Genes

Half of the human genome is derived from Transposable Elements (TEs), among which Alu, LINE-1 and SVA are particularly represented. Germline transposition of TEs generates polymorphisms between individuals and may be used to study association with phenotypes and inter-individual differences. Italy presents an increased number of isolated villages compared to other European groups, and these isolates provide a desirable study subject to understand the genetic variability of the Italian peninsula. Therefore, we focused on the association between polymorphic TEs, behavioral traits (tobacco use and alcohol consumption), and Body Mass Index (BMI) variations, which could lead to an increased risk of developing addiction-related or metabolic diseases. We identified 12,709 polymorphic TEs in 589 individuals from six isolates: classical population genetics analyses showed that while closely related to other European populations, the isolates tend to cluster amongst themselves and are dominated by drift-induced ancestral components. Several TEs were also significantly associated with behavioral traits (tobacco use or alcohol consumption) or with BMI variations and some of them have a functional role. These results suggest that polymorphic TEs may significantly impact inter-individual and inter-population phenotypic differentiation, while also functioning as variability markers and potentially having a role in susceptibility to medical conditions.

The Roma are the most numerous ethnic minority in Europe. The Iberian Roma arrived in the Iberian Peninsula five centuries ago and still today, they keep a strong group identity. Demographic and cultural reasons lie behind a high rate of Mendelian disease often related to founder variants. We have analysed exome data from 119 Iberian Roma individuals collected from 2018 to 2020. A database of variant frequency has been implemented (IRPVS) and made available online. We have analysed the carrier rate of founder private alleles as well as pathogenic variants present in the general population. Significant enrichment in structural variants involving gene clusters related to keratinization and epidermal growth suggest that evolutive mechanisms have developed towards climate and environmental adaptation. IRPVS can be accessed at http://irpvs.clinbioinfosspa.es/ AUTHOR SUMMARYReference data is necessary for the correct interpretation of genetic studies. Although most genetic variants are present in all populations, ancestry has an important impact in the genetic background. For that reason databases of genetic variant in populations are developed specifically for different ethnicities, being an important tool for genetic diagnosis. The Roma are the most numerous ethnic minority in Europe. In this study we have collected samples from healthy Roma individuals from Iberian descent and implemented a database of genetic variant to facilitate genetic diagnosis in this population. Analysis of structural variants that are specific to the Iberian Roma not found in other healthy population for which genetic data are available suggest evolution towards environmental adaptation.

BackgroundNext-generation sequencing (NGS) has transformed high-throughput DNA and RNA analysis, facilitating the rapid identification of clinically relevant genetic variants. Opioid Use Disorder (OUD), a chronic condition characterized by relapse and remission cycles, poses significant challenges for genomic investigations. While whole-exome sequencing (WES) and whole-genome sequencing (WGS) serve as robust approaches for variant detection, their high cost restricts widespread use. RNA sequencing (RNA-Seq) presents a viable alternative; however, the complexity of the transcriptome complicates reliable variant identification. Despite these challenges, RNA-Seq has emerged as a valuable tool for detecting single nucleotide polymorphisms (SNPs) in conditions with limited WES data, such as OUD. MethodsIn this study, RNA-Seq data from postmortem ventral midbrain specimens of chronic opioid users (PRJNA492904) were analyzed to identify variants associated with OUD. Given its established involvement in opioid addiction and impulsivity, we hypothesized that the NRXN3 gene would harbor a significant number of variants. Variant analysis was conducted across eight genes: BDNF, DRD2, DRD3, NRXN3, OPRD1, OPRM1, and NGFB--with a primary focus on NRXN. ResultsOur results revealed that NRXN3 exhibited the highest variant burden among the analyzed genes, highlighting its potential role in OUD pathogenesis and reinforcing its association with opioid addiction. ConclusionOur study highlights the significance of transcriptomic variant analysis in opioid addiction and underscores the potential of NRXN3 variants as biomarkers or therapeutic targets, warranting further investigation.

