP-C mutant that affects its kinetochore interactions. Our analysis identified KIF18A, whose knockout resulted in synthetic lethality with the CENP-C mutant. Further analysis revealed that the synthetic defect was due to a reduction in CENP-E function in the CENP-C mutant. Our work suggests that KIF18A promotes chromosome alignment in cooperation with CENP-E downstream of CENP-C during early prometaphase. Thus, our analysis enables us to dissect parallel molecular mechanisms for chromosome congression and identify sensitivities and biomarkers that might guide anti-KIF18A chemotherapeutics.

Kinesins

The effects of mutagen-sensitive mutants of Drosophila melanogaster in nonmutagenized cells.

The effects of 13 mutagen-sensitive (mus) mutants (representing seven loci) on mitotic chromosome stability in nonmutagenized cells have been examined genetically. To do this, mus-bearing flies heterozygous for the recessive somatic-cell marker, multiple wing hairs (mwh), were examined for increased frequencies of mwh clones in the wing blade. Mutants at the mus-103, mus-104 and mus-106 loci do not affect the frequency of mwh clones, while mus-101, mus-102, mus-105 and mus-109 alleles cause increases in the frequency of mwh clones. These data show that the wild-type alleles of latter four loci specify functions that are required for chromosome stability in nonmutagenized cells. Analysis of the size distribution of mwh clones produced by these mutants suggests that most chromosome instability caused by these mutants is the consequence of chromosome breakage; in the presence of mus-105 and mus-109 alleles a small fraction of the mwh clones are produced by an event (mitotic recombination, mutation, nondisjunction) that produces euploid clones. To inquire whether any of the extant alleles of the mus-101, mus-102, mus-105 and mus-109 loci might be leaky alleles of loci that carry out essential mitotic functions, chromosome stability in females homozygous for alleles of these loci has been compared to that of females carrying one dose of a mutant over a deficiency for that mus locus. These comparisons show that the extant alleles at the mus-101, mus-109 and mus-105 loci are all leaky mutants. It is suggested that all three of these loci may specify essential mitotic functions.

Animals

The influence of culture medium composition on the incidence of chromosomal breakage.

In patients with chromosomal instability and healthy subjects, significant differences were observed in the chromosomal breakage incidence in simultaneous lymphocyte cultures set up with TC medium 199, Eagle's Minimum Essential Medium, or RPMI, or RPMI 1629. The importance of the choice of culture medium for mutagenicity testing and studies of so-called spontaneous breakage is shown. Cultures incubated with TC Medium 199 showed the highest chromosomal breakage incidence.

Ascorbic Acid

Somatic rearrangement of chromosome 14 in human lymphocytes.

Ataxia-telangiectasia is a rare genetic disorder associated with immune deficiency, chromosome instability, and a predisposition to lymphoid malignancy. We have detected chromosomally anomalous clones of lymphocytes in eight patients with this disorder. Chromosome banding disclosed that the clones are consistently marked by structural rearrangement of the long arm (q) of chromosome 14. A translocation involving 14q was found in clones obtained from seven of the eight patients whereas a ring 14 chromosome was found in a clone obtained from the other. These findings as well as data obtained by others for patients with ataxia-telangiectasia suggest that structural rearrangement of 14q is the initial chromosomal change in lymphocyte clones of patients with this disorder. Chromosomes of lymphocytes from one of the patients were studied before and after the onset of chronic lymphocytic leukemia. Before leukemia was diagnosed, the patient had a lymphocyte clone with a 14q translocation. This clone appears to have given rise to the leukemic cells. We hypothesize that structural rearrangement of 14q is directly related to abnormal growth of lymphocytes and that it may be a step toward the development of lymphoid malignancies. Increasing evidence, provided by others, for the nonrandom involvement of 14q in African-type Burkitt's lymphoma and other lymphoid neoplasms further strengthens this hypothesis.

Adolescent

Aneuploidy selects for the acquisition of driver genes in breast cancer.

