Defining the transcriptomic and proteomic profiles of rat ageing skeletal muscle by the use of a cDNA array, 2D- and Blue native-PAGE approach A. Lombardi a,1 , E. Silvestri b,1 , F. Cioffi c , R. Senese c , A. Lanni c , F. Goglia b , P. de Lange c, ⁎ , M. Moreno b, ⁎ a Dipartimento delle Scienze Biologiche, Sezione Fisiologia, Università degli Studi di Napoli “Federico II”, Via Mezzocannone 8, 80134 Napoli, Italy b Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy c Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy ARTICLE DATA ABSTRACT Article history: Received 15 October 2008 Accepted 19 February 2009 We defined the transcriptomic and proteomic profiles of rat ageing skeletal muscle using a combined cDNA array, 2D- and Blue native-PAGE approach. This was allowed to obtain an overview of the interrelated events leading to the transcriptome/proteome/mitoproteome changes likely to underlie the structural/metabolic features of aged skeletal muscle. The main differences were found in genes/proteins related to energy metabolism, mitochondrial pathways, myofibrillar filaments, and detoxification. Concerning the abundance of mitochondrial OXPHOS complexes as well as their supramolecular organization and activity, mitochondria from old rats, when compared with those from young rats, contained significantly lower amounts of complex I (NADH:ubiquinone oxidoreductase), V (FoF1-ATP synthase), and III (ubiquinol:cytochrome c oxidoreductase). The same mitochondria contained a significantly larger amount of complex II (succinate:ubiquinone oxidoreductase), but an unchanged amount of complex IV (cytochrome c oxidase, COX). When comparing the supercomplex profiles between young and old muscle mitochondria, the densitometric analysis revealed that lighter supercomplexes were significantly reduced in older mitochondria, and that in the older group the major supercomplex bands were those representing heavier supercomplexes, likely suggesting a compensatory mechanism that, in ageing muscle, is functionally directed towards substrate channeling and catalytic enhancement advantaging the respirosome. © 2009 Elsevier B.V. All rights reserved. Keywords: Rat gastrocnemius muscle Two-dimensional gel electrophoresis Blue native Page cDNA array 1. Introduction Normal aging in humans and other animal species is asso- ciated with a physiological decline in skeletal muscle mass [1]. Muscle loss at a later age (also known as sarcopenia) is associated with numerous health consequences (such as alterations in muscle strength, quality, and functionality), leading to an increased prevalence of falls and fractures, greater morbidity, and loss of autonomy. Sarcopenia can be considered to be the consequence of complex multifactorial processes [2] that are still not com- pletely understood. The reduction in muscle mass — which is associated with alterations in muscle cross-sectional and physiological areas, and in voluntary force and relaxation rate JOURNAL OF PROTEOMICS 72 (2009) 708 – 721 ⁎ Corresponding authors. Moreno is to be contacted at Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy. Tel. +39 0824 305124; fax: +39 0824 23013. de Lange, Dipartimento di Scienze della Vita, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy. Tel.: +39 0823 274580; fax: +39 0823 274570. E-mail addresses: pieter.delange@unina2.it (P. de Lange), moreno@unisannio.it (M. Moreno). 1 These two authors contributed equally to the manuscript. 1874-3919/$ – see front matter © 2009 Elsevier B.V. All rights reserved. doi:10.1016/j.jprot.2009.02.007 available at www.sciencedirect.com www.elsevier.com/locate/jprot