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Structural complexity and mechanistic diversity of MECOM rearrangements in myeloid neoplasms.

Rearrangements involving MECOM at chromosome 3q26.2 are recurrent in myeloid neoplasms, classically represented by inv(3)(q21q26.2) and t(3;3)(q21;q26.2), which reposition the GATA2-distal haematopoietic enhancer and drive aberrant EVI1 overexpression. However, the full structural and mechanistic diversity of MECOM rearrangements (MECOM-r) is yet to be explored. We retrospectively analysed 97 cases with cytogenetically defined MECOM-r and identified 12 with complex rearrangements using GTG-banded karyotyping and tri-colour interphase/metaphase fluorescence in situ hybridisation analyses. These 12 cases demonstrated remarkable structural heterogeneity. The abnormalities encompassed translocations, inversions, insertions, duplications, and deletions, which often coexisted within the same specimen as multiple rearranged subclones. Insertional events emerged as a distinct mechanism of MECOM activation. These encompassed insertions of MYNN and/or MECOM into chromosomes 1 and 6, insertion of chromosome 8 segment into MECOM, and inverted insertions between homologous chromosome 3 segments. Recurrent breakpoints at 3q21 across multiple cases, together with localised copy number imbalances frequently involving the MYNN and GOLIM4 loci at 3q26.2, underscore the architectural fragility of these two regions. Co-occurring abnormalities such as -5/del(5q), -7/del(7q), and TP53 loss were common, reflecting a permissive genomic background for chromosomal reassembly. Our findings expand the mechanistic landscape of MECOM-r beyond canonical inv(3)/t(3;3), establishing 3q21 and 3q26.2 as structural 'hotspots' and genomic instability hubs. Distinct from fusion-driven oncogenes such as KMT2A, MECOM activation results from enhancer hijacking and regional structural remodelling, leading to EVI1 overexpression and clonal evolution in myeloid malignancies.

Humans

The Neanderthal-Derived 3p21 Haplotype at LZTFL1 in Modern-Day Moroccans Is Associated With COVID-19 Severity and Further Suggests the Presence of Neanderthals in North Africa.

There is considerable variability in the clinical presentation of COVID-19 among patients infected with SARS-CoV-2. Genome-wide association studies (GWASs) have identified the 12q24.13 and 3p21.31 regions, derived from Neanderthal DNA, as the human genetic loci most strongly associated with COVID-19 severity. We examined in this study the 3p locus in the Moroccan population by analysing allele and haplotype frequencies at the LZTFL1 gene and their associations with COVID-19 outcomes. Three SNPs at LZTFL1, tagging the Neanderthal-derived COVID-19 risk haplotype, were sequenced by Sanger's method in 102 ambulatory participants and 105 hospitalized patients and have been compared to 118 controls negative for SARS-CoV-2 infection using logistic regression analysis. Results showed that the prevalence of the lead variant rs11385942 in this locus was 8.9%, whereas the variants rs35044562 and rs13078854, which tag the Neanderthal haplotype, were present in only 6.3%. Our study showed that only the rs35044562-T and rs13078854-A alleles were associated with a 2.5-fold increased risk of severe COVID-19 (p = 0.028). These two alleles, in LD with the rs11385942-AA one, form the haplotype inherited from the Neanderthal, the only haplotype associated with COVID-19 severity in the Moroccan population (p = 0.030), whereas sub-Saharan African and the rare local haplotype also containing the rs11385942 variant do not influence the COVID-19 outcomes 19 (p > 0.05). Furthermore, our study showed that the Neanderthal haplotype at 3p21 locus exists in the inhabitants of Morocco at a frequency close to that of Europeans and suggests a close connection between North Africa and Eurasia.

Adult

Non-Coding c.*6C>T Variant in RBM8A Associated With Thrombocytopenia-Absent Radius (TAR) Syndrome in Three Indian Patients.

