Biology subjects

Meyer, S.

Publications and source records attributed to Meyer, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Whole genome sequencing of endometrial cancer identifies novel subgroups, drivers, and actionable alterations

Endometrial cancer (EC) is the most common gynaecological malignancy in high income countries, and is increasing in incidence. While molecular stratification has improved its management, precision care is hampered by incomplete characterization of the EC genome. We address this by analysis of whole genome sequencing (WGS) of 665 ECs generated by the UK Genomics England 100,000 Genome Project (100kGP). 5% of cases were associated with germline pathogenic variants in cancer genes, including BRCA1 which we confirmed predisposes to EC. We identified 107 putative coding driver genes, 35% of which had no prior established role in EC. Novel structural variants included gains of MYCN and loss of its negative regulator NEDD4.1 which were significantly mutually exclusive in copy number (CN) high tumours. Immunogenomic analysis confirmed selection for driver alterations of low immunogenicity based on patient HLA haplotype, and pervasive immune escape through multiple mechanisms. Unsupervised clustering of mutational signatures and genomic alterations identified known and novel molecular subgroups, including a CN-high subset with mutational signatures of homologous recombination deficiency (HRD) and favourable outcome. Independent prognostic value of single nucleotide variant (SNV) burden, CN burden and multiple coding drivers, along with the identification of targetable molecular alterations in over one-third of cases, underscores the promise of WGS for precision medicine in EC.

genomics↗

bioRxiv2026

A confirmatory, dual-centric non-human primate study on the efficacy of novel oropharyngeal spray immunization with an adenoviral vector vaccine against RSV -- Important lessons learned

In a confirmatory study, we evaluated the immunogenicity and protective efficacy of a heterologous prime-boost vaccination strategy against respiratory syncytial virus (RSV) in non-human primates. Building on prior evidence of protective mucosal immunity induced by intramuscular DNA priming followed by an oropharyngeal adenoviral boost, we conducted a randomized, blinded, dual-centre study across two European primate research facilities. Rhesus macaques received a codon-optimized RSV-F DNA vaccine via electroporation, followed by two mucosal administrations of a recombinant adenovirus serotype 5 vector encoding the same antigen. Control groups included animals vaccinated with irrelevant influenza antigens and a comparator group mimicking natural immunity induced by primary RSV infection. Systemic and mucosal immune responses, including RSV-F-specific antibodies and tissue-resident memory T cells, were monitored longitudinally. Here, we detected robust immune responses, but with some variability between the two centres. However, following experimental RSV challenge performed 22 weeks after the final immunization, RSV-vaccinated animals demonstrated markedly reduced viral replication in both upper and lower respiratory tracts. However, unexpected RSV-specific immunity in the control group at one single study site prevented confirmation of the predefined primary endpoint. Overall, these results support the potential of mucosal adenoviral boosting following DNA priming to induce protective immunity against RSV, while highlighting challenges associated with multi-centre preclinical vaccine studies.

immunology↗

bioRxiv2025

Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

Chromosomal topology and transcription are tightly coupled, yet the quantitative impact of topological constraints on transcription, supercoiling, and the potential coupling between neighboring genes in vivo remains unclear. In this work, we constructed synthetic chromosomal domains in Escherichia coli that contained two genes inside a topology-controllable domain and a third gene outside. Using three-color single-molecule fluorescence in situ hybridization (smFISH), we measured transcription output from the three genes in individual cells under conditions in which gene orientation, domain formation state, and global chromosomal supercoiling density were varied. We found that topological domain formation repressed transcription, diminished gene orientation-dependent differences in transcription, and modulated the supercoiling sensitivity of genes located both within and near the domain. Relaxing global negative supercoiling through gyrase inhibition broadly repressed transcription; increasing global negative supercoiling level through topoisomerase I inhibition repressed highly expressed genes, while activating lowly expressed ones. Besides single-gene effects, we also observed an intrinsic coupling between neighboring genes with a non-monotonic dependence on the underlying supercoiling state, which shifted with domain topology and gene syntax. Our results establish chromosome topology as a major regulator of both transcription levels and the coupling between adjacent genes.

biophysics↗

bioRxiv2025

Sympathetic signaling directs macrophage efferocytosis in thermogenic adipose tissue

Brown adipose tissue (BAT) undergoes significant remodeling upon thermogenic activation. During this process, brown adipocytes and immune cells, such as macrophages, contribute to thermogenesis and energy expenditure. Among the various functions exerted by macrophages, the clearance of dying cells, known as efferocytosis, is a key regulator of tissue remodeling across multiple organs in both physiological and pathological contexts. However, whether macrophages contribute to BAT remodeling and thermogenic adaptation through efferocytosis, and what drives efferocytosis in BAT, remain unknown. Here, we identify norepinephrine (NE), which is highly released in BAT upon cold challenge, as a tissue-specific trigger of macrophage efferocytosis. Transcriptomic and lipidomic analyses of BAT after cold exposure revealed a population of lipid-handling macrophages enriched in efferocytosis-related transcripts. Consistently, cold exposure enhanced the efferocytic capacity of BAT macrophages. These effects were recapitulated by stimulation of macrophages with NE and were dependent on {beta}2-adrenergic signaling and the efferocytic receptors AXL and MERTK. Mice lacking Axl and Mertk in macrophages exhibited impaired lipolysis, reduced thermogenic gene expression, and increased adipose tissue inflammation. Together, our findings identify a so far neglected role for NE in adipose tissue, linking sympathetic activation to macrophage efferocytosis and thereby promoting tissue remodeling and metabolic adaptation. Uncovering the role of NE in one of the core functions of macrophages, efferocytosis, not only expands our understanding of the multifaceted effects of NE on the immune system but also highlights therapeutic potential for targeting impaired efferocytosis in metabolic disorders. One sentence summaryNorepinephrine is a novel trigger of macrophage efferocytosis in brown adipose tissue, linking sympathetic signaling to metabolic adaptation and macrophage tissue remodeling responses through {beta}2-adrenergic and Axl/Mertk pathways.

immunology↗

bioRxiv2025

Anti-vitronectin single-chain variable fragment targeting the hemopexin-like domain decreases age-related macular degeneration indicators in ex vivo models of the retinal pigment epithelium

Vitronectin is a prominent constituent of the extracelluar matrix (ECM) that plays a key role in inflammation by regulating cell adhesion, migration, and complement activation. Together with other inflammatory biomarkers, lipids, and hydroxyapatite, an ECM component, vitronectin, accumulates in abnormal deposits and drusen associated with age-related macular degeneration (AMD). Using an engineered polypeptide (VnHX) containing the hexmopexin-like domain (HX) of vitronectin, we found that the HX domain directly promotes hydroxyapatite (HAP) accumulation. Next, we screened humanized single-chain variable fragments (scFvs) against vitronectin that inhibit the interaction between VnHX and HAP, leveraging the binding of VnHX to HAP. We then tested these scFvs for their ability to block Vn-containg deposits secreted by stem cell-derived retinal pigment epithelium (RPE). In this in vitro drusen model, treatment with the anti-vitronectin antibodies decreased vitronectin accumulation. Furthermore, the antibody treatment led to decreased accumulation of C5b-9 and clusterin, indicating alterations in the complement pathway and cellular stress. These results support that vitronectin has a functional role drusen accumulation and possibly in AMD progression. Vitronectin would be a novel, promising therapeutic target for AMD.

cell biology↗

bioRxiv2025

UFMylation orchestrates chromatin engagement of core NHEJ components to promote DNA double-strand break repair

DNA double-strand breaks (DSBs) are highly cytotoxic lesions whose misrepair can lead to genomic instability, cancer and developmental disorders. Through systematic screening of understudied ubiquitin-like modifiers (UBLs), we identify UFM1 as a previously unrecognised regulator of non-homologous end-joining (NHEJ). Using a structure-guided chemical biology strategy, we develop a photo-crosslinkable UFM1 probe and, together with high-resolution NMR, uncover non-canonical UFM1-binding regions in core NHEJ components, including XRCC4. Mechanistically, proximity-dependent proteomics reveals Ku70 as a key UFMylation substrate, establishing a functional axis in which XRCC4 engages UFMylated Ku70 to promote the chromatin assembly of NHEJ factors. Perturbation of UFM1 signalling, via UFSP2 depletion or a hypomorphic UBA5 allele in patient-derived fibroblasts, impairs these processes, linking UFMylation defects to altered regulation of DSB repair. Our findings define a complete UFM1 signalling module in genome maintenance and uncover a molecular connection between hereditary UFMylation disorders and dysregulated DSB repair pathways.

molecular biology↗

bioRxiv2025

Modeling human phenotypes in the nematode C. elegans during an undergraduate developmental biology course

Caenorhabditis elegans is a widely used model organism in biomedical research due to its genetic tractability, short life cycle, and conservation of many developmental processes with humans. In this study, undergraduate students conducted nine independent experiments during a Developmental Biology course to model human phenotypes using C. elegans. Each group selected a human phenotype of interest, identified a gene associated with the phenotype, and then determined the orthologous or homologous gene in C. elegans. By obtaining mutants and designing phenotypic assays, students investigated the extent to which the worm models could recapitulate aspects of the human condition. This collective work highlights both the potential and limitations of C. elegans as a model for human phenotypic variation and disease and demonstrates the value of undergraduate inquiry as a catalyst for scientific engagement and research-based learning.

scientific communication and education↗

bioRxiv2025

Differential effect of supercoiling on bacterial transcription in topological domains

DNA supercoiling (SC), the over- and under-winding of DNA, is generated by transcription as described in the twin-domain model. Conversely, SC also impacts transcription through torsional stress. SC therefore regulates transcription independent of transcription factor binding, the classic protein-based transcription regulatory mechanism, particularly in the context of chromosomal topological domains and the actions of topoisomerases. SC-coupled transcription has inspired several computational models, but a systematic and quantitative assessment of the parameters controlling this complex interplay is missing. There is also a lack of comparison to various experimental results regarding the effects of topological variables such as topoisomerase binding rates and domain size on transcription strength and noise. In this work we developed a quantitative model to describe SC-coupled transcription. We analyzed the effects of topoisomerase activities on the transcription of a single isolated gene with varying promoter strengths and in a topological domain of varying sizes. These simulations revealed qualitatively different roles of the two topoisomerases. Topoisomerase I is specifically required for strongly expressed genes that may be hindered by stalled RNAP, whereas gyrase activity favors the expression of all genes by enhancing transcription initiation and modulating the burstiness of transcription. A new analysis of transcriptomics data in several bacterial species showed that these simulations replicate a global relationship between promoters strength and response to variations in topoisomerase activities. Our work demonstrates how SC contributes to differential gene regulation and transcriptional bursting in mechanistic details and unites computational and experimental work. Author SummaryWe are interested in understanding how bacteria regulate the expression of their genes. One mechanism by which bacteria can do so is through the over- and under-winding of their DNA, termed DNA supercoiling. Because bacteria can use enzymes called topoisomerases to regulate the supercoiling level of their DNA, these enzymes can serve as gene regulators. It is difficult, however, to understand how topoisomerases act as gene regulators through experiments alone. Currently, there is no method of measuring the supercoiling level along a stretch of DNA over an extended period of time in living cells. We therefore developed a computational model of gene transcription coupled to supercoiling dynamics. Unlike some previously existing models, we consider continuous response curves of topoisomerases activities in response to the local supercoiling level and the ability of gyrase to perform several catalytic cycles per binding event. We also perform extensive comparisons between our model and existing gene expression and transcriptomics data, which is essential to ensuring the biological relevance of computational modeling efforts. We replicate and provide detailed explanations for several experimental observations, including the connection between supercoiling and transcriptional bursts and the selective gene expression modulation by topoisomerase inhibition that is based on the promoter strength.

biophysics↗

bioRxiv2024

Single-Cell Atlas of AML Reveals Age-Related Gene Regulatory Networks in t(8;21) AML

BackgroundAcute myeloid leukemia (AML) is characterized by cellular and genetic heterogeneity, which correlates with clinical course. Although single-cell RNA sequencing (scRNA-seq) reflects this diversity to some extent, the low sample numbers in individual studies limit the analytic potential when comparing specific patient groups. ResultsWe performed large scale integration of published scRNA-seq datasets to create a unique single-cell transcriptomic atlas for AML (AML scAtlas), totaling 748,679 cells, from 159 AML patients and 44 healthy donors from 20 different studies. This is the largest single-cell data resource for AML to our knowledge, publicly available at https://cellxgene.bmh.manchester.ac.uk/AML/. This AML scAtlas allowed investigations into 20 patients with t(8;21) AML, where we explored the clinical importance of age, given the in-utero origin of pediatric disease. We uncovered age-associated gene regulatory network (GRN) signatures, which we validated using bulk RNA sequencing data to delineate distinct groups with divergent biological characteristics. Furthermore, using an additional multiomic dataset (scRNA-seq and scATAC-seq), we validated our initial findings and created a de-noised enhancer-driven GRN reflecting the previously defined age-related signatures. ConclusionsApplying integrated data analysis of the AML scAtlas, we reveal age-dependent gene regulation in t(8;21) AML, potentially reflecting immature/fetal HSC origin in prenatal origin disease vs postnatal origin. Our analysis revealed that BCLAF1, which is particularly enriched in pediatric AML with t(8;21) of inferred in-utero origin, is a promising prognostic indicator. The AML scAtlas provides a powerful resource to investigate molecular mechanisms underlying different AML subtypes.

cancer biology↗

bioRxiv2024

A novel combination of CDK4/6 and PI3K inhibitors exhibits highly synergistic activity and translational potential in Ewing sarcoma.

Ewing sarcoma is a highly aggressive solid malignancy affecting children and young adults. Ewing sarcoma is driven primarily by EWSR1::FLI1, a fusion oncoprotein that has been notoriously difficult to target with traditional pharmacologic agents. There are numerous examples of preclinical promising combinations of small molecules that are never tested in pediatric clinical trials because agents fail to reach the market due to limited efficacy for common adult cancers. Moreover, the effectiveness of single-agent therapies for cancer treatment is often limited. To address these limitations, we selected 28 compounds that were largely FDA approved or in late stages of clinical development and known to regulate important pathways in Ewing sarcoma. We performed a drug screen in Ewing sarcoma cell lines with 180 combinations of tyrosine kinase inhibitors, cell cycle inhibitors, and conventional chemotherapy. The results of the screen revealed that a PI3K inhibitor, copanlisib, combined with a CDK4/6 inhibitor, ribociclib, exhibited strong synergistic anti-Ewing sarcoma activity. Using proteomic methods such as a reverse-phase protein array and western immunoblotting, we demonstrated that this combination induced a downregulation of the PI3K/AKT pathway as well as proteins involved in cell cycle regulation. We further confirmed these in vitro data using bulk RNA-sequencing. To evaluate the phenotypic effect of the PI3K/CDK4/6 inhibition in Ewing sarcoma lines, we performed apoptosis and cell cycle analyses using flow cytometry and demonstrated that ribociclib primarily induced a G0/G1 arrest with minimal effect on Ewing cell viability but significantly enhanced the apoptotic effect of copanlisib treatment. In a xenograft model of Ewing sarcoma, we demonstrated that the combination therapy significantly prolonged survival compared to treatment with either vehicle or single-agent therapy alone. Our findings identify a new candidate therapy combination for Ewing sarcoma using FDA-approved drugs and provide a resource of additional potential synergistic combinations for future validation. Statement of translational relevanceTreatment of patients with newly diagnosed Ewing sarcoma involves intensive multi- agent chemotherapy, radiation, and surgery, often leading to long-term toxicities. Children with relapsed or metastatic disease experience poor outcomes with five-year overall survival rates of only 15 to 30 percent. Therefore, new therapeutic approaches are urgently needed. Our drug screen revealed several promising combinations with synergistic anti-Ewing sarcoma activity including the PI3K inhibitor copanlisib with the CDK4/6 inhibitor ribociclib. This combination also significantly improved survival in a mouse xenograft model of Ewing sarcoma compared to treatment with vehicle or either drug alone. Pre-clinical validation of a combination therapy composed of two FDA- approved drugs nominates this combination for early phase trials for patients with with relapsed or refractory Ewing sarcoma, a group of patients greatly in need of new therapeutic opportunities. The data generated by our drug screen may also be used as a resource to identify other promising combinations for future validation as Ewing sarcoma therapies.

cancer biology↗

bioRxiv2024

Repetitive magnetic stimuli over the motor cortex impair consolidation of a balance task by suppressing up-regulation of intracortical inhibition

Low-frequency repetitive transcranial magnetic stimulation (rTMS) over the primary motor cortex (M1) was shown to impair short-term consolidation of a balance task, emphasizing the importance of M1 in balance skill consolidation. However, the disruptive mechanisms of rTMS on neural consolidation processes and their persistence across multiple balance acquisition sessions remain unclear. GABAergic processes are crucial for motor consolidation and, at the same time, are up-regulated when learning balance skills. Therefore, this study investigated the impact of rTMS on GABA-mediated short-interval intracortical inhibition (SICI) and consolidation of balance performance. Participants (n=31) underwent six balance acquisition sessions on a rocker board, each followed by rTMS (n=15) or sham-rTMS (n=16). In the PRE-measurement, SICI was assessed at baseline and after balance acquisition with subsequent rTMS/sham-rTMS. In the POST-measurement, this procedure was repeated to assess the influence of motor memory reactivation on SICI. In addition, SICI-PRE and SICI-POST were compared to assess long-term processes. Both groups achieved similar improvements within the balance acquisition sessions. However, they did not consolidate equally well indicated by significant declines in performance for the rTMS group (p = 0.006) in the subsequent sessions. Both short-(p = 0.014) and long-term (p = 0.038) adaptations in SICI were affected by rTMS: while the sham-rTMS group up-regulated SICI, rTMS led to reductions in inhibition. The interfering effect of rTMS on both balance consolidation and up-regulation of SICI suggests that increased intracortical inhibition is an important factor to protect and consolidate the newly acquired motor memory.

neuroscience↗

bioRxiv2023

Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution

While classical models of transcriptional regulation focus on transcription factors binding at promoters, gene expression is also influenced by chromosome organization. Understanding this spatial regulation strongly benefits from integrated and quantitative spatial analyses of genome-scale data such as RNA-Seq and ChIP-Seq. We introduce Genome Regulation Analysis Tool Incorporating Organization and Spatial Architecture (GRATIOSA), a Python package making such combined analyses more automatic, systematic and reproducible. While current software focuses on initial analysis steps (read mapping and counting), GRAsTIOSA proposes an integrated framework for subsequent analyses, providing a broad range of spatially-resolved quantitative data comparisons and representations. As an example, we quantitatively assess the validity and extension of the twin-supercoiled domain model in Escherichia coli genome-wide transcription, using recent topoisomerase ChIP-Seq data. We show that topoisomerases are locally recruited by the 40% most highly expressed transcription units, with a magnitude correlating with the expression level. The recruitment of topoisomerase I extends to around 10 kb upstream, whereas DNA gyrase is recruited at least 30 kb downstream of transcription units. This organization is the primary determinant of topoisomerase I recruitment, whereas gyrase binding is additionally modulated at larger 100-200 kb length-scale. Further analyses of spatial regulation will be facilitated by GRATIOSA.

bioinformatics↗

bioRxiv2023

Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket

To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate binding pocket. Of 631 fragments soaked, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (2 hits) or at crystal packing interfaces (3 hits). Notably, two fragments with a pose sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. Our structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography. SynopsisAn X-ray crystallographic screen on SARS-CoV-2 3CL protease resulted in 29 fragment hits, including two isatin-based reversible covalent binders, and revealed a strong influence of the crystal form used for fragment soaking on the bound conformation of three additional reference fragments.

biophysics↗

bioRxiv2023

BMP2 and BMP7 cooperate with H3.3K27M to promote quiescence and invasiveness in pediatric diffuse midline gliomas

Pediatric diffuse midline gliomas (pDMG) are an aggressive type of childhood cancer with a fatal outcome. Their major epigenetic determinism has become clear, notably with the identification of K27M mutations in histone H3. However, the synergistic oncogenic mechanisms that induce and maintain tumor cell phenotype have yet to be deciphered. In 20 to 30% of cases, these tumors have an altered BMP signaling pathway with an oncogenic mutation on the BMP type I receptor ALK2, encoded by ACVR1. However, the potential impact of the BMP pathway in tumors non-mutated for ACVR1 is less clear. By integrating bulk, single-cell and spatial transcriptomic data, we show here that the BMP signaling pathway is activated at similar levels between ACVR1 wild-type and mutant tumors and identify BMP2 and BMP7 as putative activators of the pathway in a specific subpopulation of cells. By using both pediatric isogenic glioma lines genetically modified to overexpress H3.3K27M and patients-derived DIPG cell lines, we demonstrate that BMP2/7 synergizes with H3.3K27M to induce a transcriptomic rewiring associated with a quiescent but invasive cell state. These data suggest a generic oncogenic role for the BMP pathway in gliomagenesis of pDMG and pave the way for specific targeting of downstream effectors mediating the K27M/BMP crosstalk.

cancer biology↗

bioRxiv2023

FAM104 proteins promote the nuclear localization of p97/VCP

The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis and DNA damage repair, and its de-regulation is linked to neuro-muscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97-cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. FAM104 proteins bind p97 directly via a novel, alpha-helical motif and associate with the p97- UFD1-NPL4 complex in cells. FAM104 proteins localize to the nucleus and promote both the nuclear import and chromatin binding of p97. Loss of FAM104 proteins results in slow growth and hypersensitivity to p97 inhibition in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.

cell biology↗

bioRxiv2023

Resolving genotype-phenotype discrepancies of the Kidd blood group using nanopore sequencing

