Chromosomal fragility, structural rearrangements and mobile element activity may reflect dynamic epigenetic mechanisms of importance in neurobehavioural genetics

A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes

The sheer number of gene variants and the extent of the observed clinical and molecular heterogeneity recorded in neuropsychiatric disorders (NPDs) could be due to the magnified downstream effects initiated by a smaller group of genomic higher-order alterations in response to endogenous or environmental stress. Chromosomal common fragile sites (CFS) are functionally linked with microRNAs, gene copy number variants (CNVs), sub-microscopic deletions and duplications of DNA, rare single-nucleotide variants (SNVs/SNPs), and small insertions/deletions (indels), as well as chromosomal translocations, gene duplications, altered methylation, microRNA and L1 transposon activity, and 3-D chromosomal topology characteristics. These genomic structural features have been linked with various NPDs in mostly isolated reports and have usually only been viewed as areas harboring potential candidate genes of interest. The suggestion to use a higher level entry point (the 'fragilome' and associated features) activated by a central mechanism ('stress') for studying NPD genetics has the potential to unify the existing vast number of different observations in this field. This approach may explain the continuum of gene findings distributed between affected and unaffected individuals, the clustering of NPD phenotypes and overlapping comorbidities, the extensive clinical and molecular heterogeneity, and the association with certain other medical disorders.

Analysis of chromatin instability of somatic cells in sheep

Cytogenetic tests are highly reliable, sensitive indicators of the early effects of genomic instability. Their results provide information on the organism’s susceptibility to exogenous and endogenous factors and are measures of the degree of repair of DNA damage. Our study assessed spontaneously occurring damage in following four breeds of sheep: Polish Heath, Polish Lowland (Zelazna variety), Polish Blackhead, and Berrichon du Cher. Instability was identified using the following three different tests: a sister chromatid exchange (SCE) assay, identification of fragile sites, and the comet assay. The distribution of instabilities varied depending on the breed. The mean frequency of SCEs was 5.13 ± 1.58, whereas that of fragile sites was 3.30 ± 1.24. The mean level of DNA damage (% head DNA) was 96.52 ± 6.59. The most damage to genetic material was observed in the Berrichon du Cher sheep, and the least in the Polish Heath sheep. The tests used are reliable biomarkers of genome stability in animal breeds, as well as in individuals within breeds.

Identification of chromosome instability in Japanese quail (Coturnix japonica)

1. A study of the incidence of chromosome instability in the Japanese quail as assessed by sister chromatid exchange (SCE) and fragile site identification in chromosomes was conducted in two parent breeds and their F1 and F2 generations. 2. The mean incidence of SCEs was 6.02 ± 0.45 and the frequency of fragile sites was 1.17 ± 0.79. 3. There were moderately negative correlations of 0.51-0.64 between chromosome instability and fertility in the F1 and 0.10-0.23 in the F2. The hatch of fertilised eggs was negatively correlated with the number of SCE in male (0.31) and female (0.33) F1 and was lower in P (0.18 and 0.19, respectively), whereas the correlations were similar for the number of fragile sites in both generations (0.51-0.62).

Assessment of chromosome instability in geese (Anser anser)

Wójcik, E. and Smalec, E. 2012. Assessment of chromosome instability in geese ( Anser anser ). Can. J. Anim. Sci. 92: 49–57. The basic test applied in the research of chromosome instability is the test of sister chromatid exchange (SCE). It makes it possible to identify single-and double-strand DNA damage caused by genotoxic factors and those that disrupt DNA damage repair mechanisms. Fragile sites in chromosomes can be found in all organisms. They are chromosome sites showing susceptibility to breakages and discontinuities in specific conditions of cell culture and also following induction with chemical substances. Chromosome instability of Anser anser geese was assessed in the research, focussing on sister chromatid exchange and the identification of fragile sites. The mean SCE/cell was 4.75±1.00. Most SCEs were identified in the proximal part of the chromosomes. Fragile sites were also identified in the chromosomes during the research. Altogether, 138 breakages were observed in the chromosomes. Apart from identifying chromosome damage, the particular instances of damage were located in the chromosomes.

Common chromosomal fragile sites (CFS) may be involved in normal and traumatic cognitive stress memory consolidation and altered nervous system immunity

Previous reports of specific patterns of increased fragility at common chromosomal fragile sites (CFS) found in association with certain neurobehavioural disorders did not attract attention at the time due to a shift towards molecular approaches to delineate neuropsychiatric disorder candidate genes. Links with miRNA, altered methylation and the origin of copy number variation indicate that CFS region characteristics may be part of chromatinomic mechanisms that are increasingly linked with neuroplasticity and memory. Current reports of large-scale double-stranded DNA breaks in differentiating neurons and evidence of ongoing DNA demethylation of specific gene promoters in adult hippocampus may shed new light on the dynamic epigenetic changes that are increasingly appreciated as contributing to long-term memory consolidation. The expression of immune recombination activating genes in key stress-induced memory regions suggests the adoption by the brain of this ancient pattern recognition and memory system to establish a structural basis for long-term memory through controlled chromosomal breakage at highly specific genomic regions. It is furthermore considered that these mechanisms for management of epigenetic information related to stress memory could be linked, in some instances, with the transfer of the somatically acquired information to the germline. Here, rearranged sequences can be subjected to further selection and possible eventual retrotranscription to become part of the more stable coding machinery if proven to be crucial for survival and reproduction. While linkage of cognitive memory with stress and fear circuitry and memory establishment through structural DNA modification is proposed as a normal process, inappropriate activation of immune-like genomic rearrangement processes through traumatic stress memory may have the potential to lead to undesirable activation of neuro-inflammatory processes. These theories could have a significant impact on the interpretation of risks posed by heredity and the environment and the search for neuropsychiatric candidate genes.

Does HIV-1/AIDS-associated frontotemporal neuropathology following perinatal infection influence the development of moral behaviour?

While HIV encephalopathy and the AIDS dementia complex are considered hallmark neurologic manifestations of HIV-1 infection, increasing evidence of a continuum of nervous system involvement indicates the existence of an unrecognized number of individuals with milder, mostly cognitive and/or behavioural effects. Questions are raised whether HIV-related frontotemporal neuropathology during critical developmental stages could affect development of the brain networks documented to be involved in moral decisions, and whether this could contribute to the phenomenon of delinquency in an unknown percentage of the current generation of approximately 18-25 year old survivors of early childhood or vertically acquired HIV infection. Carefully planned and executed long term, prospective controlled studies using environmental, clinical, neurological, behavioural, genetic, immune and functional neuroimaging correlates would be required to elucidate whether HIV-specific neuropathology could indeed act as an independent risk factor for the development of a frontotemporal sociopathy syndrome. If such an association is proven, the accelerated development of neurospecific therapies should be a priority, especially for clinically and immunologically stable HIV-infected children. It may be necessary to institute such treatment as early as possible in perinatally infected cases, and maybe even during intrauterine life if HIV-1 is demonstrated to also act as a neurobehavioural teratogen for the developing fetal brain. It may, however, prove to be difficult to separate primary neurobiological from environmental factors, since the epigenetic effects on the host genome of retroviral insertion influencing behavioural gene expression characteristics, and altered gene expression following early life stresses may involve overlapping neurodevelopmental gene regulatory networks. In the meantime it remains necessary to prevent or ameliorate frequent neuropsychiatric morbidity from whatever causes.

Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 ( approximately 75 Mb position) and 3q21.3-q22.1 ( approximately 130 Mb position) (six lines). All locations are shown based on NCBI Build 36.1 human genome sequence. The last two regions participated in three of four chromosome 3 inversions during primate evolution. Regions at 75, 127, and 131 Mb positions carry a large ( approximately 250 kb) segmental duplication (tumor break-prone segmental duplication [TBSD]). TBSD homologous sequences were found at 15 sites on different chromosomes. They were located within bands frequently involved in carcinoma-associated breaks. Thirteen of them have been involved in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from specific organization of the chromosomal region, associated with location at a boundary between different CG-content isochores and with the presence of TBSDs and "instability elements," including satellite repeats and retroviral sequences.

