Gene expression profiles displayed by peripheral blood mononuclear cells from patients with type 2 diabetes mellitus focusing on biological processes implicated on the pathogenesis of the disease Fernanda S. Manoel-Caetano a, b, 1 , Danilo J. Xavier b, 1 , Adriane F. Evangelista b , Paula Takahashi b , Cristhianna V. Collares b , Denis Puthier c , Maria C. Foss-Freitas d , Milton C. Foss d , Eduardo A. Donadi d , Geraldo A. Passos b, e , Elza T. Sakamoto-Hojo a, b, ⁎ a Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo — USP, Ribeirão Preto, SP, Brazil b Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo — USP, Ribeirão Preto, SP, Brazil c Inserm U928, TAGC, Aix–Marseille Université IFR137, Marseille, France d Department of Medical Clinic, Faculty of Medicine of Ribeirão Preto, University of São Paulo — USP, Ribeirão Preto, SP, Brazil e Department of Morphology, Stomatology, and Physiology, School of Dentistry of Ribeirão Preto, University of São Paulo — USP, Ribeirão Preto, SP, Brazil abstract article info Article history: Accepted 11 September 2012 Available online 2 October 2012 Keywords: Type 2 diabetes mellitus Gene expression Inflammatory response Oxidative stress DNA repair Gene set analysis Patients with type 2 diabetes mellitus (T2DM) exhibit insulin resistance associated with obesity and inflamma- tory response, besides an increased level of oxidative DNA damage as a consequence of the hyperglycemic con- dition and the generation of reactive oxygen species (ROS). In order to provide information on the mechanisms involved in the pathophysiology of T2DM, we analyzed the transcriptional expression patterns exhibited by peripheral blood mononuclear cells (PBMCs) from patients with T2DM compared to non-diabetic subjects, by investigating several biological processes: inflammatory and immune responses, responses to oxidative stress and hypoxia, fatty acid processing, and DNA repair. PBMCs were obtained from 20 T2DM patients and eight non-diabetic subjects. Total RNA was hybridized to Agilent whole human genome 4×44K one-color oligo- microarray. Microarray data were analyzed using the GeneSpring GX 11.0 software (Agilent). We used BRB- ArrayTools software (gene set analysis — GSA) to investigate significant gene sets and the Genomica tool to study a possible influence of clinical features on gene expression profiles. We showed that PBMCs from T2DM patients presented significant changes in gene expression, exhibiting 1320 differentially expressed genes compared to the control group. A great number of genes were involved in biological processes implicated in the pathogenesis of T2DM. Among the genes with high fold-change values, the up-regulated ones were associated with fatty acid metabolism and protection against lipid-induced oxidative stress, while the down-regulated ones were implicated in the suppression of pro-inflammatory cytokines production and DNA repair. Moreover, we identified two significant signaling pathways: adipocytokine, related to insulin resistance; and ceramide, related to oxidative stress and induction of apoptosis. In addition, expression profiles were not influenced by patient features, such as age, gender, obesity, pre/post-menopause age, neuropathy, glycemia, and HbA 1c percentage. Hence, by studying expression profiles of PBMCs, we provided quantitative and qualitative differences and similarities between T2DM patients and non-diabetic individuals, contributing with new perspectives for a better understanding of the disease. © 2012 Elsevier B.V. All rights reserved. 1. Introduction Type 2 diabetes mellitus (T2DM) is described as a progressive meta- bolic syndrome characterized by an initial peripheral insulin resistance in adipose tissue, liver, and skeletal muscle, and subsequent pancreatic beta cells dysfunction in an attempt to compensate for insulin resistance (Saltiel, 2001). The development of insulin resistance and the disease progression have both been associated with obesity (Stumvoll et al., 2005; Kahn et al., 2006; Belkina and Denis, 2010). According to the World Health Organization, about 90% of diabetic patients develop T2DM mainly because of excess body weight (WHO, 2011). The world Gene 511 (2012) 151–160 Abbreviations: BMI, body mass index; FA, fatty acid; FC, fold-change; FFA, free fatty acid; GO, gene ontology; GSA, gene set analysis; HbA 1c , glycated hemoglobin; IGA, individual gene analysis; IKK, I-kappa-B kinase; IL, interleukin; IRS, insulin receptor substrate; JNK, c-jun N-terminal kinase; NF-κB, nuclear factor-kappa B; OGTT, oral glucose tolerance test; OXPHOS, oxidative phosphorylation; PBMC, peripheral blood mononuclear cell; PCNA, proliferating cell nuclear antigen; RIN, RNA integrity number; ROS, reactive oxygen species; SOCs, suppressors of cytokine signaling; T2DM, type 2 diabetes mellitus; TLR, toll-like receptor; TNFα, tumor necrosis factor-alpha. ⁎ Corresponding author at: Department of Biology — Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo — USP, Ribeirão Preto, SP, Av. Bandeirantes, 3900, Monte Alegre, 14040-901, Ribeirão Preto/SP, Brazil. Tel.: +55 16 3602 3827; fax: +55 16 3602 0222. E-mail address: etshojo@usp.br (E.T. Sakamoto-Hojo). 1 These authors contributed equally to this work. 0378-1119/$ – see front matter © 2012 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.gene.2012.09.090 Contents lists available at SciVerse ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene