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Woerner J, Sriram V, Nam Y, Verma A, Kim D. Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network. Bioinformatics 2024; 40:btae126. [PMID: 38527901 PMCID: PMC10963079 DOI: 10.1093/bioinformatics/btae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/17/2024] [Indexed: 03/27/2024] Open
Abstract
MOTIVATION Many diseases, particularly cardiometabolic disorders, exhibit complex multimorbidities with one another. An intuitive way to model the connections between phenotypes is with a disease-disease network (DDN), where nodes represent diseases and edges represent associations, such as shared single-nucleotide polymorphisms (SNPs), between pairs of diseases. To gain further genetic understanding of molecular contributors to disease associations, we propose a novel version of the shared-SNP DDN (ssDDN), denoted as ssDDN+, which includes connections between diseases derived from genetic correlations with intermediate endophenotypes. We hypothesize that a ssDDN+ can provide complementary information to the disease connections in a ssDDN, yielding insight into the role of clinical laboratory measurements in disease interactions. RESULTS Using PheWAS summary statistics from the UK Biobank, we constructed a ssDDN+ revealing hundreds of genetic correlations between diseases and quantitative traits. Our augmented network uncovers genetic associations across different disease categories, connects relevant cardiometabolic diseases, and highlights specific biomarkers that are associated with cross-phenotype associations. Out of the 31 clinical measurements under consideration, HDL-C connects the greatest number of diseases and is strongly associated with both type 2 diabetes and heart failure. Triglycerides, another blood lipid with known genetic causes in non-mendelian diseases, also adds a substantial number of edges to the ssDDN. This work demonstrates how association with clinical biomarkers can better explain the shared genetics between cardiometabolic disorders. Our study can facilitate future network-based investigations of cross-phenotype associations involving pleiotropy and genetic heterogeneity, potentially uncovering sources of missing heritability in multimorbidities. AVAILABILITY AND IMPLEMENTATION The generated ssDDN+ can be explored at https://hdpm.biomedinfolab.com/ddn/biomarkerDDN.
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Affiliation(s)
- Jakob Woerner
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Vivek Sriram
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Anurag Verma
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
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Woerner J, Sriram V, Nam Y, Verma A, Kim D. Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.11.23289852. [PMID: 37293013 PMCID: PMC10246076 DOI: 10.1101/2023.05.11.23289852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many diseases exhibit complex multimorbidities with one another. An intuitive way to model the connections between phenotypes is with a disease-disease network (DDN), where nodes represent diseases and edges represent associations, such as shared single-nucleotide polymorphisms (SNPs), between pairs of diseases. To gain further genetic understanding of molecular contributors to disease associations, we propose a novel version of the shared-SNP DDN (ssDDN), denoted as ssDDN+, which includes connections between diseases derived from genetic correlations with endophenotypes. We hypothesize that a ssDDN+ can provide complementary information to the disease connections in a ssDDN, yielding insight into the role of clinical laboratory measurements in disease interactions. Using PheWAS summary statistics from the UK Biobank, we constructed a ssDDN+ revealing hundreds of genetic correlations between disease phenotypes and quantitative traits. Our augmented network uncovers genetic associations across different disease categories, connects relevant cardiometabolic diseases, and highlights specific biomarkers that are associated with cross-phenotype associations. Out of the 31 clinical measurements under consideration, HDL-C connects the greatest number of diseases and is strongly associated with both type 2 diabetes and diabetic retinopathy. Triglycerides, another blood lipid with known genetics causes in non-mendelian diseases, also adds a substantial number of edges to the ssDDN. Our study can facilitate future network-based investigations of cross-phenotype associations involving pleiotropy and genetic heterogeneity, potentially uncovering sources of missing heritability in multimorbidities.