With large-scale human genome and exome sequencing, a lot of focus has gone in studying variations present in genomes and their associations to various diseases. Since major emphasis has been put on their variations, less focus has been given to invariant genes in the population. Here we present 60,706 genomes from the ExAC database to identify population specific invariant genes. Out of 1,336 total genes drawn from various population specific invariant genes, 423 were identified to be mostly (allele frequency less than 0.001) invariant across different populations. 46 of these invariant genes showed absolute invariance in all populations. Most of these common invariant genes have homologs in primates, rodents and placental mammals while 8 of them were unique to human genome and 3 genes still had unknown functions. Surprisingly, a majority were found to be X-linked and around 50% of these genes were not expressed in any tissues. The functional analysis showed that the invariant genes are not only involved in fundamental functions like transcription and translation but also in various developmental processes. The variations in many of these invariant genes were found to be associated with cancer, developmental diseases and dominant genetic disorders.

BackgroundRetrotransposons are genetic elements that jump within the genome via an RNA intermediate. Although they had a strong impact on human genome evolution, only a very tiny fraction of them can be reactivated nowadays, most often with neutral or detrimental consequences. The pathological outcomes associated with such genetic alterations are poorly investigated in the clinic, merely due to their difficult detection. ResultsWe developed a strategy to detect rare retrotransposon mediated insertions in Whole Exome Sequencing data from 65 familial breast cancer patients. When restricting our search to high confidence retrotransposition events occurring in less than 10% of the samples, we identified only ten different Alu elements, two L1 elements, one SVA and two processed pseudogenes. Only two of these insertions occurred within protein coding sequences and interestingly, several of the targeted genes have been previously linked to cancer, in three cases even to increased breast cancer risk (GHR, DMBT1 and NEK10). When investigating the molecular consequences of four Alu insertions at the mRNA level, we found that the element present in the 3UTR of GHR repressed expression of the corresponding allele. oMreover, the analysis of a near exonic Alu insertion in PTPN14 (a mediator of P53 tumor suppressor activity) revealed that this gene was imprinted and that the presence of an intronic Alu element can lead to loss of imprinting. ConclusionsOur data underline the relevance of incorporating the search for uncommon retrotransposition events in Next Generation Sequencing pipelines when analyzing patients with a suspected genetic disease.

Among all types of mutations, single nucleotide polymorphisms are the most common type of genomic variation. In our study, we explore the counts of single nucleotide polymorphisms in particular exons and introns of the human genome based on the data set of 1,222 individuals of Polish origin that comprises 41,836,187 polymorphisms. In particular, chromosomes 1 and 22 were considered as representatives of two markedly different DNA molecules, since HSA01 represents the longest and HSA22 is one of the shortest chromosomes. The results demonstrate that outer (first, last) exons as well as the first introns harbour significantly more SNPs than other genic regions. The observed differences in counts reflect the distinct functional roles of those genomic units.

Prader-Willi syndrome (PWS) is a rare multisystemic disorder characterized by obesity, endocrine dysfunctions, and psychiatric comorbidities, which imply frequent use of psychotropic medications. They account for atypical responses to standard dosages of psychiatric drugs. Pharmacogenetics could be part of the reason for this situation, potentially offering a valuable tool for individualized treatment. This study analyzed allelic and phenotypic frequency distributions of five of the main cytochrome P450 enzymes (CYP2D6, CYP2B6, CYP2C19, CYP2C9, CYP3A4) involved in psychiatric drug metabolism in 47 patients with genetically confirmed diagnosis of PWS and compared them to reference frequencies in the general European population. Allelic frequency comparisons between the European reference population and the overall PWS cohort revealed a significant global difference for CYP2B6, with CYP2C19 and CYP2D6 showing trends toward significance. Although no global allelic differences remained significant after false discovery rate correction, post-hoc analyses consistently identified an enrichment of reduced- or non-functional alleles CYP2B619 and CYP2D610 in patients with PWS. Predicted metabolizer phenotype analyses showed a significant shift toward intermediate metabolizers of CYP3A4 in the PWS cohort, with corresponding depletion of normal metabolizers. Subgroup analyses indicated that allelic differences were more pronounced in maternal uniparental disomy and non-deletion subtypes, particularly for CYP2B6, although no significant differences were observed between PWS genetic subtypes. Overall, results imply potential differences in metabolizing activity in PWS patients, and subsequent implications in drug efficacy and tolerability. These results support the idea that pharmacogenetic testing may improve therapeutic decision-making in PWS for psychiatric treatment. Larger studies are needed to confirm these preliminary results.

Lipoprotein (a) [LP(a)] is a risk factor for cardiovascular diseases and mainly regulated by the complex LPA gene. We investigated the types of variation in the LPA gene and their predictive performance on LP(a) concentration. We determined the Kringle IV-type 2 (KIV-2) copy number (CN) using the DRAGEN LPA Caller (DLC) and a read-depth based CN estimator in 8351 whole genome sequencing samples from the GENESIS-HD study. The pentanucleotide repeat in the promoter region was genotyped with GangSTR and ExpansionHunter. LP(a) concentration was available in 4861 population-based subjects. Predictive performance on LP(a) concentration was investigated using random forests. The agreement of the KIV-2 CN between the two specialized callers was high (r=0.9966; 95% confidence interval [CI] 0.9965-0.9968). Allele-specific KIV-2 CN could be determined in 47.0% of the subjects using the DLC. Lp(a) concentration can be better predicted from allele-specific KIV-2 CN than total KIV-2 CN. Two single nucleotide variants 4925G>A and rs41272114 further improved prediction. The genetically complex LPA gene can be analyzed with excellent agreement between different callers. The allele-specific KIV-2 CN is more important for predicting LP(a) concentration than the total KIV-2 CN. It would be important that the allele-specific KIV-2 CN is determinable in all subjects.

The X-chromosome is among the largest human chromosomes. It differs from autosomes by a number of important features including hemizygosity in males, an almost complete inactivation of one copy in females, and unique patterns of recombination. We used data from the Catalog of Published Genome Wide Association Studies to compare densities of the GWAS-detected SNPs on the X-chromosome and autosomes. The density of GWAS-detected SNPs on the X-chromosome is 6-fold lower compared to the density of the GWAS-detected SNPs on autosomes. Differences between the X-chromosome and autosomes cannot be explained by differences in the overall SNP density, lower X-chromosome coverage by genotyping platforms or low call rate of X-chromosomal SNPs. Similar differences in the density of GWAS-detected SNPs were found in female-only GWASs (e.g. ovarian cancer GWASs). We hypothesized that the lower density of GWAS-detected SNPs on the X-chromosome compared to autosomes is not a result of a methodological bias, e.g. differences in coverage or call rates, but has a real underlying biological reason - a lower density of functional SNPs on the X-chromosome versus autosomes. This hypothesis is supported by the observation that (i) the overall SNP density of X-chromosome is lower compared to the SNP density on autosomes and that (ii) the density of genic SNPs on the X-chromosome is lower compared to autosomes while densities of intergenic SNPs are similar. Author summaryOne of the most striking observations from the Genome Wide Association Studies (GWAS) is that the density of GWAS hits is much lower on X-chromosome compared to autosomes. This was initially explained by technical/analytical reasons such as lower coverage and lack of adequate methods to analyze X-chromosomal SNPs. Since then, a better coverage and better analytical methods to analyze X-chromosomal SNPs were developed. We recently revisited the issue and found that the density of GWAS hits on X-chromosome is at least 5-fold lower compared to autosomes. We demonstrated that the difference cannot be explained by technical or analytical reasons. We proposed a hypothesis of a real biological phenomenon underlying X versus autosomal differences in the density of GWAS-detected SNPs, namely that X-chromosome has a lower density of functional polymorphisms compared to autosomes because of a stronger selection against X-chromosomal mutations since X-chromosomal variants are more exposed to natural selection due to hemizygosity in males and X-chromosome inactivation in females. The hypothesis is supported by the analysis of the densities of intergenic, intronic and exonic SNPs on human chromosomes.

High cholesterol levels have been associated with cardiovascular diseases, and lowering them has been a key focus in the treatment of such diseases. Statins are drugs used with that aim, and can be divided in the lipophilic Simvastatin and the hydrophilic Rosuvastatin. Regardless of the statin type, a high proportion ([~]70%) of patients stop using statins due to suffering from side effects on skeletal muscle, such as myalgia, and muscle cramps. Thus, there has been a considerable effort in understanding how statins contribute to these side effects. A catalogue of genes and molecular pathways that change upon statin treatment has been recently published, allowing further understanding how the side effects occur. However, Transposable Elements (TEs) were not studied. TEs can move within a genome, and they are highly repetitive, representing about half of the human genome. Currently, most TEs in the human genome are inactive, but it has been shown that TEs can still transcribe, and that either via their transposition or their transcriptional activity, can influence gene expression. Here, using novel computational tools to accurately estimate TE expression, we studied their activity and predicted their potential impact on gene expression. We developed a catalogue of TEs expressed upon statin treatment, and the putative genes whose expression might be influenced by TEs. Overall, we speculate that based on our findings, TEs might be a key target in order to understand statin-mediated side effects.

The fishing cat, Prionailurus viverrinus, displays a fish hunting behavior uncommon among most other cats. Estimated population declines in the wild increase the significance of its existing zoo populations, particularly with a recent high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. We hypothesize that its small captive population may harbor TCC risk variants at the germline level. To aid conservation efforts and investigate the genetics of TCC, we present a new fishing cat chromosomescale assembly, reaffirm its close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify and characterize single nucleotide variants (SNVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Among genes previously associated with bladder cancer risk in human BRCA2 was found to have the highest number of missense mutations in fishing cats, with only two variants exhibiting a predominance in TCC cats. These new fishing cat genomic resources will aid efforts to improve their genetic fitness and enhance the comparative study of feline genomes.

BackgroundAlport syndrome is a progressive and hereditary nephropathy, characterized by hematuria and proteinuria, and extrarenal manifestations as hearing loss and eye abnormalities. The disease can be expressed as autosomal recessive or dominant, caused by variants in COL4A3 and COL4A4 loci, respectively, or X-linked caused by variants in COL4A5 locus. MethodsTwo unrelated families with Alport Syndrome from northeast of Brazil were studied and whole exome sequencing were performed. DNA sequences were mapped against the human genome (GRCh38/hg38 build) to identify associated mutations. ResultsVariant analysis showed deleterious variants in COL4A3 and COL4A4 loci in chromosome 2. Two variants were detected with alternative alleles in a homozygous state in the probands. One novel premature stop codon at position 481 of COL4A3 protein is present in one family and one frameshift mutation leading to a premature stop codon at position 786 of COL4A4 protein in the other family. Both Alport cases presented their variants surrounded by a broad runs of homozygosity (ROH). ConclusionsThe autosome recessive inheritance coupled with the runs of homozygosity in both families suggest inbreeding.

HCT116 is a colorectal cancer cell line frequently used in anti-tumor drug development experiments as well as in studies of the molecular machinery of eukaryotic cells. It is well characterized by the presence of several single-nucleotide and short mutations in multiple oncogenes and tumor suppressor genes, including KRAS, PIK3CA, MLH1, CTNNB1, CDKN2A, TGFBR2, and BRCA2. However, its landscape of large genomic rearrangements (LGRs) and copy number variants (CNVs) is still far from being fully understood. Therefore, the aim of this study was to identify LGRs and CNVs in several HCT116 cell line samples using Oxford Nanopore sequencing technology, including three samples from the SRA NCBI database, and to compare common and unique variants across all samples. Using the recently developed eLaRodON tool, we identified 22,666 common LGRs, among which more than 70% of tandem duplications and deletions larger than 80 kb were confirmed by CNV analysis. Among LGRs affecting protein-coding sequences, two in-frame rearrangements were identified: a deletion of exons 4-6 and a duplication of exon 10 in the CCSER1 gene, which encodes a cell division regulator protein. Given its high rearrangement rate in various tumors and the clinical significance of its overexpression, this finding may be potentially useful in future research on this cell line. Regarding differences between samples, we found that LGRs in the laboratory sample and in one of the three SRA NCBI samples occurred more frequently via ALR/Alpha repeats than via Alu repeats, in contrast to common LGRs and those unique to the other samples, a finding that may indicate the presence of unique mechanisms of genomic instability. Thus, this study reveals a broad spectrum of large genomic rearrangements and copy number variants that can be identified in the HCT116 cell line using Oxford Nanopore sequencing, including rearrangements specific to distinct cell line samples.

