{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Burak Özkan"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15734"],"description":["Amyotrophic lateral sclerosis (ALS) is conceptualized as a progressive motor neuron degeneration, but emerging evidence suggests systemic manifestations beyond the neuromuscular system. Altered bone structure and metabolism has been shown to be part of the ALS clinical presentation; it remains unclear whether the bone phenotype is secondary to muscle denervation and reduced loading, or it is due to an autonomous process. We investigated skeletal involvement in the SOD1(G93A) mouse model at presymptomatic (P45) and symptomatic (P110) stage through biomechanical and transcriptomic approaches. Biomechanical three-point bending tests revealed significant reductions in femoral rigidity and maximum bending force in SOD1 mutants at P45, indicating early structural deficits. Micro-CT analysis demonstrated reduced trabecular bone mineral density and thickness at P45, with progressive trabecular loss and cortical thinning by P110. Histological examination revealed marked osteoblast loss at P45 with minimal changes in osteoclast activity, suggesting impaired bone formation as the primary early mechanism. Transcriptomic analysis of bone tissue and cultured osteoblasts from P45 mice identified dysregulation of bone differentiation pathways, including downregulation of osteoblast differentiation genes and upregulation of negative regulators of ossification. Notably, unfolded protein response was upregulated in SOD1 osteoblasts and E2F targets and G2M checkpoint genes were significantly downregulated. Immunohistochemistry confirmed increased p16Ink4a level in SOD1 osteoblasts, indicating cellular senescence as a key pathological mechanism. These findings suggest that bone deterioration in ALS reflects intrinsic defects in bone that precede motor symptoms. Understanding these mechanisms may lead to targeted interventions to preserve skeletal integrity in ALS patients and potentially reveal novel insights into ALS pathogenesis beyond the neuromuscular system."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Bone tissue: After euthanasia, femurs were dissected and cleared of soft tissue. Articular cartilage was trimmed. Bone marrow was removed by PBS flushing and brief centrifugation. Bones were snap-frozen in liquid N₂ and kept on dry ice until processing. Primary osteoblasts: Long bones (femora/tibiae/humeri/radii-ulnae) were dissected, soft tissue removed, marrow flushed with PBS, and bone chips (1–2 mm²) prepared for outgrowth culture (see growth protocol).","Growth Protocol - Primary osteoblasts were established as outgrowth cultures from long-bone chips. Chips were rinsed and plated in α-MEM supplemented with 15% FBS, 1% penicillin/streptomycin, and 1% L-glutamine. Cultures were maintained ~6 weeks with routine medium changes until ~80% confluence, then harvested for RNA.","Sample Treatment - No experimental treatments were applied to RNA-seq samples. Cells were cultured under basal conditions as described in the growth protocol.","Library Construction - Poly(A)-selected, strand-specific (second-strand/dUTP) mRNA libraries were prepared from 1 µg total RNA using an Illumina-compatible kit, according to the manufacturer’s protocol. Adapter-ligated cDNA was PCR-amplified with limited cycles, size-selected for ~300–500 bp inserts, and QC’d by Bioanalyzer and qPCR.","Nucleic Acid Extraction - Pulverized bone powder or cell pellets were lysed in guanidinium-based buffer (RLT + β-mercaptoethanol). Total RNA was extracted using Qiagen RNeasy with on-column DNase digestion, following the manufacturer’s instructions. RNA quantity/quality were assessed by spectrophotometry and Bioanalyzer; only samples with RIN > 7 were used.","Sequencing - Libraries were pooled equimolarly and sequenced on an Illumina platform (NovaSeq 6000) in paired-end mode (2×150 bp). Base calling and de-multiplexing used the instrument’s standard pipeline to generate gzipped FASTQ files."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw reads were adapter/quality-trimmed (Trimmomatic) and assessed with FastQC. Reads were aligned to the mouse reference genome (GRCm39) with STAR. Deposited processed data include raw and DESeq2 size-factor normalization counts."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Burak Özkan"],"additional_accession":[]},"is_claimable":false,"name":"Early loss of bone mass in the SOD1(G93A) ALS mouse model is associated with loss of sensitivity to osteogenic factors and enhanced bone senescence","description":"Amyotrophic lateral sclerosis (ALS) is conceptualized as a progressive motor neuron degeneration, but emerging evidence suggests systemic manifestations beyond the neuromuscular system. Altered bone structure and metabolism has been shown to be part of the ALS clinical presentation; it remains unclear whether the bone phenotype is secondary to muscle denervation and reduced loading, or it is due to an autonomous process. We investigated skeletal involvement in the SOD1(G93A) mouse model at presymptomatic (P45) and symptomatic (P110) stage through biomechanical and transcriptomic approaches. Biomechanical three-point bending tests revealed significant reductions in femoral rigidity and maximum bending force in SOD1 mutants at P45, indicating early structural deficits. Micro-CT analysis demonstrated reduced trabecular bone mineral density and thickness at P45, with progressive trabecular loss and cortical thinning by P110. Histological examination revealed marked osteoblast loss at P45 with minimal changes in osteoclast activity, suggesting impaired bone formation as the primary early mechanism. Transcriptomic analysis of bone tissue and cultured osteoblasts from P45 mice identified dysregulation of bone differentiation pathways, including downregulation of osteoblast differentiation genes and upregulation of negative regulators of ossification. Notably, unfolded protein response was upregulated in SOD1 osteoblasts and E2F targets and G2M checkpoint genes were significantly downregulated. Immunohistochemistry confirmed increased p16Ink4a level in SOD1 osteoblasts, indicating cellular senescence as a key pathological mechanism. These findings suggest that bone deterioration in ALS reflects intrinsic defects in bone that precede motor symptoms. Understanding these mechanisms may lead to targeted interventions to preserve skeletal integrity in ALS patients and potentially reveal novel insights into ALS pathogenesis beyond the neuromuscular system.","dates":{"release":"2025-11-30T00:00:00Z","modification":"2026-05-27T17:08:23.326Z","creation":"2025-10-15T14:17:34.963Z"},"accession":"E-MTAB-15734","cross_references":{"ENA":["ERP182239"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}