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Small RNAome profiling from human skeletal muscle: Novel miRNAs and their targets associated with cancer cachexia

ABSTRACT: Background: MicroRNAs (miRs) are small non-coding RNAs that regulate gene (mRNA) expression. Although pathological role of miRs have been studied in muscle wasting conditions such as age, obesity, starvation and muscular dystrophy, their roles in Cancer Cachexia CC are still emerging. Objectives: (i) to profile human skeletal muscle expressed miRs; (ii) to identify differentially expressed (DE) miRs between cachectic and non-cachectic cancer patients; (iii) to identify mRNA targets for the DE miRs to gain mechanistic insights and (iv) to investigate if miRs show potential prognostic and predictive value. Methods: 43 cancer patients were included, of which 19 were cachectic cases exhibiting pre-illness weight loss ≥ 5% and 24 non-cachectic cancer controls who were weight stable in the preceding 6 months. Total RNA isolated from muscle biopsies were subjected to next generation sequencing (NGS). Results: 781 miRs were profiled and 82 miRs with read counts of ≥ 5 in 80% of samples were retained for analysis. We identified 7 DE miRs (up-regulated, fold change of ≥1.4 at p< 0.05). Potential mRNA targets for the DE miRs were identified using previously described human skeletal muscle mRNA expression data (n=90) and identified 212 potential mRNA targets. Ingenuity Pathway Analysis identified 41 pathways (p<0.05) including pathways of myogenesis and inflammation. qRT-PCR analysis of representative miRs, showed similar direction of effect (p<0.05) as in NGS. And lastly, we evaluated the identified miRs for prognostic and predictive value. Conclusions: We identified seven novel miRs associated with CC and pathways that are regulated in CC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE75473 | GEO | 2017/01/09

SECONDARY ACCESSION(S): PRJNA304384

REPOSITORIES: GEO

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Project description:Cancer cachexia (CC) is a poorly understood cause of morbidity and mortality, which has no efficacious treatment or generally-accepted management strategy. The consensus definition for CC identified skeletal muscle loss as a key marker in the diagnosis and classification of cachexia. The importance of fat wasting however, is less understood. During cachexia, different adipose depots demonstrate differential wasting rates. Studies from animal models have suggested adipose tissue may be a key driver of muscle wasting through fat-muscle crosstalk but human studies in this area are lacking. We performed global gene expression profiling of intra-abdominal (IAAT) and subcutaneous (SAT) adipose from weight stable and cachectic cancer patients and healthy controls. Cachexia was defined as >2% weight loss plus low CT-muscularity. Biopsies of SAT and IAAT were taken from patients undergoing resection for oesophago-gastric cancer, and healthy controls (donor nephrectomy) (n=16 and 8 respectively). RNA was isolated and reverse transcribed. cDNA was hybridised to the Affymetrix Clariom S Microarray and data was analysed using R/Bioconductor. Differential expression of genes was assessed using empirical Bayes and moderated-t-statistic approaches. Category enrichment analysis was used with a tissue-specific background to examine the biological context of differentially expressed genes. Selected differentially regulated genes were validated by qPCR. ELISA for Intelectin-1 was performed on IAAT samples for the corresponding patients. The current cohort plus 12 additional patients from each group also had plasma Intelectin-1 ELISA carried out. In IAAT versus SAT comparisons there were 2101, 1722 and 1659 significantly regulated genes in the cachectic, weight stable and control groups respectively. There were 2200 significantly regulated genes from IAAT in cachectic patients compared to controls and 1253 significantly regulated genes from IAAT in weight stable cancer patients compared to controls. The gene showing the largest difference in expression was Intelectin-1 (Omentin-1) (FDR corrected p=0.0001); a novel adipocytokine associated with weight loss in other groups. Genes involving inflammation were enriched in cancer and control IAAT versus SAT though different groups of genes contributed. Energy metabolism and fat browning genesets were downregulated in cancer IAAT as were key fat browning genes (e.g. UCP1). SAT and IAAT have unique gene expression signatures. IAAT is metabolically active in cancer, and maybe a target for therapeutic manipulation. IAAT may play a fundamental role in cachexia, but the downregulation of energy metabolism genes implies a limited role for fat browning in human cachectic patients, in contrast to pre-clinical models.

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Small RNAome profiling from human skeletal muscle: Novel miRNAs and their targets associated with cancer cachexia

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