NRASQ61K melanoma tumor formation is reduced by p38-MAPK14 activation in zebrafish models and NRAS-mutated human melanoma cells.

Oncogenic BRAF and NRAS mutations drive human melanoma initiation. We used transgenic zebrafish to model NRAS mutant melanoma and the rapid tumor onset allowed us to study candidate tumor suppressors. We identified P38α-MAPK14 as a potential tumor suppressor in The Cancer Genome Atlas melanoma cohort of NRAS mutant melanomas, and overexpression significantly increased the time to tumor onset in transgenic zebrafish with NRAS-driven melanoma. Pharmacological activation of P38α-MAPK14 using anisomycin reduced in vitro viability of melanoma cultures, which we confirmed by stable overexpression of p38α. We observed that the viability of MEK-inhibitor resistant melanoma cells could be reduced by combined treatment of anisomycin and MEK-inhibition. Our study demonstrates that activating the p38α-MAPK14 pathway in the presence of oncogenic NRAS abrogates melanoma in vitro and in vivo.This project has received funding from the European Union’s Horizon 2020 432 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 641458. The 433 work carried out at the University of Edinburgh was partly funded by EEP, MRC HGU Programme 434 (MC_UU_00007/9), European Research Council (ZF-MEL-CHEMBIO-648489), and L'Oreal-Melanoma 435 Research Alliance (401181)

NRASQ61K melanoma tumor formation is reduced by p38-MAPK14 activation in zebrafish models and NRAS-mutated human melanoma cells.

Oncogenic BRAF and NRAS mutations drive human melanoma initiation. We used transgenic zebrafish to model NRAS mutant melanoma and the rapid tumor onset allowed us to study candidate tumor suppressors. We identified P38α-MAPK14 as a potential tumor suppressor in The Cancer Genome Atlas melanoma cohort of NRAS mutant melanomas, and overexpression significantly increased the time to tumor onset in transgenic zebrafish with NRAS-driven melanoma. Pharmacological activation of P38α-MAPK14 using anisomycin reduced in vitro viability of melanoma cultures, which we confirmed by stable overexpression of p38α. We observed that the viability of MEK-inhibitor resistant melanoma cells could be reduced by combined treatment of anisomycin and MEK-inhibition. Our study demonstrates that activating the p38α-MAPK14 pathway in the presence of oncogenic NRAS abrogates melanoma in vitro and in vivo.This project has received funding from the European Union’s Horizon 2020 432 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 641458. The 433 work carried out at the University of Edinburgh was partly funded by EEP, MRC HGU Programme 434 (MC_UU_00007/9), European Research Council (ZF-MEL-CHEMBIO-648489), and L'Oreal-Melanoma 435 Research Alliance (401181)

Behavioral and Gene Regulatory Responses to Developmental Drug Exposures in Zebrafish.

Developmental consequences of prenatal drug exposure have been reported in many human cohorts and animal studies. The long-lasting impact on the offspring-including motor and cognitive impairments, cranial and cardiac anomalies and increased prevalence of ADHD-is a socioeconomic burden worldwide. Identifying the molecular changes leading to developmental consequences could help ameliorate the deficits and limit the impact. In this study, we have used zebrafish, a well-established behavioral and genetic model with conserved drug response and reward pathways, to identify changes in behavior and cellular pathways in response to developmental exposure to amphetamine, nicotine or oxycodone. In the presence of the drug, exposed animals showed altered behavior, consistent with effects seen in mammalian systems, including impaired locomotion and altered habituation to acoustic startle. Differences in responses seen following acute and chronic exposure suggest adaptation to the presence of the drug. Transcriptomic analysis of exposed larvae revealed differential expression of numerous genes and alterations in many pathways, including those related to cell death, immunity and circadian rhythm regulation. Differential expression of circadian rhythm genes did not correlate with behavioral changes in the larvae, however, two of the circadian genes, arntl2 and per2, were also differentially expressed at later stages of development, suggesting a long-lasting impact of developmental exposures on circadian gene expression. The immediate-early genes, egr1, egr4, fosab, and junbb, which are associated with synaptic plasticity, were downregulated by all three drugs and in situ hybridization showed that the expression for all four genes was reduced across all neuroanatomical regions, including brain regions implicated in reward processing, addiction and other psychiatric conditions. We anticipate that these early changes in gene expression in response to drug exposure are likely to contribute to the consequences of prenatal exposure and their discovery might pave the way to therapeutic intervention to ameliorate the long-lasting deficits

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy.

In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy

\ua9 The Author(s) 2024.In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3−/−; ttn.1+/−) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases

Total Nucleic Acid Extraction from Single Zebrafish Embryos for Genotyping and RNA-seq.

