Overexpression of eIF-5A2 in mice causes accelerated organismal aging by increasing chromosome instability

Weighted single-step genome-wide association study for direct and maternal genetic effects associated with birth and weaning weights in sheep

Body weight is an important economic trait for sheep meat production, and its genetic improvement is considered one of the main goals in the sheep breeding program. Identifying genomic regions that are associated with growth-related traits accelerates the process of animal breeding through marker-assisted selection, which leads to increased response to selection. In this study, we conducted a weighted single-step genome-wide association study (WssGWAS) to identify potential candidate genes for direct and maternal genetic effects associated with birth weight (BW) and weaning weight (WW) in Baluchi sheep. The data used in this research included 13,408 birth and 13,170 weaning records collected at Abbas-Abad Baluchi Sheep Breeding Station, Mashhad-Iran. Genotypic data of 94 lambs genotyped by Illumina 50K SNP BeadChip for 54,241 markers were used. The proportion of variance explained by genomic windows was calculated by summing the variance of SNPs within 1 megabase (Mb). The top 10 window genomic regions explaining the highest percentages of additive and maternal genetic variances were selected as candidate window genomic regions associated with body weights. Our findings showed that for BW, the top-ranked genomic regions (1 Mb windows) explained 4.30 and 4.92% of the direct additive and maternal genetic variances, respectively. The direct additive genetic variance explained by the genomic window regions varied from 0.31 on chromosome 1 to 0.59 on chromosome 8. The highest (0.84%) and lowest (0.32%) maternal genetic variances were explained by genomic windows on chromosome 10 and 17, respectively. For WW, the top 10 genomic regions explained 6.38 and 5.76% of the direct additive and maternal genetic variances, respectively. The highest and lowest contribution of direct additive genetic variances were 1.37% and 0.42%, respectively, both explained by genomic regions on chromosome 2. For maternal effects on WW, the highest (1.38%) and lowest (0.41%) genetic variances were explained by genomic windows on chromosome 2. Further investigation of these regions identified several possible candidate genes associated with body weight. Gene ontology analysis using the DAVID database identified several functional terms, such as translation repressor activity, nucleic acid binding, dehydroascorbic acid transporter activity, growth factor activity and SH2 domain binding.

Moonlighting translation factors: multifunctionality drives diverse gene regulation

Translation factors have traditionally been viewed as proteins that drive ribosome function and ensure accurate mRNA translation. Recent discoveries have highlighted that these factors can also moonlight in gene regulation, but through functions distinct from their canonical roles in protein synthesis. Notably, the additional functions that translation factors encode are diverse, ranging from transcriptional control and extracellular signaling to RNA binding, and are highly regulated in response to external cues and the intrinsic cellular state. Thus, this multifunctionality of translation factors provides an additional mechanism for exquisite control of gene expression.

Eukaryotic Initiation Factor 5A2 Regulates Expression of Antiviral Genes

Translation factors are essential for regulation of protein synthesis. The eukaryotic translation initiation factor 5A (eIF5A) family is made up of two paralogues - eIF5A1 and eIF5A2 - which display high sequence homology but distinct tissue tropism. While eIF5A1 directly binds to the ribosome and regulates translation initiation, elongation, and termination, the molecular function of eIF5A2 remains poorly understood. Here, we engineer an eIF5A2 knockout allele in the SW480 colon cancer cell line. Using ribosome profiling and RNA-Sequencing, we reveal that eIF5A2 is functionally distinct from eIF5A1 and does not regulate transcript-specific or global protein synthesis. Instead, eIF5A2 knockout leads to decreased intrinsic antiviral gene expression, including members of the IFITM and APOBEC3 family. Furthermore, cells lacking eIF5A2 display increased permissiveness to virus infection. Our results uncover eIF5A2 as a factor involved regulating the antiviral transcriptome, and reveal an example of how gene duplications of translation factors can result in proteins with distinct functions.

miRNome Profiling Detects miR-101-3p and miR-142-5p as Putative Blood Biomarkers of Frailty Syndrome

