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PubMed2025

Type and position of repeat interruptions as determinants of disease severity and expansion size in Friedreich ataxia.

PURPOSE: In Friedreich ataxia (FRDA) the size of the smaller GAA expansion is a major determinant of disease severity; interruption motifs were identified after the discovery of the pathogenic expansions; however, their impact is only recently investigated. METHODS: 164 patients with FRDA with biallelic expansions and 15 patients without FRDA were analyzed for interruption(s) number, position, and motif. Expansion size and age at onset of ataxia (AAO) were determined for patients with FRDA. RESULTS: Three groups of patients with FRDA were identified by the simultaneous analysis of the precise distance ("depth") between the interruptions (mostly nontriplet) and the 3' end of the expansion (P < .001), the smaller expansion size (P < .001), and AAO (P < .001). Classical FRDA corresponds to absence of interruption or interruption depth < 8 repeats, with AAO often <15 years (area under the curve [AUC] = 0.90; 95% CI, 0.84-0.96); LOFA to interruption depth of 8 to 18 repeats (AUC = 0.97; 95% CI, 0.94-1), with AAO 15 to 34 years (AUC = 1; 95% CI, 1-1); and vLOFA to interruption depth > 18 (AUC = 0.97; 95% CI, 0.92-1), with AAO > 34 years. Multiple (>5) triplet interruptions hamper further expansion. CONCLUSION: This study provides the molecular basis for a novel classification of FRDA that should be recommended for correct diagnosis.

Humans↗

PubMed2026

Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells.

Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. An updated Clinical Nanopore Cas9-Targeted Sequencing workflow is presented for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the Oxford Nanopore Technologies wf-human-variation Epi2Me workflow, including the Straglr tool to analyze base-called reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 and introduces new gene panels for ataxia, myopathy, neurodegeneration, and amyotrophic lateral sclerosis/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. In this work, the use of multiplexing, Flongle flow cells, and single-gene targeting were explored as alternatives to panel-based approaches in the Clinical Nanopore Cas9-Targeted Sequencing workflow, finding that only single-gene targeting provides compatibility and reliable performance.

Journal Article↗

PubMed2026

Toward the clinical application of long-read sequencing in repeat-expansion disorders.

Repeat-expansion disorders (REDs) are a mechanistically and clinically well-defined subgroup of rare diseases caused by the expansion of short tandem repeats (STRs). These expansions can exceed several kilobases and show complex features, such as noncanonical secondary structures, somatic instability, repeat interruptions and allele-specific methylation. These characteristics are highly relevant for understanding disease mechanisms, clinical variability, prognosis and potentially therapeutic decision-making, but cannot be fully resolved using traditional diagnostic methods or short-read sequencing technologies. By contrast, long-read sequencing (LRS) enables accurate investigation of STR complexity in a single assay, facilitates the discovery of new pathogenic repeat expansions and drives advances in diagnostics, clinical and basic research, which may allow for better patient stratification in future clinical trials. This Perspective discusses recent LRS-driven discoveries, methodological and bioinformatic advances, and emerging diagnostic applications to illustrate the potential of LRS in reshaping both research and clinical practice.

Humans↗

PubMed1979

Pattern of milk flow in breast-fed infants.

122 six-day-old infants were test-weighed during breast feeding. Cross-sectional data collection avoided repeated interruptions of individual feeds. Milk flow conformed to a definite pattern: a mean of 50% of the feed from each breast was taken in the first two minutes of sucking and a mean of 80-90% was taken by four minutes. The second half of a ten-minute feed from either breast was almost non-nutritive. Preliminary studies suggest that the pattern is the same after one month of lactation.

Breast Feeding↗

PubMed2024

Bulk serum extracellular vesicles from stressed mice show a distinct proteome and induce behavioral and molecular changes in naive mice.

Chronic stress can trigger several pathologies including mood disorders for which no clear diagnostic molecular markers have been established yet. Attractive biomarker sources are extracellular vesicles (EVs). Evs are released by cells in health and disease and contain genetic material, proteins and lipids characteristic of the cell state. Here we show that Evs recovered from the blood of animals exposed to a repeated interrupted stress protocol (RIS) have a different protein profile compared to those obtained from control animals. Proteomic analysis indicated that proteins differentially present in bulk serum Evs from stressed animals were implicated in metabolic and inflammatory pathways and several of them were previously related to psychiatric disorders. Interestingly, these serum Evs carry brain-enriched proteins including the stress-responsive neuronal protein M6a. Then, we used an in-utero electroporation strategy to selectively overexpress M6a-GFP in brain neurons and found that M6a-GFP could also be detected in bulk serum Evs suggesting a neuronal origin. Finally, to determine if these Evs could have functional consequences, we administered Evs from control and RIS animals intranasally to naïve mice. Animals receiving stress EVs showed changes in behavior and brain M6a levels similar to those observed in physically stressed animals. Such changes could therefore be attributed, or at least in part, to EV protein transfer. Altogether these findings show that EVs may participate in stress signaling and propose proteins carried by EVs as a valuable source of biomarkers for stress-induced diseases.

Animals↗

PubMed2024

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes.

BACKGROUND: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. RESULTS: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. CONCLUSIONS: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Animals↗

PubMed2026

Dissecting the relationship between haplotypes around ATXN2 CAG repeats and the number of CAA interruptions by long-read sequencing.

BACKGROUND: CAG repeat expansions in ATXN2 are implicated as risk factors for several neurological diseases, including spinocerebellar ataxia type 2 (SCA2) when >=33 CAG repeats are present, and amyotrophic lateral sclerosis (ALS) when 27-33 CAG repeats are present. However, how haplotypes around the repeats and CAA interruptions within the repeats are associated with disease phenotypes remains poorly understood. Previous studies on haplotypes around ATXN2 were limited to SNPs very close to the repeats (<5kb) or were based on statistical inference only. METHODS: Here, we used long-read sequencing on the Oxford Nanopore Technologies (ONT) platform to simultaneously infer haplotypes around ATXN2, the number of CAG repeats, and the number of CAA interruptions, along with NYGC ALS Consortium NGS dataset. We further sequenced 41 individuals (EUR = 39) with neurological diseases with intermediate repeats by ONT. RESULTS: We found that haplotypes around ATXN2 and the number of interruptions show ethnicity-specific and ALS-specific distribution. Three CAA interruptions are present at low prevalence (~1%) in control populations in multiple ancestry groups, but high prevalence (~55%) in ALS individuals with intermediate repeats. Furthermore, we examined 159 individuals with ALS (~90% European ancestry) with intermediate ATXN2 repeats and found a unique haplotype in ALS individuals with three CAA interruptions, which can be tagged by an SNV, rs148019457. We also validated that the rs148019457-G allele is only present in haplotypes with three CAA interruptions. CONCLUSIONS: In summary, our study shows that 3 CAA interruptions are rarely seen in healthy controls but are common in those with expanded ATXN2 CAG repeats who have neurological disorders, and that rs148019457 tags a specific haplotype with 3 CAA interruptions within expanded ATXN2 CAG repeats in individuals of European ancestry. These results have implications for the development of precision genomic medicine for neurological disorders, and the tag SNP may help identify those with interruptions from existing population genotyping data.

ATXN2↗

PubMed2026

Loss of interruption in the HTT CAG repeat is associated with somatic expansion and loss of medium spiny neurons in Huntington's disease.

Synonymous loss-of-interruption variants in the expanded CAG repeat sequence of Huntingtin (HTT) accelerate the clinical onset and progression of Huntington's disease (HD). Medium spiny neurons (MSNs) are gradually lost in HD and undergo selective somatic CAG expansion, but it is unclear how somatic expansion relates to MSN pathology. Here, we show that MSNs with large (111-150 CAG) and very large (>150 CAG) somatic expansions are rare in early manifest HD but accumulate in proportion with duration of disease. In patients with the deleterious CAG-CCG loss-of-interruption (CAG-CCG LOI) modifier, the proportion of MSNs with large and very large expansions is increased ∼5-fold despite reduced small somatic expansions in blood, and caudate MSN counts are reduced. Our findings suggest that increased somatic CAG expansion contributes to accelerated striatal MSN pathology and onset of HD but that MSNs with very large genomic CAG expansions can persist among surviving neurons of the HD brain.

Huntington’s disease↗

PubMed1976

Mechanism of escape, extrasystolic, and parasystolic arrhythmias. Study on an electrical analogue.

A simple analogue of the heart consisting of a system of neon relaxation oscillators is presented. The analogue may display rhythm patterns similar to sinus rhythm, escape rhythm, isorrhythmic dissociation with synchronization, atrial extrasystoles, ventricular extrasystoles, and parasystole. The strict rules followed by these arrhythmias, as well as the deviations from the rules commonly followed by the equivalent heart arrhythmias, may be easily reproduced on the analogue. Such features are the Treppe phenomenon and captured beats in escape rhythm, fixed coupling intervals in extrasystoles, partial or complete atrioventricular block in very premature atrial extrasystoles, prolongation of the period following an atrial extrasystole, interpolated premature beats, complete compensatory pause and the rule of bigeminy in ventricular extrasystoles, slight instability of the parasystolic period, multiple length parasystolic periods slightly different from the exact multiples of the parasystolic idioperiod, preference of the parasystoles for certain phase in the sinus cycle, synchronization at a phase difference and fluctuation repeatedly and without interruption from a parasystolic to an extrasystolic rhythm and synchronization in escape rhythm with isorrhythmic dissociation. The mechanisms involved in these phenomena are discussed in detail. The striking similarity between the properties of the cardiac pacemakers and those of the relaxation oscillators on the one hand and betwen the rhythm patterns of the heart and those of the analogue on the other may permit the hypothesis that the mechanisms operating in the analogue may be used in analyzing and understanding heart arrhythmias.

Arrhythmias, Cardiac↗

PubMed2026

Progressive cardiac phenotypes and reduced reversibility from long-term CUGexp RNA expression in a DM1 mouse model.

Myotonic dystrophy type 1 (DM1) is caused by an expanded CTG repeat in the DMPK gene, resulting in mutant transcripts that form expanded CUG (CUGexp) RNA foci and sequester muscleblind-like (MBNL) RNA-binding proteins. DM1 is multisystemic, with progressive worsening of disease manifestations in affected tissues. Disease progression is attributed to somatic expansion of the CTG repeats with age, resulting in production of CUGexp RNA with enhanced intrinsic toxicity due to increased MBNL sequestration. To determine the degree to which cardiac disease progression can occur independently of repeat expansion, we used a transgenic DM1 mouse model with inducible heart-specific expression of a stable, interrupted 960-CUG-repeat RNA. Sustained CUGexp RNA expression caused progressive cardiac enlargement, contractile dysfunction, conduction delay, myocardial fibrosis, and reduced survival, while MBNL-dependent splicing defects remained static, consistent with the stable repeat length. We also determined the degree of reversibility after different periods of CUGexp RNA expression by shutting off the repeat-containing transgene. Suppression of CUGexp RNA expression rescued cardiac abnormalities, but reversibility declined with longer exposure to the toxic RNA. These findings demonstrate that prolonged expression of stable CUGexp RNA drives progressive cardiac pathology, revealing a mechanism of disease progression in DM1 in addition to somatic expansion.

Animals↗

PubMed2026

Clinical Application of Long-Read Sequencing for FMR1 Gene Mutation Detection in Populations From Shandong, China.