Due to substantial improvement in read accuracy, third-generation long-read sequencing holds great potential in blood group diagnostics, particularly in cases where traditional genotyping or sequencing techniques, primarily targeting exons, fail to explain serological phenotypes. In this study, we employed Oxford Nanopore sequencing to resolve all genotype-phenotype discrepancies in the Kidd blood group system (JK, encoded by SLC14A1) observed over seven years of routine high-throughput donor genotyping using a mass spectrometry based platform at Blood Transfusion Service Zurich. Discrepant results from standard serological typing and donor genotyping were confirmed by commercial PCR-SSP kits. To resolve discrepancies, we amplified the entire coding region of SLC14A1 ([~]24 kb, exons 3 to 10) in two overlapping long-range PCRs in all samples. Amplicons were barcoded and sequenced on a MinION flow cell. Sanger sequencing and bridge-PCRs were used to confirm findings. Among 11,972 donors with both serological and genotype data available for the Kidd system, we identified 10 cases with unexplained conflicting results. Five were linked to known weak and null alleles caused by variants not included in the routine donor genotyping. In two cases, we identified novel null alleles on the JK*01 (Gly40Asp; c.119G>A) and JK*02 (Gly242Glu; c.725G>A) haplotype, respectively. Remarkably, the remaining three cases were associated with a yet unknown deletion of [~]5 kb spanning exons 9-10 of the JK*01 allele, which other molecular methods had failed to detect. Overall, nanopore sequencing demonstrated reliable and accurate performance for detecting both single-nucleotide and structural variants. It possesses the potential to become a robust tool in the molecular diagnostic portfolio, particularly for addressing challenging structural variants such as hybrid genes, deletions and duplications.

genetics↗

bioRxiv2023

Novel regulatory variant in ABO intronic RUNX1 binding site inducing A3 phenotype

Background and ObjectivesMixed-field agglutination in ABO phenotyping (A3, B3) has been linked to genetically different blood cell populations like in chimerism, or to rare variants in either ABO exon 7 or regulatory regions. Clarification of such cases is challenging and would greatly benefit from sequencing technologies that allow resolving full-gene haplotypes at high resolution. Materials and MethodsWe used long-read sequencing by Oxford Nanopore Technologies to sequence the entire ABO gene, amplified in two overlapping long-range PCR fragments, in a blood donor presented with A3B phenotype. Confirmation analyses were carried out by Sanger sequencing and included samples from other family members. ResultsOur data revealed a novel heterozygous g.10924C>A variant on the ABO*A-allele located in the transcription factor binding site for RUNX1 in intron 1 (+5.8 kb site). Inheritance was shown by the results of the donors mother, who shared the novel variant and the anti-A specific mixed-field agglutination. ConclusionWe discovered a regulatory variant in the 8-bp RUNX1 motif of ABO, which extends current knowledge of three other variants affecting the same motif and also leading to A3 or B3 phenotypes. Overall, long-range PCR combined with nanopore sequencing proved powerful and showed great potential as emerging strategy for resolving cases with cryptic ABO phenotypes.

genetics↗

bioRxiv2023

Alterations of the TGFb-sequestration complex member ADAMTSL1 levels are associated with muscular defects and rhabdomyosarcoma aggressiveness

Rhabdomyosarcoma (RMS) is the most frequent form of paediatric soft-tissue sarcoma and remains a medical challenge, holding in failure current therapeutic strategies. RMS shares histological features with cells of the muscle lineage and this cancer is thought to arise from malignant transformation of myogenic precursors. It has been proposed that RMS and myogenesis could represent the "Jekyll and Hyde" of skeletal muscle. The underlying idea is that some early steps of myogenic differentiation are blocked in RMS, and that understanding how the normal process has gone awry could help to decipher the biological underpinnings of tumorigenesis and tumor escape. It is widely agreed that extracellular matrix (ECM) interferes in skeletal muscle regeneration and that defects in ECM components are clinically significant. The challenge is now to decipher actors and mechanisms responsible for the transmission of signals to muscle cells and the subsequent alterations that could be associated with RMS. Using an original transgenic mice model, we show here that ADAMTSL1 is involved in skeletal muscle regeneration. As previously reported for other members of its family, ADAMTSL1 is part of the TGF-{beta}-ECM-sequestering complex and likely positively regulates TGF-{beta}-pathway activity. Last, we observed that ADAMTSL1 expression behaves as a strong prognostic factor in the aggressive fusion-positive RMS and correlates with a neural-like phenotype of tumor cells, resulting from gain of SMAD2/3/4 targets.

cancer biology↗