Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases

AbstractBACKGROUND: Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult.PRINCIPAL FINDINGS: We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell.CONCLUSIONS: For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases.AVAILABILITY: The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download

Lateral periodontal cysts: a retrospective study of 11 cases

Objective: To describe the clinical, radiological and histopathological features of lateral periodontal cysts among patients diagnosed in different centers (Vall d"Hebron General Hospital, Granollers General Hospital, the Teknon Medical Center, and the Master of Oral Surgery and Implantology of the University of Barcelona Dental School; Barcelona, Spain). Study design: A retrospective observational study was made of 11 lateral periodontal cysts, all of which were diagnosed following a thorough clinical examination, radiological study and posterior histological study. Results: The mean patient age was 37 years, and males predominated over females. The mean lesion size was 1.25 cm. A single relapse was recorded 7 years after removal of the initial lesion. All the cysts were surgically removed. Discussion and conclusions: Lateral periodontal cysts are very infrequent, and are characterized by the preserved vitality of the adjacent teeth. Identification of the lesion is initially based on the clinical findings, though histological study is required to confirm the diagnosis. The treatment of choice is the surgical removal, though occasional relapses have been documented

Lateral periodontal cysts: a retrospective study of 11 cases

Objective: To describe the clinical, radiological and histopathological features of lateral periodontal cysts among patients diagnosed in different centers (Vall d"Hebron General Hospital, Granollers General Hospital, the Teknon Medical Center, and the Master of Oral Surgery and Implantology of the University of Barcelona Dental School; Barcelona, Spain). Study design: A retrospective observational study was made of 11 lateral periodontal cysts, all of which were diagnosed following a thorough clinical examination, radiological study and posterior histological study. Results: The mean patient age was 37 years, and males predominated over females. The mean lesion size was 1.25 cm. A single relapse was recorded 7 years after removal of the initial lesion. All the cysts were surgically removed. Discussion and conclusions: Lateral periodontal cysts are very infrequent, and are characterized by the preserved vitality of the adjacent teeth. Identification of the lesion is initially based on the clinical findings, though histological study is required to confirm the diagnosis. The treatment of choice is the surgical removal, though occasional relapses have been documented

Dental implications in oral cancer patients

Objectives. A study is made of the dental implications of oral cancer, with a view to avoiding the complications that appear once oncological treatment is started. Patients and Methods. The study comprised a total of 22 patients diagnosed with oral cancer according to clinical and histological criteria in the Service of Maxillofacial Surgery (Dental Clinic of the University of Barcelona, Spain) during the period 1996-2005, and posteriorly treated in different hospital centers in Barcelona. Results. Of the 22 patients diagnosed with oral cancer in our Service, the present study finally analyzed the 12 subjects who reported for the dental controls. As regards the remaining 10 patients, 5 had died and 5 could not be located; these subjects were thus excluded from the analysis. All of the smokers had abandoned the habit. The most common tumor location was the lateral margin of the tongue. None of the patients visited the dentist regularly before the diagnosis of oral cancer. T1N0M0 was the most common tumor stage. Surgery was carried out in 50% of the cases, while 8.4% of the patients received radiotherapy and 41.6% underwent surgery with postoperative radiotherapy. In turn, 66.6% of the patients reported treatment sequelae such as dysgeusia, xerostomia or speech difficulties, and one patient suffered osteoradionecrosis. Forty-one percent of the patients did not undergo regular dental controls after cancer treatment. As regards oral and dental health, 16.6% presented caries, and 50% had active periodontal disease. Conclusions. Protocols are available for preventing the complications of oral cancer treatment, and thus for improving patient quality of life. However, important shortcomings in the application of such protocols on the part of the public health authorities make it difficult to reach these objectives

Dental implications in oral cancer patients

Objectives. A study is made of the dental implications of oral cancer, with a view to avoiding the complications that appear once oncological treatment is started. Patients and Methods. The study comprised a total of 22 patients diagnosed with oral cancer according to clinical and histological criteria in the Service of Maxillofacial Surgery (Dental Clinic of the University of Barcelona, Spain) during the period 1996-2005, and posteriorly treated in different hospital centers in Barcelona. Results. Of the 22 patients diagnosed with oral cancer in our Service, the present study finally analyzed the 12 subjects who reported for the dental controls. As regards the remaining 10 patients, 5 had died and 5 could not be located; these subjects were thus excluded from the analysis. All of the smokers had abandoned the habit. The most common tumor location was the lateral margin of the tongue. None of the patients visited the dentist regularly before the diagnosis of oral cancer. T1N0M0 was the most common tumor stage. Surgery was carried out in 50% of the cases, while 8.4% of the patients received radiotherapy and 41.6% underwent surgery with postoperative radiotherapy. In turn, 66.6% of the patients reported treatment sequelae such as dysgeusia, xerostomia or speech difficulties, and one patient suffered osteoradionecrosis. Forty-one percent of the patients did not undergo regular dental controls after cancer treatment. As regards oral and dental health, 16.6% presented caries, and 50% had active periodontal disease. Conclusions. Protocols are available for preventing the complications of oral cancer treatment, and thus for improving patient quality of life. However, important shortcomings in the application of such protocols on the part of the public health authorities make it difficult to reach these objectives