Thrombocytopenia-absent radius (TAR) syndrome is a rare genetic disorder characterized by the absence of radius in the forearms and a decrease in platelet count. The molecular basis of TAR syndrome is linked to a heterozygous minimal deletion within the 1q21.1 region spanning 200 k bases (kb), resulting in a null allele and a nucleotide variation in RBM8A resulting in a hypomorphic allele. Previous studies have identified pathogenic variants in the coding regions of the RBM8A gene as the cause of TAR syndrome. However, the involvement of non-coding variants in disease pathogenesis remains largely unexplored. We investigated the association of a non-coding 3' UTR variant, c.*6C>T, in RBM8A with TAR syndrome in three individuals from two unrelated families of Indian origin. Our study provides evidence that this variant is associated with decreased stability of the transcript and is a hypomorphic allele with disease-causing impact when in trans with a null allele (1q21.1 deletion). The present work is the first application of an mRNA stability assay to directly detect RNA degradation in patients with non-coding RBM8A variants causing TAR syndrome.

Humans

Enhancement of banding patterns in human metaphase chromosomes by energy transfer.

Intermolecular energy transfer between appropriately chosen pairs of dyes can be used to induce or enhance banding patterns in human metaphase chromosomes. Energy transfer, calibrated by fluorometric studies on soluble dye.DNA complexes, can also be detected by photometric measurements on cytological preparations of metaphase chromosomes stained with pairs of fluorochromes. If a fluorescent dye with one type of binding or quantum yield specificity (e.g., quinacrine, 33258 Hoechst, or chromomycin A(3)) is employed together with a counterstain (e.g., actinomycin D, 7-aminoactinomycin D, or methyl green) exhibiting a complementary base pair binding specificity and satisfying spectral overlap criteria for energy transfer, contrast in fluorescence from the first dye is enhanced in specific subsets of standard chromosome bands. Extensive energy transfer presumably suppress donor fluorescence except in chromosomal region containing clusters of at least 20 base pairs predominantly of one type, within which the donor but not the acceptor can bind and fluoresce. Quinacrine-bright polymorphic regions are especially resistant to fluorescence quenching by counterstains with G.C binding specificity, strengthening the evidence that these latter regions are highly enriched for A.T base pair clusters. The ability to highlight selectively many such polymorphic regions may prove of further, practical, utility in a number of cytogenetic problems.

Chromosomes, Human

Structure of the human fetal globin gene locus.

We have derived a 'map' of restriction enzyme sites in and around the human gamma-globin genes. This has enabled us to show that there are two gamma-globin genes per haploid set, that the genes contain 'introns' within the same regions of DNA as the human beta and delta-globin genes, and that the genes are 3,500 base pairs apart. We conclude that the correct gene organisation of the human beta-like globin locus is GgammaAgammadeltabeta.

Chromosome Mapping

The nucleolar cycle in man.

Tissue cultures of human embryonal kidney and ovary were examined. In the nuclei of both tissues, one to ten nucleoli have been found. The maximum number of nucleoli is connected with the gene expression of rDNA of the 10 nucleolus organizers of chromosome pairs Nos. 13, 14, 15, 21 and 22, which have secondary constrictions and are the satellite chromosomes in man. The small percentage of cells with 10, 9 and 8 nucleoli is attributed to the rapid association of 3 of the homologous acrocentrics (perhaps of group D). Two of the satellite (SAT) pairs probably associate later after mitosis. The process of fusion is dynamic, resulting in one interphase nucleous--a manifestation of the association of all SAT chromosomes. Dissociation of the nucleolus occurs upon entering prophase, due to the condensation of the chromosomes and retreat of rDNA to the respective secondary constrictions. As a result, the nucleolar number increases again. The pattern of the nucleolar kinetics within the course of one mitotic division is described.

Cell Nucleolus

The structure of the human beta-globin gene in beta-thalassaemia.

Twenty-one cases of beta 0 and beta +-thalassaemia have been analysed by restriction endonuclease mapping. In most cases no deletion in the regions surrounding the beta- and delta-globin genes could be detected. However, in a single Asian case of beta 0-thalassaemia, homozygous clinically, one of the homologous chromosomes contained a beta-globin gene with a deletion of 600 base pairs of DNA and comprising most or all of the 3' end of the structural gene including the EcoRI restriction site within the beta-globin coding sequence.

DNA

HCG stimulation test in children with abnormal sexual development.