BACKGROUND: Fragile X syndrome (FXS) is a common inherited intellectual disability. In this study, long-read sequencing was used for the FMR1 gene detection. METHODS: Men with familial inherited intellectual disability and women with indications for FXS screening were defined as high-risk populations and were included in this study along with non-high-risk reproductive-aged women. PCR-capillary electrophoresis was used for preliminary screening of non-high-risk reproductive-aged women, and long-read sequencing was performed on abnormal samples and samples from high-risk populations. Prenatal diagnosis using long-read sequencing was performed for pregnant women in need. RESULTS: The prevalence of mutation in high-risk females was 3.10% (7/226). 3 mutations were detected in male samples, with a mutation ratio of approximately 8.3% (3/36). The three most common CGG repeats were 29, 30, and 36, respectively. Analysis of AGG interruption pattern in 242 samples identified 908 AGG interruptions, involving 67 different patterns. The most frequent AGG interruption pattern was (CGG)9AGG(CGG)9AGG(CGG)9. Furthermore, long-read sequencing was successfully applied for prenatal diagnosis in two pregnant women, and dynamic mutation of CGG repeat was detected within one family. CONCLUSION: Long-read sequencing-based assay cannot only accurately detect CGG repeat and AGG interruption, but also simultaneously identify other abnormalities of the FMR1 gene. Long-read sequencing offers a broader detection scope and better characterization of FXS-related genetic features.

Humans↗

PubMed1979

Inhibitory role of brain stem serotoninergic neuron system on thyroid function in rat.

Thyroid function was investigated in adult male rats following the use experimental procedures which inhibit the activity of serotoninergic neuron system. Pharmacological blockade of the biosynthesis of sertonin by repeated administration of para-chlorophenylalanine (pCPA), or interruption (by Halász knife) of the serotoninergic pathways of the brain stem which terminate on hypothalamic nuclei equally resulted in an augmentation of the following parameters of hypothalamo-hypophysial-thyroid activity: T/S ratio, pituitary and blood TSH levels and blood thyroxine concentration as well as TRH content of the hypothalamus. The results suggest that the central nervous serotoninergic neuron system plays an inhibitory role in the regulation of TSH secretion, presumably acting upon the hypothalamus, thereby inhibiting hypothalamic TRH secretion.

Animals↗

PubMed1977

Mechanisms of B cell tolerance: I. Dynamic nature of the induction of hapten-specific unresponsiveness by hapten-conjugated pneumococcal polysaccharide.

Exposure of 2,4-dinitrophenyl (DNP)-hemocyanin-primed spleen cells to DNP-conjugated pneumococcal polysaccharide (DNP-S3) in vivo or in vitro renders such cells unresponsive to DNP-hemocyanin challenge following adoptive transfer. The unresponsiveness is hapten-specific, independent of the presence of T cells and adherent cells, and not due to either toxic effect of S3 or carry-over of tolerogenic amounts of cell-bound DNP-S3, and thus presumably represents a model of B cell tolerance. The degree of suppression induced depends upon the dose of the tolerogen and most strikingly on the duration of exposure of cells to the tolerogen. Thus 2 to 6 h exposure to DNP-S3 has an insignificant effect on anti-DNP responses, while 24 and 48 h exposures in vitro and in vivo are highly suppressive. Such a dynamic process of tolerance induction suggests a "multiple hit" phenomenon, implying the generation of suppressive signals by repeated cycles of tolerogen-receptor interactions. The process can be interrupted by removal of extracellular DNP-S3, although this does not reverse the unresponsiveness that has already been induced.

Animals↗

PubMed1979

Cytarabine and thioguanine for acute nonlymphocytic leukemia. Another look.

A modification of the protocol of cytarabine and thioguanine was used for remission induction in patients with acute nonlymphocytic leukemia. First, synchronization of the mitotically active leukemia cells was attempted by administering cytarabine alone in a dose of 5 mg/kg of body weight 24 hours prior to initiating daily therapy with both drugs. Second, in order to recover dormant leukemic cells into the proliferative pool, both drugs were continued without interruption and without regard to the suppression of the circulating leukocyte and platelet count until bone marrow aspirates, repeated daily if necessary, were free of leukemic blast cells. This usually resulted in severe but reversible bone marrow hypoplasia, and 16 of 21 patients (76%) so treated achieved complete hematologic remission.

Adolescent↗

PubMed1978

Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries.