Effectiveness of substituting cyclosporin A with tacrolimus in reducing gingival overgrowth in renal transplant patients

Objectives: This study aims to evaluate the effectiveness of periodontal therapy combined with tacrolimus in the suppression of gingival overgrowth (GO) and the effect on GO of changing from cyclosporin A to tacrolimus. Patients and Methods: Sixteen renal transplant patients, averaging 52 years of age, whose kidney function was stable and were receiving treatment with cyclosporin A, were randomly assigned to one of two groups. In the experimental group, patients were instructed in oral hygiene and underwent periodontal treatment, whereas in the control group, only oral hygiene instructions were given. After the first visit and the change of medication from cyclosporine to tacrolimus in both groups, periodic clinical revisions were carried out for 3 months in order to assess the evolution of GO. Results: All patients showed a progressive decrease in GO. There were no statistically significant differences between the two groups (p>0.05). A greater decrease in GO occurred within the first month after changing the medication. Conclusions: No improved effectiveness in reducing GO was observed for periodontal therapy in combination with tacrolimus. Tacrolimus is an alternative to cyclosporine when attempting to avoid GO in patients with kidney transplants

Diabetes mellitus, periapical inflammation and endodontic treatment outcome

The possible connection between chronic oral inflammatory processes, such as apical periodontitis and periodontal disease (PD), and systemic health is one of the most interesting aspects faced by the medical and dental scientific community. Chronic apical periodontitis shares important characteristics with PD: 1) both are chronic infections of the oral cavity, 2) the Gram-negative anaerobic microbiota found in both diseases is comparable, and 3) in both infectious processes increased local levels of inflammatory mediators may have an impact on systemic levels. One of the systemic disorders linked to PD is diabetes mellitus (DM); is therefore plausible to assume that chronic apical periodontitis and endodontic treatment are also associated with DM. The status of knowledge regarding the relationship between DM and endodontics is reviewed. Upon review, we conclude that there are data in the literature that associate DM with a higher prevalence of periapical lesions, greater size of the osteolityc lesions, greater likelihood of asymptomatic infections and worse prognosis for root filled teeth. The results of some studies suggest that periapical disease may contribute to diabetic metabolic dyscontrol

Recent human evolution has shaped geographical differences in susceptibility to disease

Background: Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies.Results: We report three main findings. First, contrary to previous results, genes associated to complex diseases present lower degrees of genetic differentiation among human populations than average genome-wide levels. Second, also contrary to previous results, the differences in replicability of disease associated-loci between Europeans and East Asians are highly correlated with genetic differentiation between these populations. Finally, highly replicated genes present increased levels of high-frequency derived alleles in European and Asian populations when compared to African populations. Conclusions: Our findings highlight the heterogeneous nature of the genetic etiology of complex disease, confirm the importance of the recent evolutionary history of our species in current patterns of disease susceptibility and could cast doubts on the status as false positives of some associations that have failed to replicate across populations.

Design and evaluation of a panel os single-nucleotide polymorphisms in microRNA genomic regions for association studies in human disease

MicroRNAs (miRNA) are recognized posttranscriptional gene repressors involved in the control of almost every biological process. Allelic variants in these regions may be an important source of phenotypic diversity and contribute to disease susceptibility. We analyzed the genomic organization of 325 human miRNAs (release 7.1, miRBase) to construct a panel of 768 single-nucleotide polymorphisms (SNPs) covering approximately 1 Mb of genomic DNA, including 131 isolated miRNAs (40%) and 194 miRNAs arranged in 48 miRNA clusters, as well as their 5-kb flanking regions. Of these miRNAs, 37% were inside known protein-coding genes, which were significantly associated with biological functions regarding neurological, psychological or nutritional disorders. SNP coverage analysis revealed a lower SNP density in miRNAs compared with the average of the genome, with only 24 SNPs located in the 325 miRNAs studied. Further genotyping of 340 unrelated Spanish individuals showed that more than half of the SNPs in miRNAs were either rare or monomorphic, in agreement with the reported selective constraint on human miRNAs. A comparison of the minor allele frequencies between Spanish and HapMap population samples confirmed the applicability of this SNP panel to the study of complex disorders among the Spanish population, and revealed two miRNA regions, hsa-mir-26a-2 in the CTDSP2 gene and hsa-mir-128-1 in the R3HDM1 gene, showing geographical allelic frequency variation among the four HapMap populations, probably because of differences in natural selection. The designed miRNA SNP panel could help to identify still hidden links between miRNAs and human disease.