RNA sequencing allows for the quantification of the transcriptome of embryos to investigate transcriptional responses to various perturbations (e.g., mutations, infections, drug treatments). Previous protocols either lack the option to genotype individual samples, or are laborious and therefore difficult to do at a large scale. We have developed a protocol to extract total nucleic acid from individual zebrafish embryos. Individual embryos are lysed in 96-well plates and nucleic acid is extracted using SPRI beads. The total nucleic acid can be genotyped and then DNase I treated to produce RNA samples for sequencing. This protocol allows for processing large numbers of individual samples, with the ability to genotype each sample, which makes it possible to undertake transcriptomic analysis on mutants at timepoints before the phenotype is visible. Graphic abstract: Extraction of total nucleic acid from individual zebrafish embryos for genotyping and RNA-seq

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy.

Acknowledgements: We acknowledge H. Luque, L. Phillips, J. Casement, O. Magnuson, D. Nguyen and Y. Hu for technical support; R. García-Tercero and C. Díaz for sample collection; E. Zorio, M.E. Leach, D. Bharucha-Goebel, J. Dastgir and C. Konersman for clinical expertise and M. Gautel for helpful advice. We also thank CureCMD for their help in patient recruitment and the patients for donating their samples. The research leading to these results has received funding from the European Community’s Seventh Framework Program (FP7/2007-2013; 2012-305121) ‘Integrated European—omics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)’ (to A. Töpf, V.S., I.T.Z. and F.M.); the European Union’s Horizon 2020 research and innovation program (Solve-RD project; 779257 to A. Töpf); Muscular Dystrophy UK and Muscular Dystrophy Association US (mda577346 to F.M.); Päulon Säätiö (to M. Savarese); Academy of Finland, Sigrid Juselius Foundation (to B.U.); core funding to the Sanger Institute by the Wellcome Trust (098051 and 206194 to E.M.B.-N., J.P. and N.W.); EURO-NMD and Fundación Gemio (to J.J.V., N.M. and P.M.); Intramural Research Grant (2-5, 29-4) for Neurological and Psychiatric Disorders of NCNP and AMED (JP20ek0109490h0001 to I.N.); Inserm, CNRS, University of Strasbourg, Labex INRT (ANR-10-LABX-0030 and ANR-10-IDEX-0002-02), France Génomique (ANR-10-INBS-09) and Fondation Maladies Rares for the ‘Myocapture’ sequencing project, AFM-Téléthon (22734), the European Joint program (EJPRD2019-126 IDOLS-G and ANR-19-RAR4-0002 to J.L., X.L. and V.B.); Intramural funds from the NIH National Institute of Neurological Disorders and Stroke (to C.G.B.); the Dutch Princess Beatrix Muscle Fund and the Dutch Spieren voor Spieren Muscle fund (to C.E.E.); PI16/00316 supported by the Instituto de Salud Carlos III (ISCIII), Madrid and the Generalitat Valenciana (grant PROMETEO/2019/075 to N.M.); Australian NHMRC Neil Hamilton Fairley Early Career Research Fellowship (GNT1090428 to E.C.O.); Starship Foundation A+7340 (to G.L.O.); Early Career Award from the Thrasher Research Fund (to S.S.); U54 HD090255 from the NIH Eunice Kennedy Shriver National Institute of Child Health and Human Development (to A.H.B.); Wellcome Center for Mitochondrial Research (203105/Z/16/Z), the Mitochondrial Disease Patient Cohort (UK; G0800674), the Medical Research Council International Center for Genomic Medicine in Neuromuscular Disease (MR/S005021/1), the Medical Research Council (MR/W019027/1), the Lily Foundation, Mito Foundation, the Pathological Society, the UK NIHR Biomedical Research Center for Ageing and Age-related Disease award to the Newcastle upon Tyne Foundation Hospitals NHS Trust and the UK NHS Highly Specialized Service for Rare Mitochondrial Disorders of Adults and Children (to R.W.T.). MYO–SEQ was funded by Sanofi Genzyme, Ultragenyx, LGMD2I Research Fund, Samantha J Brazzo Foundation, LGMD2D Foundation, Kurt+Peter Foundation, Muscular Dystrophy UK and Coalition to Cure Calpain 3. Sequencing and analysis for relevant families (Supplementary Note) were provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics (Broad CMG) and were funded by the National Human Genome Research Institute, the National Eye Institute and the National Heart, Lung and Blood Institute under grant UM1 HG008900 and the National Human Genome Research Institute under grants U01HG0011755 and R01 HG009141. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. DNA samples for NeurOmics and MYO–SEQ were provided by the John Walton Muscular Dystrophy Research Center Biobank. This facility is supported by the NIHR Newcastle Biomedical Research Center. Newcastle University’s Electron Microscopy Research Services and equipment Hitachi HT7800 120 kV TEM microscope are funded by BBSRC grant reference BB/R013942/1.Funder: Genzyme (Genzyme Corporation); doi: https://doi.org/10.13039/100004329Funder: Ultragenyx Pharmaceutical (Ultragenyx Pharmaceutical Inc.); doi: https://doi.org/10.13039/100013220Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): 2012-305121In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases