B cell–derived chronic lymphocytic leukemia (B-CLL) represents a common malignancy whose cell derivation and pathogenesis are unknown. Recent studies have shown that >50% of CLLs display hypermutated immunoglobulin variable region (IgV) sequences and a more favorable prognosis, suggesting that they may represent a distinct subset of CLLs which have transited through germinal centers (GCs), the physiologic site of IgV hypermutation. To further investigate the phenotype of CLLs, their cellular derivation and their relationship to normal B cells, we have analyzed their gene expression profiles using oligonucleotide-based DNA chip microarrays representative of ∼12,000 genes. The results show that CLLs display a common and characteristic gene expression profile that is largely independent of their IgV genotype. Nevertheless, a restricted number of genes (<30) have been identified whose differential expression can distinguish IgV mutated versus unmutated cases and identify them in independent panels of cases. Comparison of CLL profiles with those of purified normal B cell subpopulations indicates that the common CLL profile is more related to memory B cells than to those derived from naive B cells, CD5+ B cells, and GC centroblasts and centrocytes. Finally, this analysis has identified a subset of genes specifically expressed by CLL cells of potential pathogenetic and clinical relevance.

Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound pairs, from the most synergistic to the most antagonistic, based on gene-expression profiles of human B cells treated with individual compounds at multiple time points and concentrations. Using scoring metrics based on experimental dose-response curves, we assessed 32 methods (31 community-generated approaches and SynGen), four of which performed significantly better than random guessing. We highlight similarities between the methods. Although the accuracy of predictions was not optimal, we find that computational prediction of compound-pair activity is possible, and that community challenges can be useful to advance the field of in silico compound-synergy prediction.

Summary Genome-wide identification of the mechanism of action (MoA) of small-molecule compounds characterizing their targets, effectors, and activity modulators, represents a highly relevant yet elusive goal, with critical implications for assessment of compound efficacy and toxicity. Current approaches are labor-intensive and mostly limited to elucidating high-affinity binding target proteins. We introduce a regulatory network-based approach that elucidates genome-wide MoA proteins based on the assessment of the global dysregulation of their molecular interactions following compound perturbation. Analysis of cellular perturbation profiles identified established MoA proteins for 70% of the tested compounds and elucidated novel proteins that were experimentally validated. Finally, unknown-MoA compound analysis revealed altretamine, an anticancer drug, as an inhibitor of glutathione peroxidase 4 lipid repair activity, which was experimentally confirmed, thus revealing unexpected similarity to the activity of sulfasalazine. This suggests that regulatory network analysis can provide valuable mechanistic insight into the elucidation of small molecule MoA and compound similarity.

Patients with hereditary hemochromatosis (HH), a disease characterized by a progressive iron overload that is responsible for all of its clinical manifestations, are at high risk of developing liver cancer. 1-3 It has been suggested that iron plays a key role in the occurrence of hepatic cancer although, in most cases, it develops several years after iron depletion. [4][5][6] The possible role of iron as a factor facilitating the development of liver cancer has been also suggested by the finding of increased iron content in the non-neoplastic livers of non-HH patients undergoing liver transplantation for hepatocellular carcinoma (HCC). 7 It has long been debated whether excess iron also facilitates the occurrence of extrahepatic cancers in patients with or without HH. In comparison with the general population, a significantly higher risk of esophageal cancer and skin melanoma has been found in Danish HH patients, 8 and of lung and intestinal cancer in a series of English HH patients 9 ; however, no increased risk of extrahepatic cancer was found in Australian HH patients against those with chronic liver diseases of different etiology. 10 In addition, an increased risk of colorectal and gastric cancers and hematologic malignancies was found in a large series of subjects heterozygous for HH. 11 To verify whether excess iron facilitates the development of liver and nonliver cancers, we prospectively followed 230 HH patients and compared the cancer development rate with that observed in a group of patients with histologically proven non-iron-related chronic liver disease (CLD), matched by sex, age, duration of follow-up, and the severity of the clinical findings. PATIENTS AND METHODS PatientsTwo hundred thirty consecutive patients with HH and all consecutive patients with non-iron-related CLD attending our outpatient liver unit were enrolled in the study between January 1975 and December 1996 and were prospectively followed-up until December 1998 (censoring date). Each HH patient was matched individually to a control case according to age (Ϯ5 years), sex, duration of follow-up (Ϯ5 years), and the severity of liver disease.Hereditary Hemochromatosis Group. The diagnosis of HH was based on standard criteria including exclusion of known causes of iron overload, hepatic iron index (liver iron concentration/age) greater than 1.9, iron removed by weekly phlebotomy to reach the depletion greater than 5 g in men and greater than 3 g in women, and presence of a gradient of liver siderosis from periportal hepatocytes to centrolobular veins. 12 Furthermore, genetic studies of HFE mutations were performed in 200 patients: 62% were homozygotes and 6% heterozygotes for the C282Y mutation; 4% were compound heterozygotes for C282Y and H63D mutations, and 28% carried a wildtype HFE genotype. In Table 1 we report the baseline transferrin saturation percentage, serum ferritin, hepatic iron index, and the amount of iron removed to reach iron depletion of HH patients