Human disease and drug pharmacology, complex as real life

In the past decades drug discovery practice has escaped from the complexity of the formerly used phenotypic screening in animals to focus on assessing drug effects on isolated protein targets in the search for drugs that exclusively and potently hit one selected target, thought to be critical for a given disease, while not affecting at all any other target to avoid the occurrence of side-effects. However, reality does not conform to these expectations, and, conversely, this approach has been concurrent with increased attrition figures in late-stage clinical trials, precisely due to lack of efficacy and safety. In this context, a network biology perspective of human disease and treatment has burst into the drug discovery scenario to bring it back to the consideration of the complexity of living organisms and particularly of the (patho)physiological environment where protein targets are (mal)functioning and where drugs have to exert their restoring action. Under this perspective, it has been found that usually there is not one but several disease-causing genes and, therefore, not one but several relevant protein targets to be hit, which do not work on isolation but in a highly interconnected manner, and that most known drugs are inherently promiscuous. In this light, the rationale behind the currently prevailing single-target-based drug discovery approach might even seem a Utopia, while, conversely, the notion that the complexity of human disease must be tackled with complex polypharmacological therapeutic interventions constitutes a difficult-torefuse argument that is spurring the development of multitarget therapies.

The Rose Bengal test in human brucellosis: a neglected test for the diagnosis of a neglected disease

Brucellosis is a highly contagious zoonosis affecting livestock and human beings. The human disease lacks pathognomonic symptoms and laboratory tests are essential for its diagnosis. However, most tests are difficult to implement in the areas and countries were brucellosis is endemic. Here, we compared the simple and cheap Rose Bengal Test (RBT) with serum agglutination, Coombs, competitive ELISA, Brucellacapt, lateral flow immunochromatography for IgM and IgG detection and immunoprecipitation with Brucella proteins. We tested 208 sera from patients with brucellosis proved by bacteriological isolation, 20 contacts with no brucellosis, and 1559 sera of persons with no recent contact or brucellosis symptoms. RBT was highly sensitive in acute and long evolution brucellosis cases and this related to its ability to detect IgM, IgG and IgA, to the absence of prozones, and to the agglutinating activity of blocking IgA at the pH of the test. RBT was also highly specific in the sera of persons with no contact with Brucella. No test in this study outperformed RBT, and none was fully satisfactory in distinguishing contacts from infected patients. When modified to test serum dilutions, a diagnostic titer >4 in RBT resulted in 87.4% sensitivity (infected patients) and 100% specificity (contacts). We discuss the limitations of serological tests in the diagnosis of human brucellosis, particularly in the more chronic forms, and conclude that simplicity and affordability of RBT make it close to the ideal test for small and understaffed hospitals and laboratories.

Human disease and drug pharmacology, complex as real life

In the past decades drug discovery practice has escaped from the complexity of the formerly used phenotypic screening in animals to focus on assessing drug effects on isolated protein targets in the search for drugs that exclusively and potently hit one selected target, thought to be critical for a given disease, while not affecting at all any other target to avoid the occurrence of side-effects. However, reality does not conform to these expectations, and, conversely, this approach has been concurrent with increased attrition figures in late-stage clinical trials, precisely due to lack of efficacy and safety. In this context, a network biology perspective of human disease and treatment has burst into the drug discovery scenario to bring it back to the consideration of the complexity of living organisms and particularly of the (patho)physiological environment where protein targets are (mal)functioning and where drugs have to exert their restoring action. Under this perspective, it has been found that usually there is not one but several disease-causing genes and, therefore, not one but several relevant protein targets to be hit, which do not work on isolation but in a highly interconnected manner, and that most known drugs are inherently promiscuous. In this light, the rationale behind the currently prevailing single-target-based drug discovery approach might even seem a Utopia, while, conversely, the notion that the complexity of human disease must be tackled with complex polypharmacological therapeutic interventions constitutes a difficult-torefuse argument that is spurring the development of multitarget therapies.