Human cytomegalovirus (HCMV) and hearing impairment: infection of fibroblast cells with HCMV induces chromosome breaks at 1q23.3, between loci DFNA7 and DFNA49 -- both involved in dominantly inherited, sensorineural, hearing impairment

Human cytomegalovirus (HCMV) infection is the most common congenital infection in developed countries and is responsible for a substantial fraction of sensorineural hearing impairment (SNHI) in children. The risk of hearing impairment is associated with viral load in urine and blood collected during the first postnatal month. However, although inner ear abnormalities are observed in some children with HCMV-induced SNHI, the exact mechanism whereby congenital HCMV infection causes hearing impairment is unknown. Earlier studies using standard cytogenetic mapping techniques showed that infection of S-phase human fibroblast cells with HCMV resulted in two specific, site-directed, chromosome breaks at band positions 1q21 and 1q42 which include loci involved in dominantly and recessively inherited hearing impairment, respectively. These findings suggested that cells infected with HCMV might provide a reservoir for genetic damage and, in a clinical perspective, a scenario could be envisioned whereby hearing impairment could result from early DNA damage of dividing fetal cells rather than viral replication and cell lysis. In this work we demonstrate, using fine mapping techniques, that HCMV infection in S-phase fibroblast cells induces genetic damage at 1q23.3, within a maximal region of 37 kb, containing five low copy repeat (LCR) elements. The breakpoint is situated between two hearing impairment (HI) loci, DFNA49 and DFNA7, and in close proximity to the MPZ gene previously shown to be involved in autosomal dominant Charcot-Marie-Tooth syndrome (CMT1B) with auditory neuropathy.

Modeling non-random deletions in cancer

Chromosome deletions do abound in cancer and are detected in certain regions in a non-random manner. Although their relevance remains elusive, it is a general agreement that segmental losses provide the cell with selective growth advantage. Consequently these may contain genes and/or regulatory sequences that control normal growth and inhibit malignancy. We have developed a monochromosomal hybrid based experimental model for the generation and functional analysis of deletions, that is called "elimination test" (Et). Focused on human chromosome 3 - that was known to carry multiple 3p deletions - the Et was expected to restrict a 3p tumor suppressor region to a sufficiently small segment that permits the selection of a critically important candidate gene. Surprisingly, we detected three regions that were lost in all or majority of tumors: CER1 (3p21.3, Mb: 43.32-45.74), CER2 (3p22, Mb: 37.83-39.06) and FER (3p14.3-p21.2, Mb: 50.12-58.03). In contrast a 3q26-qter region (CRR) was regularly retained. CER1 - our main focus - contains multiple genes that may inhibit tumor growth, but 3 genes, RIS1, LF (LTF) and LIMD1 have already the necessary experimental support to be considered bona fide tumor suppressors. Tumor suppressor region borders display instability features including: (1) they break in evolution and in tumors, (2) they evolve horizontally, and (3) they are enriched with pseudogene insertions. The most remarkable features at the breakpoint cluster regions were segmental duplications that drive horizontal evolution and contribute to cancer associated instability.

Is there an emerging endosymbiotic relationship between mycobacteria and the human host based on horizontal transfer of genetic sequences?

While not negating the seriousness of tuberculosis and the need to prevent and combat the disease effectively, the large percentage of infected, apparently healthy individuals who harbour latent infections warrants consideration whether an endosymbiotic relationship is being established between mycobacteria and man. By means of a gene decay process eliminating their most metabolically important pathogenic genes associated with an increasing need for host gene products during prolonged intracellular survival, mycobacteria appears to be undergoing a process of establishing a less dangerous relationship with its host. To have tolerated this relationship over time, humans must have benefited. This is suggested to have occurred via changes in DNA higher order structure altering combinatorially regulated gene expression allowing increased cerebrodiversity. It can be expected that, beyond a certain threshold, negative effects ensued, leading to neuropathology and increased susceptibility for certain psychiatric disorders. These processes have probably been happening since the earliest contact with mycobacteria, but recently may have become modified by the emergence of epidemic tuberculosis and waves of increased oxidative stress following the circumstances associated with the Industrial Revolution and the more recent AIDS pandemic. The organism seems to have uniquely exploited the normal stress reaction of the host. Genomic stresses include changes associated with glucocorticoid effects as well as upregulated reactive oxygen species and stress/(heat shock) protein production, the latter two of which result in host cell cycle delay. Subsequently replication dependent chromosomal fragile sites appear in the host genome and together with upregulated chaperonins and mobile element activation, the scene is set for sequence exchange between the organism and host. If proven, these events raise the possibility of modifying chromatin epigenetically to retain the proposed advantages while silencing pathogenicity factors.