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Sporadic porphyria cutanea tarda (PCT) is caused by a reduced activity of uroporphyrinogen decarboxylase (URO-D) in the liver. Mild to moderate iron overload is common in PCT, as iron is one of the factors which trigger the clinical manifestations of the disease through the inactivation of URO-D. A role for genetic hemochromatosis in the development of iron overload in sporadic PCT has been hypothesized in the past. The aim of this work was to investigate whether mutations of HFE, which is a candidate gene for hemochromatosis, play the role of genetic susceptibility factors for PCT in Italian patients, who have a high prevalence of acquired triggering factors, such as hepatitis C virus (HCV) chronic infection and alcohol. We determined HFE genotypes of 68 male patients with PCT. Our data do not confirm an association of PCT with the Cys282Tyr HFE mutation, strongly associated with hemochromatosis in Northern European countries. A second mutation of HFE, His63Asp, however, had a significantly increased frequency as it was present in half of the patients. Surprisingly, the presence of the His63Asp mutation was not related to the iron status of patients, suggesting that a subtle abnormality of iron metabolism induced by this mutation could escape detection by the standard parameters of iron status. In PCT patients with liver disease, the presence of the mutation could contribute to the inactivation of URO-D, either directly or through a synergistic action with other factors that cause liver damage. (HEPATOLOGY 1998;27;181-184.)

Multiple myeloma (MM) is the most common form of plasma cell dyscrasia, characterized by a marked heterogeneity of genetic lesions and clinical course. It may develop from a premalignant condition (monoclonal gammopathy of undetermined significance, MGUS) or progress from intramedullary to extramedullary forms (plasma cell leukemia, PCL). To provide insights into the molecular characterization of plasma cell dyscrasias and to investigate the contribution of specific genetic lesions to the biological and clinical heterogeneity of MM, we analysed the gene expression profiles of plasma cells isolated from seven MGUS, 39 MM and six PCL patients by means of DNA microarrays. MMs resulted highly heterogeneous at transcriptional level, whereas the differential expression of genes mainly involved in DNA metabolism and proliferation distinguished MGUS from PCLs and the majority of MM cases. The clustering of MM patients was mainly driven by the presence of the most recurrent translocations involving the immunoglobulin heavy-chain locus. Distinct gene expression patterns have been found to be associated with different lesions: the overexpression of CCND2 and genes involved in cell adhesion pathways was observed in cases with deregulated MAF and MAFB, whereas genes upregulated in cases with the t(4;14) showed apoptosis-related functions. The peculiar finding in patients with the t(11;14) was the downregulation of the a-subunit of the IL-6 receptor. In addition, we identified a set of cancer germline antigens specifically expressed in a subgroup of MM patients characterized by an aggressive clinical evolution, a finding that could have implications for patient classification and immunotherapy.

Our data contribute to the understanding of the molecular and biologic features of distinct MM subtypes. The identification of a distinctive gene expression pattern in TC2 patients may improve risk stratification and indicate novel therapeutic targets.