Chromosome instability is highly prevalent in cancer and drives large-scale chromosomal imbalances, known as aneuploidies1-4. How aneuploidy contributes to tumorigenesis remains difficult to study due to the vast numbers of genes affected. Here we established a CRISPR knockout- and activation-linked assay (CRISPR-KOALA), enabling high-throughput bidirectional genetic screens in immunocompetent mouse models of cancer. We developed a compendium of the ten most frequent human chromosome-arm-level alterations in basal-like breast cancer (BLBC), a disease type that is driven by large copy-number alterations (CNAs)5-8. Using CRISPR-KOALA, we screened the mouse orthologues of 3,752 genes on these arms and identified 90 cancer driver genes, the function of the vast majority of which is unknown. These genes drive distinct signalling pathways including MAPK, HIPPO and WNT, reflecting the high degree of BLBC heterogeneity. Manipulating the identified cancer driver genes overcomes the need for CNAs in Trp53-mutant BLBC mouse models. Mechanistically, we identify that PLGRKT is a potent oncogene that lies on chromosome 9p and show that its tumour-promoting activity is associated with highly stress-resistant mitochondria and an increased ability to detoxify reactive oxygen species. Together, our findings reveal that arm-level CNAs can function to select specific driver genes to promote heterogeneous biological processes.

Animals

Differential sensitivity of Xeroderma pigmentosum cells of different repair capacities towards the chromosome breaking action of carcinogens and mutagens.

The sensitivity of cultured fibroblasts obtained from four unrelated Xeroderma pigmentosum patients (XP-K, XP-C, XP-E and XP-H), which showed different DNA repair levels, was examined. The frequency of metaphase plates with chromosome aberrations and the frequency of breaks and exchanges per chromosome complement were estimated following exposure to the carcinogens 4-nitroquinoline-1-oxide (4NQO),N-acetoxy-2-acetyl-aminofluorene (N-acetoxy-2-AAF), and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), and to the mutagen daunomycin. The frequency of chromosome aberrations (breaks and exchanges) increased in the order (XP-K less than XP-C less than XP-E less than XP-H) with decreasing DNA repair capacity of the XP cells examined (XP-K greater than XP-C greater than XP-E greater than XP-H) following 4NQO and N-acetoxy-2-AAF. MNNG induced DNA repair synthesis and chromosome aberrations in the four XP cell types at levels comparable to those in fibroblasts of non-afflicted persons. Daunomycin triggered no DNA repair synthesis but induced similar frequencies of chromosome aberrations in the XP cells and controls. Heterozygous XP cells from parents of XP-K, XP-E and XP-C responded as control cells towards the three carcinogens and the mutagen used. Xeroderma pigmentosum can be considered to be an "induced" chromosome instability syndrome, in contrast to Bloom's syndrome or Fanconi's anaemia, which are "spontaneous" chromosome breakage syndromes according to German's definition.

4-Nitroquinoline-1-oxide

Mutagenic effects of isonicotinic acid hydracide in Fanconi's anemia.

Isonicotinic acid hydracide (INH) increases substantially the chromosomal instability in Fanconi's anemia (FA) cells. The same concentrations of INH do not significantly break chromosomes in heterozygous or normal cells. INH does not induce alkylation or cross-links in the DNA, like other mutagens known to increase breakage in FA cells. Possible mechanisms of the effect of INH are discussed. One consequence of this experiment is the possibility of an exact and doubtless prenatal diagnosis of a homozygous FA fetus.

Adolescent

[Chromosome effect of cyclophosphamide in various strains of mice].

The chromosomes of four different mouse strains were examined after administration of a single dose of cyclophosphamide, 100 mg/kg. Chromosomal breaks and rearrangements were produced in C3H mice three to four times as frequently and in AKR mice twice as frequently as in C57 B1 and XLII Orl mice. This indicates that cytogenetic investigations in mutation research using mice as in vivo test systems may be variable depending on the mouse strain employed. Because the effect of the alkylating agent was not pronounced in the two strains having a high incidence of cancer and leukemia (C3H and AKR), the possibility of a relationship between chromosomal instability and cancer proneness is discussed.

Animals

Ultraviolet radiation--induced chromosomal abnormalities in fetal fibroblasts from New Zealand black mice.

Fibroblasts from New Zealand Black mouse fetuses manifest increased frequency of chromosomal breaks and interchanges after exposure to ultraviolet radiation when compared with cells from BABL/c fetuses. This chromosomal instability is similar to what has been reported in cells from patients with xeroderma pigmentosum and may be related to the chromosomally abnormal clones and malignancy previously reported in adult New Zealand Black mice.

Animals

Klinefelter's syndrome and bladder cancer.

A patient with Klinefelter's syndrome is described who also had transitional cell carcinoma of the bladder. His mother and maternal grandfather died of neoplasms. It is suggested that neoplasm and aneuploidy in the same family could have been caused by an inherited chromosomal instability rather than coincidence.

Adult