Plasma testosterone was estimated by radioimmunoassay in 60 children with disorders of sexual development before and after stimulation with human chorionic gonadotrophin (HCG). In 21 children the testosterone levels after 3 and 5 daily injections of 1000 units HCG were compared and good correlation was found between the paired results (r =0-93), suggesting that the 5-day HCG test has no advantage over the 3-day test. In 7 boys with apparently normal genital development the increments in plasma testosterone ranged from 2-0 to 8-5 nmol/1 after 3 injections of HCG. 10 boys with anorchia showed little response to HCG stimulation, but in patients with other disorders, such as micropenis (10), cryptorchidism (8), hermaphroditism (3), male pseudohermaphroditism (13), hypospadias (3), and sex chromosome anomalies (6), there was considerable variation in the plasma testosterone level after HCG. In 2 boys with suspected anorchia the results suggested that testes were present and this was confirmed at operation.

Adolescent

Upper airway microbiome interacts with GSDMB and ORMDL3 asthma risk SNPs to influence early-life wheeze risk.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) in the chromosome 17q12-q21 region and, independently, early-life nasal microbiota dominated by Moraxella, Streptococcus, or Haemophilus (MSH) increase risk of chronic wheeze and asthma development. OBJECTIVE: We sought to determine whether 17q12-q21 risk SNPs and nasal microbiota interact to modulate childhood wheeze risk. METHODS: Nasal wash samples from 12-month-old infants in 2 birth cohorts, COAST (Childhood Origins of Asthma; n = 180) and URECA (Urban Environment and Childhood Asthma; n = 139), underwent 16S ribosomal RNA variable region 4 sequencing. Nasal microbiota dominated by MSH or Corynebacterium, Dolosigranulum, Staphylococcus, or Bacillus (CDSB) were assessed. Paired blood was genotyped for 9 17q12-q21 risk SNPs. Logistic regression tested interactions between 17q12-q21 SNPs and MSH or CDSB on wheeze risk in the first 3 years of life. A549 lung epithelial cells, CRISPR-edited to encode the rs7216389 risk genotype (rs7216389TT) were compared to the heterozygous (rs7216389CT) line using bulk RNA sequencing. RESULTS: SNPs, particularly those in the ORMDL3 (rs8076131; odds ratio [OR]: 1.72; 95% CI: 1.09-2.71; Pint = .031) and GSDMB (rs2305480; OR: 1.72; 95% CI: 1.09-2.71; Pint = 0.042; and rs7216389; OR: 1.73; 95% CI: 1.09-2.70; Pint = .047) genes, interact with MSH microbiota to increase early-life wheeze risk (false discovery rate Pint = .016 for all), while interactions with CDSB reduce risk. A549 airway epithelial cells homozygous for rs7216389TT exhibited decreased expression of genes involved in antimicrobial responses and neutrophil recruitment and evidence increased microbial adherence compared with the heterozygous cell line. CONCLUSION: Airway microbiota interact with SNPs at the 17q12-q21 locus in genes involved in sphingolipid metabolism and intracellular antimicrobial responses, to modulate wheeze risk.

Humans

LBA technique in the detection of chromosome variants. I. Chromosomes with known sites of Q variants.

A method is described (LBA method) which used DNA replication pattern in the detection of chromosome variants in man. In Part I, results on chromosomes with known sites of Q-variants, i.e., 5 pairs of acrocentrics, as well as 3 and 4, were presented. Fourty-one variants were detected in a total of 40 acrocentrics. Twenty-eight of them were detected only by the LBA technique; 11 of them being in short arms and 17 of them in centromeres. Seven variants, including 4 of those in satellites, were detected only in QFQ-stained metaphases. Six short-arm variants were observed by both methods. It appears that a sequential QFQ-LBA technique is very useful in the detection of variants in D- or G-group chromosomes.

Centromere

Organization of the alpha-globin genes in the Chinese alpha-thalassemia syndromes.

The alpha-thalassemia syndromes are a group of inherited anemias, the clinical severity of which has been shown to increase with the number of alpha-globin structural genes deleted. Employing restriction endonuclease gene mapping, we defined the organization of the alpha-globin genes in cellular DNA from Chinese subjects with various alpha-thalassemia syndromes. The four alpha-globin genes of normals are at two loci located on a 23.0-kilobase pair (kb) Eco RI fragment. In deletion type hemoglobin-H disease the 5' alpha-globin locus is deleted and the single 3' alpha-globin locus is found on a 19.0-kb Eco RI fragment. In alpha-thalassemia-2 there are two alpha-globin genes on a 23.0-kb Eco RI fragment and one on a 19.0-kb fragment. In alpha-thalassemia-1 and the nondeletion type of hemoglobin-H disease the two alpha-globin genes are at two loci on one chromosome and none reside on the other chromosome.