Selected regions of cloned EcoRI fragments of the chicken ovalbumin gene have been sequenced. The positions where the sequences coding for ovalbumin mRNA (ov-mRNA) are interrupted in the genome have been determined, and a previously unreported interruption in the DNA sequences coding for the 5' nontranslated region of the messenger has been discovered. Because directly repeated sequences are found at exon-intron boundaries, the nucleotide sequence alone cannot define unique excision-ligation points for the processing of a possible ov-mRNA precursor. However, the sequences in these boundary regions share common features; this leads to the proposal that there are, in fact, unique excision-ligation points common to all boundaries.

Animals↗

PubMed2026

Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.

Tandem repeat (TR) expansions, including short TRs (motifs ≤6 bp) and variable number TRs (motifs >6 bp), underlie many monogenic disorders, with variable length and sequence influencing pathogenicity, penetrance, severity, and onset. Accurate genotype-phenotype correlation and disease prevalence estimation require characterization beyond repeat length. Here we present a population-scale analysis of 66 disease-associated TR loci using long-read assemblies from 2530 diverse haplotypes from 1265 unaffected donors. Integrating repeat length, motif composition, local ancestry, linkage disequilibrium, and phylogenetic analyses, we reveal extensive locus-, population-, and allele-specific variation shaping disease risk. Up to 8.5% of individuals carry expansions above established pathogenic thresholds, many containing interrupting motifs or sequence structures that attenuate pathogenicity. After excluding alleles from loci with uncertain disease association, non-pathogenic interrupted expansions, and carrier states inconsistent with inheritance patterns, ~4% carried expansions predicted to confer disease risk, largely at adult-onset loci with reduced penetrance. Ancestry-resolved analyses uncover population-specific TR architectures contributing to epidemiological disparities in repeat expansion disorders. Phylogenetic analyses identify conserved ancestral alleles and loci with recent instability. We describe variable linkage disequilibrium patterns and recombination signatures around specific disease-associated TR loci. Our findings emphasize integrating sequence, ancestry, and evolutionary context to understand the complex landscape of disease-associated TRs.

Humans↗

PubMed1978

Biochemical treatment of precancerous oral lesions: the effectiveness of various analogues of retinoic acid.

Leukoplakia is neither a clinical, aetiological nor histopathological entity. Therefore treatment is difficult particularly in multifocal and advanced lesions. Since 1970, we have tested the therapeutic effect of different derivatives of all-trans-retinoic acid. The study includes 75 cases with homogeneous leukoplakia without or with minimal epithelial dysplasia. Over 60% of the cases treated showed positive early results. In follow-ups from 1 to 6 years about 45% of cases showed complete or partial remission. The rest showed relapses or even progression. In cases with recurrence without changes in the morphological characteristics, positive effects were achieved with 1 to 4 repeated courses of therapy. All derivatives of retinoic acid tested so far have shown undesirable side effects with systematic manifestations or local symptoms: interruption of treatment (4) or reduction of dosage (9) were unavoidable for that reason. Regarding the side effects, retinoic acid should only be given under clinical supervision. Of the derivates tested to date, aromatic retinoid seems to have the best curative potential in homogenic leukoplakia.

Humans↗

PubMed1979

Prenatal diagnosis of polycystic kidneys and encephalocele (Meckel syndrome).

Two unrelated families are presented with repeated occurrences of a congenital syndrome of which the main stigmata were polycystic kidneys and occipital encephalocele (Meckel syndrome). Prenatal diagnosis, followed by interruption of pregnancy, was performed in one case. The diagnosis was based on an increase of amniotic alpha-fetoprotein (AFP), and on the mode of growth and cell types of cultured amniotic cells. In another similarly examined case the diagnosis was suspected, but the parents did not wish the pregnancy to be interrupted. The child was stillborn and malformed. AFP values are presented and discussed in relation to the observed malformations. Neural tube defects are associated with an increase of AFP in amniotic fluid, but, as in normal pregnancies, the values decrease with increasing gestational age. On the other hand, kidney malformations seem to be associated with AFP values which remain high or even increase with increasing gestational age.

Amniotic Fluid↗