Frailty is an aging-related pathology, defined as a state of increased vulnerability to stressors, leading to a limited capacity to meet homeostatic demands. Extracellular microRNAs (miRNAs) were proposed as potential biomarkers of various disease conditions, including age-related pathologies. The primary objective of this study was to identify blood miRNAs that could serve as potential biomarkers and candidate mechanisms of frailty. Using the Fried index, we enrolled 22 robust and 19 frail subjects. Blood and urine samples were analysed for several biochemical parameters. We observed that sTNF-R was robustly upregulated in the frail group, indicating the presence of an inflammatory state. Further, by RNA-seq, we profiled 2654 mature miRNAs in the whole blood of the two groups. Expression levels of selected differentially expressed miRNAs were validated by qPCR, and target prediction analyses were performed for the dysregulated miRNAs. We identified 2 miRNAs able to significantly differentiate frail patients from robust subjects. Both miR-101-3p and miR-142-5p were found to be downregulated in the frail vs. robust group. Finally, using bioinformatics targets prediction tools, we explored the potential molecular mechanisms and cellular pathways regulated by the two miRNAs and potentially involved in frailty.

Quantification of Age-Related Decline in Transcriptional Homeostasis

Age-dependent dysregulation of transcription regulatory machinery triggers modulations in the gene expression levels leading to the decline in cellular fitness. Tracking of these transcripts along the temporal axis in multiple species revealed a spectrum of evolutionarily conserved pathways, such as electron transport chain, translation regulation, DNA repair, etc. Recent shreds of evidence suggest that aging deteriorates the transcription machinery itself, indicating the hidden complexity of the aging transcriptomes. This reinforces the need for devising novel computational methods to view aging through the lens of transcriptomics. Here, we present Homeostatic Divergence Score (HDS) to quantify the extent of messenger RNA (mRNA) homeostasis by assessing the balance between spliced and unspliced mRNA repertoire in single cells. We validated its utility in two independent aging datasets, and identified sets of genes undergoing age-related breakdown of transcriptional homeostasis. Moreover, testing of our method on a subpopulation of human embryonic stem cells revealed a set of differentially processed transcripts segregating these subpopulations. Our preliminary analyses in this direction suggest that mRNA processing level information offered by single-cell RNA sequencing (scRNA-seq) data is a superior determinant of chronological age as compared to transcriptional noise.

Longevity pathways are associated with human ovarian ageing

STUDY QUESTION

Are genes known to be involved in somatic cell ageing, particularly related to longevity pathways, associated with the accelerated ageing process of the ovary?

SUMMARY ANSWER

Growth, metabolism, and cell-cycle progression-related pathways that are involved in somatic cell ageing are also associated with ovarian ageing.

WHAT IS KNOWN ALREADY

Ovarian ageing is characterized by a gradual decline in ovarian follicle quantity, a decline in oocyte quality, and lower chances of pregnancy. Genetic pathways modulating the rate of somatic cell ageing have been researched intensively. Ovarian ageing does not follow the same timeline as somatic cell ageing, as signs of ovarian ageing occur at a younger female age, while the somatic cells are still relatively young. It is not known whether the generally recognized somatic cell longevity genes also play a role during ovarian ageing. Looking at somatic cell longevity genes can lead to new hypotheses and possible treatment options for subfertility caused by ovarian ageing.

STUDY DESIGN, SIZE, DURATION

In this observational study, we analysed a dataset of individual gene expression profiles of 38 germinal vesicle (GV) oocytes from 38 women aged between 25 and 43 years. We correlated female age (calendar age in years) and biological age (factors known to be associated with ovarian ageing such as dosage of FSH needed for ovarian hyperstimulation, and antral follicle count (AFC)) with gene expression signatures of longevity pathways.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Transcripts of 38 GV oocytes were used for individual gene expression analysis. R version 3.5.1 was used to process and analyse data. The GeneAge database (build 19) was used to obtain mouse ageing-related genes. Human to mouse orthologues were obtained using the R package biomaRt. Correlations and significance between gene expression data and age were tested for using Pearson's product moment correlation coefficient using ranked expression data. Distributions were compared with an ANOVA, and the Tukey Honest Significant Difference method was used to control for the Type I error rate across multiple comparisons.

MAIN RESULTS AND THE ROLE OF CHANCE

Of the 136 genes in the GeneAge database, the expression of 15 anti-longevity genes identified in oocytes showed a positive correlation with female calendar age and FSH dosage administered during ICSI treatment, and a negative correlation with AFC. Expression of 32 pro-longevity genes was negatively correlated with calendar age and FSH dosage, and positively correlated with AFC. In general, anti- and pro-longevity genes changed in opposing directions with advancing maternal age in oocytes. Notably, the anti-longevity genes include many ‘growth’-related genes involved in the mechanistic target of rapamycin (mTOR) Complex 1 pathway, such as EIF5A2, EIF3H, EIF4E, and mTOR. The pro-longevity genes include many cell-cycle progression-related genes involved in DNA damage repair (e.g. XRCC6, ERCC2, and MSH2) or cell-cycle checkpoint regulation genes (e.g. ATM, BRCA1, TP53, TP63, TP73, and BUB1B).

LIMITATIONS, REASONS FOR CAUTION

Using mature oocytes instead of GV-stage oocytes discarded from ICSI treatments may provide different results. No correction for multiple testing was carried out on individual genes because a small set of longevity-related genes was selected a priori for the analysis. The global trend was corrected for multiple testing and remained significant. This work was an observational study and, as no additional experimental work was performed, the associations described do not directly demonstrate the involvement of such genes in oocyte ageing.

WIDER IMPLICATIONS OF THE FINDINGS

Growth, metabolism, and cell-cycle progression-related pathways that are known to be involved in somatic cell ageing were associated with ovarian ageing. If experimental data are obtained to support these associations, we suggest that interventions known to modulate these processes could benefit women suffering from ovarian ageing.

STUDY FUNDING/COMPETING INTEREST(S)

G.E.J. is supported by a VENI grant from ZonMw (https://www.zonmw.nl). Work in the Houtkooper group is financially supported by an ERC Starting grant (No. 638290), a VIDI grant from ZonMw (No. 91715305), and the Velux Stiftung (No. 1063). M.G. declares several research and educational grants from Guerbet, Merck and Ferring (all location VUmc), outside the scope of the submitted work. The other authors report no competing interest

TRIAL REGISTRATION NUMBER

N/A.

Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice

Chromosomal instability (CIN) is a hallmark of cancer, leading to aneuploid cells. To study the role that CIN plays in tumor evolution, several mouse models have been engineered over the last 2 decades. These models have unequivocally shown that systemic high-grade CIN is embryonic lethal. We and others have previously shown that embryonic lethality can be circumvented by provoking CIN in a tissue-specific fashion. In this study, we provoke systemic high-grade CIN in adult mice as an alternative to circumvent embryonic lethality. For this, we disrupt the spindle assembly checkpoint (SAC) by alleviating Mad2 or truncating Mps1, both essential genes for SAC functioning, with or without p53 inactivation. We find that disruption of the SAC leads to rapid villous atrophy, atypia and apoptosis of the epithelia of the jejunum and ileum, substantial weight loss, and death within 2-3 weeks after the start of the CIN insult. Despite this severe intestinal phenotype, most other tissues are unaffected, except for minor abnormalities in spleen, presumably due to the lower proliferation rate in these tissues. We conclude that high-grade CIN in vivo in adult mice is most toxic to the high cell turnover intestinal epithelia.

Recent insights into the cellular and molecular determinants of aging

Aging is the gradual decline of physiological functions and organismal fitness, which leads to age-dependent fitness loss, diseases and eventually mortality. Understanding the cause of aging constitutes one of most intriguing areas of research in biology. On both the cellular and molecular levels, it has been hypothesized that there are aging determinants to control the onset and progression of aging, including the loss of beneficial components and accumulation of detrimental factors. This Review highlights the recent advance in identifying various factors that affect the aging process, focusing on how these determinants affect the lifespan and fitness of a cell or organism. With more and more aging determinants revealed, further understanding about their functions and interconnections could enable the development of specific intervention to extend healthy lifespan and reduce the risk of age-related diseases.

CIN and Aneuploidy: Different Concepts, Different Consequences

Chromosomal instability (CIN) and aneuploidy are similar concepts but not synonymous. CIN is the process that leads to chromosome copy number alterations, and aneuploidy is the result. While CIN and resulting aneuploidy often cause growth defects, they are also selected for in cancer cells. Although such contradicting fates may seem paradoxical at first, they can be better understood when CIN and aneuploidy are assessed separately, taking into account the in vitro or in vivo context, the rate of CIN, and severity of the aneuploid karyotype. As CIN can only be measured in living cells, which proves to be technically challenging in vivo, aneuploidy is more frequently quantified. However, CIN rates might be more predictive for tumor outcome than assessing aneuploidy rates alone. In reviewing the literature, we therefore conclude that there is an urgent need for new models in which we can monitor chromosome mis-segregation and its consequences in vivo. Also see the video abstract here: https://youtu.be/fL3LxZduchg.

Expression of eukaryotic translation initiation factor 5A-2 (eIF5A-2) associated with poor survival in gastric cancer

Altered expression of eukaryotic translation initiation factor 5A-2 (eIF5A-2) was associated with human carcinogenesis and progression. This study assessed eIF5A-2 expression in gastric cancer tissues for association with clinicopathological parameters and survival of patients. A total of 436 gastric cancer tissues and 92 normal mucosal blocks were collected for construction of tissue microarrays and immunohistochemical assessment of eIF5A-2 expression. The data were statistically analyzed for association with clinicopathological factors and survival of patients. Immunohistochemical data showed that eIF5A-2 protein was highly expressed in gastric cancer tissues (p < 0.001). Upregulated expression of eIF5A-2 protein was associated with tumor Lauren classification, size, location, invasion, TNM stages, and lymph node and distant metastases. The 3- and 5-year cumulative survival rates of these 436 patients were 88.5 and 58.1 %, respectively. In contrast, the mean survival time of patients with increased tumor eIF5A-2 was 30.22 ± 1.23 vs. 51.29 ± 0.86 months for those with low tumor eIF5A-2 (p < 0.001). Multivariate analysis showed that eIF5A-2 expression and related tumor parameters were independent indicators of overall survival in gastric cancer patients. In conclusion, the current study indicates that overexpression of eIF5A-2 protein was associated with poor overall survival of gastric cancer patients.

Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle

Background

Cattle breeding populations are susceptible to the propagation of recessive diseases. Individual sires generate tens of thousands of progeny via artificial insemination. The frequency of deleterious alleles carried by such sires may increase considerably within few generations. Deleterious alleles manifest themselves often by missing homozygosity resulting from embryonic/fetal, perinatal or juvenile lethality of homozygotes.

Results

A scan for homozygous haplotype deficiency in 25,544 Fleckvieh cattle uncovered four haplotypes affecting reproductive and rearing success. Exploiting whole-genome resequencing data from 263 animals facilitated to pinpoint putatively causal mutations in two of these haplotypes. A mutation causing an evolutionarily unlikely substitution in SUGT1 was perfectly associated with a haplotype compromising insemination success. The mutation was not found in homozygous state in 10,363 animals (P = 1.79 × 10⁻⁵) and is thus likely to cause lethality of homozygous embryos. A frameshift mutation in SLC2A2 encoding glucose transporter 2 (GLUT2) compromises calf survival. The mutation leads to premature termination of translation and activates cryptic splice sites resulting in multiple exon variants also with premature translation termination. The affected calves exhibit stunted growth, resembling the phenotypic appearance of Fanconi-Bickel syndrome in humans (OMIM 227810), which is also caused by mutations in SLC2A2.

Conclusions

Exploiting comprehensive genotype and sequence data enabled us to reveal two deleterious alleles in SLC2A2 and SUGT1 that compromise pre- and postnatal survival in homozygous state. Our results provide the basis for genome-assisted approaches to avoiding inadvertent carrier matings and to improving reproductive and rearing success in Fleckvieh cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1483-7) contains supplementary material, which is available to authorized users.

