Cellular and tissue defects associated with insulin resistance are coincident with transcriptional abnormalities and are improved after insulin sensitization with thiazolidinedione (TZD) PPAR␥ ligands. We characterized 72 human subjects by relating their clinical phenotypes with functional pathway alterations. We transcriptionally profiled 364 biopsies harvested before and after hyperinsulinemic-euglycemic clamp studies, at baseline and after 3-month TZD treatment. We have identified molecular and functional characteristics of insulin resistant subjects and distinctions between TZD treatment responder and nonresponder subjects. Insulin resistant subjects exhibited alterations in skeletal muscle (e.g., glycolytic flux and intramuscular adipocytes) and adipose tissue (e.g., mitochondrial metabolism and inflammation) that improved relative to TZD-induced insulin sensitization. Pre-TZD treatment expression of MLXIP in muscle and HLA-DRB1 in adipose tissue from insulin resistant subjects was linearly predictive of post-TZD insulin sensitization. We have uniquely characterized coordinated cellular and tissue functional pathways that are characteristic of insulin resistance, TZD-induced insulin sensitization, and potential TZD responsiveness. muscle and adipose tissue ͉ transcriptional mechanisms ͉ diabetes ͉ branched chain amino acid (BCAA) ͉ inflammation I nsulin resistance is a pathological state in which insulin action is impaired in target tissues including liver, skeletal muscle, and adipose tissue. Insulin resistance is a defining feature of the metabolic syndrome and the primary defect leading to type 2 diabetes (1, 2). Impaired insulin-stimulated glucose uptake in skeletal muscle and lipid metabolism in adipocytes are central characteristics of insulin-resistance. Other manifestations of the condition include elevated intramuscular fat content (3), dysregulation of adipokine secretion, and chronic lowgrade inflammation in adipose tissue (4). Macrophage infiltration in adipose tissue activates inflammatory pathways that induce insulin resistance and modulate the effects of adipose tissue on whole-body metabolism (5). Several studies have shown that decreased mitochondrial protein and oxidative phosphorylation (OXPHOS) in skeletal muscle and adipocytes are also underlying factors of insulin resistance (6, 7).Thiazolidinediones (TZDs) are insulin-sensitizing drugs used to treat type 2 diabetes. TZDs enhance insulin sensitivity by improving glucose and lipid metabolism, altering adipokine secretion, and reducing adipose tissue inflammation (4, 8). Although TZDs improve insulin sensitivity and the glycemic, lipid, and inflammatory profiles of most patients, approximately 30% of diabetic subjects do not respond to TZD treatment, as gauged by fasting plasma glucose or HbA1c levels (9, 10). TZDs are ligands of peroxisome proliferator-activated receptor gamma (PPAR␥) through which they alter the expression of hundreds of genes in skeletal muscle, adipocytes, and macrophages. PPAR␥-mediated gene regulation is the predom...