China

Cloning and characterization of H4 (D10S170), a gene involved in RET rearrangements in vivo.

H4(D10S170) is a gene which we isolated because of its frequent rearrangement with the RET proto-oncogene in vivo. Its fusion to RET generates the RET/PTC1 oncogene, which has been detected in about 20% of human thyroid papillary carcinomas. We have cloned and sequenced the cDNA corresponding to the H4(D10S170) gene from a human normal thyroid cDNA library. The nucleotide sequence of the H4(D10S170) 3 kb transcript shows no significant homology to known genes and contains an open reading frame (ORF) of 585 amino acids. H4(D10S170) predicted protein has no transmembrane domain and shows extensive regions in the alpha helical conformation, which are 30% homologous to the alpha-helical domains of several proteins including tropomyosin, vimentin, keratin and the tail region of myosin heavy chain. A putative SH3 binding site is present at the carboxy terminus, which suggests that H4(D10S170) might be a cytoskeletal protein.

Amino Acid Sequence

Integrative Genomic Profiling of Newly Diagnosed Prostate Cancers Progressing on Surveillance.

OBJECTIVE: To identify molecular features associated with earlier progression to definitive therapy amongst patients with localized prostate cancer (PCa) managed on active surveillance (AS). METHODS: We performed a retrospective pilot study of 7 patients with low- to intermediate-risk PCa undergoing serial multiparametric MRI (mpMRI)-targeted biopsies of the same lesion while on AS, who all proceeded to definitive therapy. Time-to-treatment (TTT) was defined as years from first biopsy on AS to definitive therapy. Laser-capture microdissection was used to separate tumor epithelium, benign glands, high-grade prostatic intraepithelial neoplasia, and stroma in each biopsy specimen. DNA from the tumor and matched benign tissue underwent whole-exome sequencing, and RNA from all compartments underwent whole-transcriptome sequencing. Somatic mutations and copy-number alterations were compared across serial biopsies and used to reconstruct phylogenies and quantify clonal complexity. RESULTS: Tumors exhibited substantial intratumoral heterogeneity, and in 3 of 6 paired cases, serial mpMRI-targeted biopsies showed discordant somatic profiles consistent with sampling distinct major clones over time. By contrast, no single gene-level alteration, and few large-scale chromosomal events, were associated with TTT. High clonal complexity, defined as ≥3 subclones, was associated with significantly shorter TTT than low complexity (median 1.9 vs 7.2 years; P = .0082). Exploratory pathway analyses of individual tissue components suggested TTT-associated differences in inflammatory signaling and stromal-epithelial cross-talk. CONCLUSION: In this small, hypothesis-generating cohort, clonal complexity was more closely associated with earlier definitive therapy than individual genomic alterations. Larger prospective studies are needed to validate whether multiomic measures of clonal architecture can improve AS risk stratification.

Humans

Genetic damage induced by ethyl alcohol in Aspergillus nidulans.

Heterozygous diploid conidia of Aspergillus nidulans were treated during germination with ethyl alcohol in concentrations ranging from 0.25% to 20% (v/v). The diploid strain carried three recessive conidial color mutations, in addition to genetic markers on all eight pairs of linkage groups. It was thereby possible to detect events of crossing over, non-disjunction, and mutation. An increase in the dose of ethanol was associated with a decrease in conidial viability and an increase in the relative and absolute frequencies of formation of (a) normal colonies which produced colored sectors and (b) phenotypically abnormal colonies, the majority of which (83.1%) produced normal sectors. At a concentration of 5% (v/v) ethanol, the survivors included 17.59% of the former and 44.7% of the latter colonies. Genetic analysis of the various segregants suggested that the frequencies of both mitotic crossing over and non-disjunction or the misdistribution of chromosomes were increased by ethanol. Among 133 abnormal colonies which segregated normal clones, 79 (59.4%) were associated with one of these genetic events. A total of 297 haploids and 130 diploids arose as normal segregants from the abnormal colonies. There were 31 recognizable events of non-disjunction and 14 crossing over in linkage groups I and II, where these events could be distinguished. These data suggested that the predominant effect of ethanol was a disruption of chromosome distribution. A cytological examination of ethanol-treated, germinating conidia revealed an interference with the mitotic spindle apparatus. The frequency of detectable spindles decreased more than 3-fold after 8 h exposure to 5% (v/v) ethanol. This finding supported the conclusion that ethanol disrupted chromosome distribution, and suggested the mechanism by which it does so. Human clinical data on alcohol consumption were examined in light of these findings.

Aspergillus nidulans

Hijacking pre-tRNA enables LTR-retrotransposon-initiated constitutive heterochromatin formation.

Pericentric heterochromatin serves as a fundamental component of eukaryotic chromosomes, endowing specialized genomic architecture with broad functional consequences. Although it is universally marked by H3K9me3 modification, the underlying pericentric DNA sequences diverge substantially across species. Here, by leveraging a transposition reporter system combined with a genome-wide RNA interference (RNAi) screen, we identified a specialized mechanism for recruiting SUV39H methyltransferase to initiate pericentric heterochromatin formation. This pathway depends on a highly ordered complex comprising the Puf68, pre-transfer RNAs (tRNAs), and the primer binding site (PBS). Puf68 binds with high affinity to poly-U tracts in pre-tRNA 3' trailer, forming a Puf68/pre-tRNA complex that subsequently base-pairs with the PBS of nascent long terminal repeat (LTR)-retrotransposons. Through direct interaction, Puf68 recruits Su(var)3-9 to these regions, catalyzing H3K9 trimethylation. Notably, Puf68 is sufficient to initiate de novo heterochromatin assembly both at pericentric and ectopically integrated LTR-retrotransposon regions. Our findings not only uncover a previously unrecognized mechanism of heterochromatin initiation but also resolve a long-standing question of how hosts harness nascent LTR-retrotransposon transcripts.

Heterochromatin

Genetic Analysis of Early Neoplasia in the Breast: Next-Generation Sequencing of Flat Epithelial Atypia and Associated Ductal and Lobular Lesions.

The molecular features of invasive breast cancers (IBC) have been well-characterized, but less is known about the earlier stages of neoplasia, including oncogenic drivers in early intraductal lesions. Flat epithelial atypia (FEA) is considered the earliest recognized precursor in the low-grade neoplasia pathway, but its mutational repertoire has not been studied, and drivers of the transition to morphologically more advanced lesions are unknown. Herein, we utilized next-generation sequencing to analyze 39 synchronous lesions from 13 patients, including FEA (n = 12) or predominantly FEA with early atypical ductal hyperplasia (FEA/early atypical ductal hyperplasia [ADH], n = 5) and associated ADH (n = 2), ductal carcinoma in situ (ductal carcinoma in situ [DCIS], n = 11), lobular carcinoma in situ (n = 3), and/or IBC with ductal and/or lobular differentiation (n = 6). Aside from 1 DCIS sample, all sequenced lesions in each patient were clonally related to one another. Recurrent alterations in FEA and FEA/early ADH included PIK3CA (69%), NCOR1 (31%), CBFB (31%), RUNX1 (15%), and GATA3 (23%). The mutational repertoire of FEA was similar to The Cancer Genome Atlas luminal IBC, except CBFB and NCOR1 mutations, which were more frequent in FEA and (along with PIK3CA, FOXA1, and CDKN1B) not always identified in paired morphologically advanced lesions. Compared with FEA, DCIS had more mutations and chromosomal copy number changes, including aberrations in PI-3 kinase pathway, transcription factors, chromatin remodeling genes, and TP53. CDH1 mutations identified in lobular carcinoma in situ were absent in paired FEA. Analysis of cases with ductal and lobular heterogeneity, including Rosen's triad, confirmed the shared clonality of the ductal and lobular components with features of genetic divergence. IBC of no special type were genetically similar to DCIS, and tubular carcinomas were similar to FEA. The results reveal the mutational repertoire of FEA and the genetics of early breast neoplasia, highlighting the clonal relationships of FEA to ductal and lobular carcinomas. Luminal breast cancer-associated genetic alterations are present at the earliest morphologically recognized stages of neoplasia.