Roles of eukaryotic initiation factor 5A2 in human cancer

Eukaryotic initiation factor 5A (eIF5A), the only known cellular protein containing the amino acid hypusine, is an essential component of translation elongation. eIF5A2, one of the two isoforms in the eIF5A family, is reported to be a novel oncogenic protein in many types of human cancer. Both in vitro and in vivo studies showed that eIF5A2 could initiate tumor formation, enhance cancer cell growth, and increase cancer cell motility and metastasis by inducing epithelial-mesenchymal transition. Accumulatied evidence suggests that eIF5A2 is a useful biomarker in the prediction of cancer prognoses and serves as an anticancer molecular target. In this review, we will focus on updating current knowledge of the EIF5A2 gene in human cancers. The molecular mechanisms of EIF5A2 related to tumorigenesis will also be discussed.

RNA profiles of porcine embryos during genome activation reveal complex metabolic switch sensitive to in vitro conditions

Fertilization is followed by complex changes in cytoplasmic composition and extensive chromatin reprogramming which results in the abundant activation of totipotent embryonic genome at embryonic genome activation (EGA). While chromatin reprogramming has been widely studied in several species, only a handful of reports characterize changing transcriptome profiles and resulting metabolic changes in cleavage stage embryos. The aims of the current study were to investigate RNA profiles of in vivo developed (ivv) and in vitro produced (ivt) porcine embryos before (2-cell stage) and after (late 4-cell stage) EGA and determine major metabolic changes that regulate totipotency. The period before EGA was dominated by transcripts responsible for cell cycle regulation, mitosis, RNA translation and processing (including ribosomal machinery), protein catabolism, and chromatin remodelling. Following EGA an increase in the abundance of transcripts involved in transcription, translation, DNA metabolism, histone and chromatin modification, as well as protein catabolism was detected. The further analysis of members of overlapping GO terms revealed that despite that comparable cellular processes are taking place before and after EGA (RNA splicing, protein catabolism), different metabolic pathways are involved. This strongly suggests that a complex metabolic switch accompanies EGA. In vitro conditions significantly altered RNA profiles before EGA, and the character of these changes indicates that they originate from oocyte and are imposed either before oocyte aspiration or during in vitro maturation. IVT embryos have altered content of apoptotic factors, cell cycle regulation factors and spindle components, and transcription factors, which all may contribute to reduced developmental competence of embryos produced in vitro. Overall, our data are in good accordance with previously published, genome-wide profiling data in other species. Moreover, comparison with mouse and human embryos showed striking overlap in functional annotation of transcripts during the EGA, suggesting conserved basic mechanisms regulating establishment of totipotency in mammalian development.

Increased frequency of micronuclei in adults with a history of childhood sexual abuse: a discordant monozygotic twin study

BACKGROUND

Childhood sexual abuse (CSA) is a traumatic life event associated with an increased lifetime risk for psychopathology/morbidity. The long-term biological consequences of CSA-elicited stress on chromosomal stability in adults are unknown. The primary aim of this study was to determine if the rate of acquired chromosomal changes, measured using the cytokinesis-block micronucleus assay on stimulated peripheral blood lymphocytes, differs in adult female monozygotic twins discordant for CSA.

METHODS

Monozygotic twin pairs discordant for CSA were identified from a larger population-based sample of female adult twins for whom the experience of CSA was assessed by self-report (51 individuals including a reference sample). Micronuclei (MN) contain chromatin from structurally normal or abnormal chromosomes that are excluded from the daughter nuclei during cell division and serve as a biomarker to assess acquired chromosomal instability.

RESULTS

Female twins exposed to CSA exhibited a 1.63-fold average increase in their frequency of MN compared to their nonexposed genetically identical cotwins (Paired t-test, t₁₆ = 2.65, P = 0.017). No additional effects of familial factors were detected after controlling for the effect of CSA exposure. A significant interaction between CSA history and age was observed, suggesting that the biological effects of CSA on MN formation may be cumulative.

CONCLUSIONS

These data support a direct link between CSA exposure and MN formation measured in adults that is not attributable to genetic or environmental factors shared by siblings. Further research is warranted to understand the biological basis for the observed increase in acquired chromosomal findings in people exposed to CSA and to determine if acquired somatic chromosomal abnormalities/somatic clonal mosaicism might mediate the adult pathology associated with CSA.