STUDY QUESTIONIs Tcte1 mutation causative for male infertility? SUMMARY ANSWERCollected data underline the complex and devastating effect of the single-gene mutation on testicular molecular network, leading to male reproductive failure. WHAT IS KNOWN ALREADYLatest data revealed mutations in genes related to axonemal dynein arms as causative for morphology and motility abnormalities in spermatozoa of infertile males, including dysplasia of fibrous sheath (DFS) and multiple morphological abnormalities in the sperm flagella (MMAF). The nexin-dynein regulatory complex (N-DRC) coordinates the dynein arm activity, and is built from DRC1-DRC7 proteins. DRC5 (TCTE1) - one of N-DRC element, has been already reported as a candidate for abnormal sperm flagella beating, however, only in restricted manner with no clear explanation of respective observations. STUDY DESIGN, SIZE, DURATIONUsing CRISPR/Cas9 genome editing technique, mouse knockout line of Tcte1 gene was created on the basis of C57Bl/6J strain. Then, the mouse reproductive potential, semen characteristics, testicular gene expression level, sperm ATP and testis apoptosis level measurements have been performed, followed by visualization of N-DRC proteins in sperm, and protein modeling in silico. Also, a pilot genomic sequencing study of samples from human infertile males (n=248) was applied for screening of TCTE1 variants. PARTICIPANTS/MATERIALS, SETTING, METHODSTo check the reproductive potential of KO mice, adult animals were crossed for delivery of three litters per caged pair, but no longer than for 6 months, in various combinations of zygosity. All experiments were performed for wild type (WT - control group), heterozygous Tcte1+/-, and homozygous Tcte1-/- male mice. Gross anatomy was performed on testis and epididymis, followed by semen analysis. Sequencing of RNA (RNAseq; Illumina) has been done for mice testis tissues. STRING interactions have been checked for protein-protein interactions, based on changed expression level of corresponding genes identified in the mouse testis RNAseq experiments. Immunofluorescence in situ staining was performed to detect the N-DRC complex proteins: Tcte1 (Drc5), Drc7, Fbxl13 (Drc6), and Eps8l1 (Drc3) in mouse spermatozoa. To determine the ATP amount in spermatozoa, the luminescence level was measured. Also, immunofluorescent in situ staining was performed to check the level of apoptosis via caspase 3 visualization on mouse testis samples. DNA from whole blood samples of infertile males (n=137 non-obstructive azoospermia or cryptozoospermia, n=111 samples with spectrum of oligoasthenoteratozoospermia, including n=47 with asthenozoospermia) has been extracted to perform genomic sequencing (WGS, WES or Sanger). Protein prediction modeling of human identified variants and the exon 3 structure deleted in mouse knockout has been also performed. MAIN RESULTS AND THE ROLE OF CHANCENo progeny at all was found for homozygous males with revealed oligoasthenoteratozoospermia, while heterozygous animals (fertile) manifested oligozoospermia, suggesting haploinsufficiency. RNA-sequencing of the testicular tissue showed the influence of Tcte1 mutations on the expression pattern of 21 genes responsible for mitochondrial ATP processing, linked with apoptosis, or spermatogenesis. In Tcte1-/- males the protein revealed only residual amounts in sperm head nucleus, and was not transported to sperm flagella, as other N-DRC components. Decreased ATP level (2.4-fold lower) was found in spermatozoa of homozygous mice, together with disturbed tail:midpiece ratio, leading to abnormal sperm tail beating. Casp3-positive signals (indicating apoptosis) were observed in spermatogonia only, at similar level in all three mouse genotypes. Mutation screening of human infertile males revealed 1 novel and 5 ultrarare heterogeneous variants (predicted as disease causing) in 6.05% of patients studied. Protein prediction modeling of identified variants revealed changes in the protein surface charge potential, leading to disruption in helix flexibility or its dynamics, thus, suggesting the disrupted TCTE1 interaction with its binding partners located within the axoneme. What does this mean for patients?Abnormal semen parameters (sperm count, motility and morphology) are known as one of the first symptoms that may be related to male fertility problems. This study aimed to determine the role of Tcte1 in male infertility using mouse knockout model. Tcte1 protein is one of the structural elements building N-DRC, a complex within an axoneme that is responsible for coordination of the sperm flagella elements activity, strictly related to sperm motility. We have found that mutations in mouse Tcte1 knockout model revealed two phenotypes, dependent on zygosity: infertile oligoasthenoteratozoospermic homozygotes, and fertile oligozoospermic heterozygotic males, suggesting haploinsufficiency mechanism. Pilot study on human samples with TCTE1 variants revealed a wide spectra of semen quality (from non-obstructive azoospermia, via cryptozoospermia, to severe oligoasthenozoospermia). Thus, TCTE1 gene is the next one that should be added to the male infertility list because of its crucial role in spermatogenesis influencing the variety of testicular molecular networks (incl. energy machinery processing) and proper sperm function.

BackgroundLynch Syndrome (LS) is an autosomal dominant hereditary syndrome associated with a diverse range of cancer types. Despite being one of the most prevalent hereditary cancer syndromes, the detection of LS remains challenging due to the absence of well-defined diagnostic criteria which would be able to select all patients who should undergo testing for LS and the limitations of existing screening methods. The implementation of an efficient screening program capable of accurately detecting the majority of LS cases remains a topic of continuous discussion in the scientific literature, with recent studies emphasizing the significance of a universal screening program. MethodsOur study aimed to develop and optimize a cost-effective universal screening method for detecting mutation in the mismatch repair (MMR) genes through mixed sample analysis. We tested five approaches in terms of the use of biological material and the analysis of mixed samples. ResultsEach approach successfully detected a specific Lynch-associated pathogenic variant in mixed in the pooled samples with frequency 5.00%, with the lowest allelic fraction recorded at 3.04%. Approach 2, which involved isolating DNA from each patient individually, demonstrated the highest average allelic fraction (7.04%). However, considering financial and time requirements, approach 1, where DNA was isolated only after mixing aliquots of whole blood, proved to be the most favorable. ConclusionThe findings of our study present a promising opportunity to improve LS detection. The identification of LS not only has the potential to prevent cancer-related morbidity and mortality but also facilitates continued progress in understanding the primary prevention of cancer.

John Henryism (JH) is a stress response mechanism that enables individuals to cope with chronic psychological stressors. Originally identified in African American males, JH has since been associated with numerous negative health outcomes such as cardiovascular disease. Despite its relationship to diseases with known genetic risk factors, little work has been reported concerning the genetics of JH. In the current study, genome-wide microarray and the JH Active Coping scale data from the CARDIA Cohort study were used to identify genetic factors associated with JH levels. Principal component analysis accounted for population stratification and evaluated six inheritance models in plink software. We also performed network analyses on the resulting significant associations (P < 5x10-8) to identify molecular pathways to health outcomes. Our GWAS results revealed 25 significant genetic associations and two suggestive associations. One of the variants identified with a suggestive association (P < 5x10-6) to JH (rs11634680) reproduces the same suggestive association from a prior study of the same dataset with the similar odds ratios and P-values between the studies. In our pathway analysis, we found a variant associated with JH (rs12448959) decreases the amount of GABA transaminase and thereby reduces the nicotine reward through the GABAergic signaling pathway. Our work provides a molecular explanation to the observational data that individuals with high levels of JH active coping skills are less prone to using smoking as stress relief.

IntroductionRibosomal (rDNA), satellite III (f-SatIII) and telomere (TR) tandem repeats perform a variety of functions in the human cell. Copy number variations (CNVs) of these repeats contributes to the global chromatin architecture and genome expression changes in response to stress or pathology. An elevated rDNA abundance and lowered contents of f-SatIII and TR were found in blood leukocytes of patients with schizophrenia. The main question of the study was: are the CNVs of the three repeat types in blood leukocytes a universal phenomenon linked to a patho4logy associated with chronic oxidative stress? Cystic fibrosis (CF), a monogenic disease was chosen as an object of the study. Materials and MethodsWe determined the rDNA, f-SatIII and TR content in the blood leukocyte genomes of 545 subjects aged 0.2 to 50 years. The subjects were divided into three groups: Control (HC-group, N = 267), CF group (N= 186) and CF(d) group (severe patients, who died after some time upon sampling, aged 17 to 40 years, N = 92). For each patient, the type of the mutation in CFTR gene had been determined earlier. Non-radioactive quantitative hybridization technique was applied to quantify the repeats. Resultsthe rDNA abundance was elevated in the DNA of CF and CF(d) groups (565{+/-}105 copies per genome, N=278) compared to HC group (445{+/-}112 copies, N=267). A patients age 3 to 16 years was associated with "severe" mutations in CFTR (98% of cases), increased f-SatIII repeat counts and decreased telomere repeat (TR) contents in genome DNA compared to the age-matched controls. The genomes of deceased patients from CF(d) group also harbored increased numbers of f-SatIII and decreased numbers of TR. Patients above 16 years with a milder course of the disease and relatively low content of "severe" CFTR mutations contained less f-SatIII and more TR in their genomic DNA. A parameter rDNA{middle dot}(f-SatIII/TR) showed a maximum difference between patients with relatively mild (age 17 to 40) and severe (age 17 to 40) forms of the pathology according to ROC analysis data (AUC = 0.86). ConclusionCystic fibrosis was associated with an increase in rDNA abundance and altered f-SatIII and TR contents in the DNA of cases compared to the controls. The severe course of the disease was characterized with high f-SatIII contents and shortened telomeres. Whereas mild CF cases were associated with low contents of f-SatIII and normal or slightly reduced telomere length. The index rDNA{middle dot} (f-SatIII/TR) might be a predictor of the patients life expectancy.

Environmental and dietary factors can exert multigenerational effects on health and development. In this study, we investigated whether early-life metabolic challenge affects the germline genome and epigenome across three generations. Using a murine model of early life obesity via litter size reduction (overnutrition group, ON) and a control group (CT), we followed the paternal lineage focusing on germline genomic and methylation changes employing Genotyping-by-Sequencing (GBS) coupled with methyl-immunoprecipitation (GBS-MeDIP). We found that unrelated ON families clustered together based on identified Single-Nucleotide Polymorphism (SNP), suggesting that the treatment may have genomic impact. Copy number variations (CNVs) events were identified in ON individuals, being enriched in Long Interspersed Nuclear Elements (LINEs) and Long Terminal Repeats (LTRs). While Principal Component Analysis (PCA) of the methylome showed no clear treatment effect, pathway enrichment and regional analyses revealed methylation changes associated with transposable elements and developmental genes. Notably, the ON group exhibited a disruption in the methylation of Repetitive Elements (RE), which was significant in the same type of RE that were also enriched in the observed CNVs. The ON also showed reduced emergence of novel SNPs in offspring compared to the CT group. These findings suggest that multigenerational metabolic challenge can constrain genetic variability and induce genome instability, potentially mediated by transposable element activity rather than widespread changes in DNA methylation. This work highlights the importance of studying both genome and epigenome dynamics under realistic, multigenerational exposure scenarios and suggests that early metabolic challenges can have long-lasting impacts on genomic architecture and evolutionary potential.

The escalating adoption of Next Generation Sequencing (NGS) in clinical diagnostics reveals genetic variations, termed secondary findings (SFs), with health implications beyond primary diagnoses. The Collaborative Spanish Variant Server (CSVS), a crowdsourced database, contains genomic data from more than 2100 unrelated Spanish individuals. Following the American College of Medical genetics (ACMG) guidelines, CSVS was analyzed, identifying pathogenic or likely pathogenic variants in 78 actionable genes (ACMG list v3.1) to ascertain SF prevalence in the Spanish population. Among 1129 samples, 60 reportable SFs were found in 5% of individuals, impacting 32 ACMG-listed genes, notably associated with cardiovascular disease (59.4%), cancer (25%), inborn errors of metabolism (6.3%), and other miscellaneous phenotypes (9.4%). The study emphasizes utilizing dynamic population databases for periodic SF assessment, aligning with evolving ACMG recommendations. These findings illuminate the prevalence of significant genetic variants, enriching understanding of secondary findings in the Spanish population.

Transposable elements (TEs) are middle-repeated DNA sequences that can move along chromosomes using internal coding and regulatory regions. By their ability to move and because they are repeated, TEs can promote mutations. Especially they can alter the expression pattern of neighboring genes and have been shown to be involved in the mammalian regulatory network evolution. Human and mouse share more than 95% of their genomes and are affected by comparable diseases, which makes the mouse a perfect model in cancer research. However not much investigation concerning the mouse TE content has been made on this topics. In human cancer condition, a global activation of TEs can been observed which may ask the question of their impact on neighboring gene functioning. In this work, we used RNA sequences of highly aggressive pancreatic tumors from mouse to analyze the gene and TE deregulation happening in this condition compared to pancreas from healthy animals. Our results show that several TE families are deregulated and that the presence of TEs is associated with the expression divergence of genes in the tumor condition. These results illustrate the potential role of TEs in the global deregulation at work in the cancer cells.