Primary Respiratory Chain Disease Causes Tissue-Specific Dysregulation of the Global Transcriptome and Nutrient-Sensing Signaling Network

Zhe Zhang,Joseph A Baur,Mai Tsukikawa,Elizabeth Mccormick,Marni J Falk,Eric Rappaport,Richard Haas,Eiko Nakamaru-Ogiso,Emily Place,Shana Mccormack,Min Peng,Julian Ostrovsky,Colleen Clarke,Erzsebet Polyak,Gail Reiner,Michael Polymenis

doi:10.1371/journal.pone.0069282

Abstract

Primary mitochondrial respiratory chain (RC) diseases are heterogeneous in etiology and manifestations but collectively impair cellular energy metabolism. Mechanism(s) by which RC dysfunction causes global cellular sequelae are poorly understood. To identify a common cellular response to RC disease, integrated gene, pathway, and systems biology analyses were performed in human primary RC disease skeletal muscle and fibroblast transcriptomes. Significant changes were evident in muscle across diverse RC complex and genetic etiologies that were consistent with prior reports in other primary RC disease models and involved dysregulation of genes involved in RNA processing, protein translation, transport, and degradation, and muscle structure. Global transcriptional and post-transcriptional dysregulation was also found to occur in a highly tissue-specific fashion. In particular, RC disease muscle had decreased transcription of cytosolic ribosomal proteins suggestive of reduced anabolic processes, increased transcription of mitochondrial ribosomal proteins, shorter 5′-UTRs that likely improve translational efficiency, and stabilization of 3′-UTRs containing AU-rich elements. RC disease fibroblasts showed a strikingly similar pattern of global transcriptome dysregulation in a reverse direction. In parallel with these transcriptional effects, RC disease dysregulated the integrated nutrient-sensing signaling network involving FOXO, PPAR, sirtuins, AMPK, and mTORC1, which collectively sense nutrient availability and regulate cellular growth. Altered activities of central nodes in the nutrient-sensing signaling network were validated by phosphokinase immunoblot analysis in RC inhibited cells. Remarkably, treating RC mutant fibroblasts with nicotinic acid to enhance sirtuin and PPAR activity also normalized mTORC1 and AMPK signaling, restored NADH/NAD+ redox balance, and improved cellular respiratory capacity. These data specifically highlight a common pathogenesis extending across different molecular and biochemical etiologies of individual RC disorders that involves global transcriptome modifications. We further identify the integrated nutrient-sensing signaling network as a common cellular response that mediates, and may be amenable to targeted therapies for, tissue-specific sequelae of primary mitochondrial RC disease.

Highlights

Primary mitochondrial disease represents a heterogeneous group of genetic disorders that directly impair activity of the energy-generating respiratory chain (RC), with manifestations of severe and typically progressive multi-organ dysfunction that may present across the age spectrum
We identified 4,367 differentially expressed genes (DEGs) with p value less than 0.05 and an estimated 12.1% false discovery rate (FDR). 2,016 of these genes were upregulated and 2,351 of these genes were downregulated in RC disease
To assess the possible therapeutic implications of our observation that central nodes of the nutrient sensing signaling network were modified in primary RC disease, we investigated the mTORC1 and AMPK activities of a fibroblast cell lines (FCLs) from a mitochondrial disease subject (Q1039) who has Leigh syndrome caused by pathogenic mitochondrial DNA (mtDNA) mutations in two complex I subunit genes (ND4 and ND6)

Summary

Introduction

Primary mitochondrial disease represents a heterogeneous group of genetic disorders that directly impair activity of the energy-generating respiratory chain (RC), with manifestations of severe and typically progressive multi-organ dysfunction that may present across the age spectrum. We found that the PPAR signaling pathway, which is involved in coordinating basic lipid metabolism, plays a central role in modulating hepatic and renal responses to primary RC dysfunction that results from a coenzyme Q biosynthetic deficiency in B6.Pdss2kd/kd mutant mice [5]. These findings suggest that a few master genes or central signaling pathways may modulate the transcriptional, translational, and/or post-translational cellular response to primary mitochondrial disease, and that this response may itself contribute to the pathogenesis of RC disease. Defining such central pathway alterations might offer novel pharmacologic targets for treating the clinical sequelae of primary RC disease

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Results

Conclusion