Humans

Molecular and Clinical Determinants of Acquired Resistance and Treatment Duration for Targeted Therapies in Colorectal Cancer.

PURPOSE: Targeted therapies have improved outcomes for patients with metastatic colorectal cancer, but their impact is limited by rapid emergence of resistance. We hypothesized that an understanding of the underlying genetic mechanisms and intrinsic tumor features that mediate resistance to therapy will guide new therapeutic strategies and ultimately allow the prevention of resistance. EXPERIMENTAL DESIGN: We assembled a series of 52 patients with paired pretreatment and progression samples who received therapy targeting EGFR (n = 17), BRAF V600E (n = 17), KRAS G12C (n = 15), or amplified HER2 (n = 3) to identify molecular and clinical factors associated with time on treatment (TOT). RESULTS: All patients stopped treatment for progression and TOT did not vary by oncogenic driver (P = 0.5). Baseline disease burden (&#x2265;3 vs. <3 sites, P = 0.02), the presence of hepatic metastases (P = 0.02), and gene amplification on baseline tissue (P = 0.03) were each associated with shorter TOT. We found evidence of chromosomal instability (CIN) at progression in patients with baseline MAPK pathway amplifications and those with acquired gene amplifications. At resistance, copy-number changes (P = 0.008) and high number (&#x2265;5) of acquired alterations (P = 0.04) were associated with shorter TOT. Patients with hepatic metastases demonstrated both higher number of emergent alterations at resistance and enrichment of mutations involving receptor tyrosine kinases. CONCLUSIONS: Our genomic analysis suggests that high baseline CIN or effective induction of enhanced mutagenesis on targeted therapy underlies rapid progression. Longer response appears to result from a progressive acquisition of genomic or chromosomal instability in the underlying cancer or from the chance event of a new resistance alteration.

Humans

The time and duration of meiosis.

Ever since meiosis was recognized as a process there has been a continuing interest in its temporal aspects. Two main types of meiotic timing experiments have been conducted: first, experiments to estimate the duration of meiosis (and sometimes its stages); second, experiments to locate the sensitive stage(s) when exposure of meiocytes to various treatments can affect meiotic chromosome behaviour (e.g. pairing or recombination). Such experiments have played an important role in increasing our understanding of the meiotic process. The duration of meiosis has been estimated in about 70 organisms, including two prokaryotes (yeast and Chlamydomonas) and the following eukaryotes: 1 Basidiomycete (Coprinus lagopus), 2 Gymnosperms (Larix decidua and Thuja plicata gracilis). at least 39 angiosperms, and at least 26 animal species. The duration of female meiosis has been estimated in far fewer species than male meiosis. However, estimates of the duration of female meiosis are available for 6 angiosperms. Drosophila melanogaster, Xenopus laevis, and several mammals. Comparison of these data shows that the duration of meiosis is one of the most variable aspects of the meiotic process, ranging from less than 6 h in yeast to more than 40 years in the human female. Developmental holds at different stages of meiosis are common in plants and animals, and inevitably prolong the meiotic division. However, even among species without developmental holds, the duration of meiosis is very variable. For instance, in animals it ranges from about 1-2 days in male Drosophila melanogaster to more than 24 days in male Homo sapiens and several Orthopterans. Despite the large variation in the duration of meiosis three generalizations can be made: (i) first prophase is always very long compared with the remaining meiotic stages, (ii) the rate of meiotic development is very slow compared with the rate of development in dividing somatic meristem cells of the same organisms under the same conditions, (iii) the duration of meiosis is characteristic of the genotype and species. Four main factors have been recognized which effect or determine the duration of meiosis, namely (1) environmental factors (e.g. temperature); (2) nuclear DNA content; (3) ploidy level of the organism; and, (4) the genotype. Because nuclear DNA content plays a major role in determining the duration of meiosis, it has been suggested that DNA influences the rate of meiotic development in two ways: first through its informational content (the genotype), and second indirectly by the physical and mechanical effects of its mass independently of its informational content (i.e. the nucleotype). Thus, the observed duration of meiosis is the result of a complex genotype-nucleotype-environment interaction. With the obvious exception of variation caused by developmental holds, changes in the duration of meiosis usually involve proportional changes in the durations of all its stages...

Animals