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Affiliation(s)
- Jakob Woerner
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vivek Sriram
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Wiśniewski OW, Dydowicz F, Salamaga S, Skulik P, Migaj J, Kałużna-Oleksy M. Risk Factors Predisposing to Angina in Patients with Non-Obstructive Coronary Arteries: A Retrospective Analysis. J Pers Med 2022; 12:jpm12071049. [PMID: 35887545 PMCID: PMC9318432 DOI: 10.3390/jpm12071049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
No hemodynamically significant atherosclerotic plaques are observed in up to 30% of patients reporting angina and undergoing coronary angiography. To investigate risk factors associated with non-obstructive coronary artery disease (NOCAD), we analyzed the medical records of, consecutively, 136 NOCAD subjects and 128 patients with significant stenosis in at least one coronary artery (the OCAD group). The blood concentrations of the TC (4.40 [3.78−5.63] mmol/L vs. 4.12 [3.42−5.01] mmol/L; p = 0.026), LDL-C (2.32 [1.80−3.50] mmol/L vs. 2.10 [1.50−2.70] mmol/L; p = 0.003), non-HDL-C (2.89 [2.29−4.19] mmol/L vs. 2.66 [2.06−3.39] mmol/L; p = 0.045), as well as the LDL-C/HDL-C ratio (1.75 [1.22−2.60] vs. 1.50 [1.10−1.95]; p = 0.018) were significantly increased in the NOCAD patients compared to the OCAD group due to the lower prevalence and intensity of the statin therapy in the NOCAD individuals (p < 0.001). Moreover, the abovementioned lipid parameters appeared to be valuable predictors of NOCAD, with the LDL-C (OR = 1.44; 95%CI = 1.14−1.82) and LDL-C/HDL-C (OR = 1.51; 95%CI = 1.13−2.02) showing the highest odds ratios. Furthermore, multivariable logistic regression models determined female sex as the independent risk factor for NOCAD (OR = 2.37; 95%CI = 1.33−4.20). Simultaneously, arterial hypertension substantially lowered the probability of NOCAD (OR = 0.21; 95%CI = 0.10−0.43). To conclude, female sex, the absence of arterial hypertension, as well as increased TC, LDL-C, non-HDL, and LDL-C/HDL-C ratio are risk factors for NOCAD in patients reporting angina, potentially as a result of poor hypercholesterolemia management.
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Affiliation(s)
- Oskar Wojciech Wiśniewski
- Faculty of Medicine, Poznan University of Medical Sciences, 10 Fredry Street, 61-701 Poznan, Poland; (F.D.); (S.S.); (P.S.)
- Correspondence:
| | - Franciszek Dydowicz
- Faculty of Medicine, Poznan University of Medical Sciences, 10 Fredry Street, 61-701 Poznan, Poland; (F.D.); (S.S.); (P.S.)
| | - Szymon Salamaga
- Faculty of Medicine, Poznan University of Medical Sciences, 10 Fredry Street, 61-701 Poznan, Poland; (F.D.); (S.S.); (P.S.)
| | - Przemysław Skulik
- Faculty of Medicine, Poznan University of Medical Sciences, 10 Fredry Street, 61-701 Poznan, Poland; (F.D.); (S.S.); (P.S.)
| | - Jacek Migaj
- 1st Department of Cardiology, Poznan University of Medical Sciences, 1/2 Dluga Street, 61-848 Poznan, Poland; (J.M.); (M.K.-O.)
| | - Marta Kałużna-Oleksy
- 1st Department of Cardiology, Poznan University of Medical Sciences, 1/2 Dluga Street, 61-848 Poznan, Poland; (J.M.); (M.K.-O.)
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Abstract
The clinical relevance of lipoprotein(a) (Lp(a)) as a cardiovascular risk factor is currently underestimated. The aim of our study was to assess the influence of increased Lp(a) values on the development and severity of coronary artery disease (CAD).In our retrospective analysis of 31,274 patients, who were hospitalized for the first time, we compared patients with isolated increased Lp(a) (> 110 mg/dl) and normal Lp(a) (< 30 mg/dl), with increased Lp(a) concentrations (30-60 mg/dl, 61-90 mg/dl, 91-110 mg/dl), and in a third analysis with additionally increased LDL cholesterol and HbA1c values.Patients with high Lp(a) levels showed a significantly higher incidence of advanced CAD with a three-vessel disease being present in 50.2 vs. 25.1 %. Patients with high Lp(a) levels had a significantly more frequent history of myocardial infarction (34.6 vs. 16.6 %, p < 0.001), surgical myocardial revascularization (40.8 vs. 20.8 %, p < 0.001) and percutaneous coronary intervention (55.3 vs. 33.6 %, p < 0.001). In addition, there was a marked difference in gender to the disadvantage of male patients regarding development and severity of CAD. CAD risk (Odds ratio) was increased 5.5-fold in patients with Lp(a) ≥ 110 mg/dl. Additionally elevated LDL and HbA1c levels were not associated with increased manifestation and severity of CAD.High Lp(a) concentration leads to an increased manifestation and severity of coronary artery disease. Additional risk factors do not aggravate manifestation of CAD.
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Rajasekhar D, Saibaba KSS, Srinivasa Rao PVLN, Latheef SAA, Subramanyam G. Lipoprotein (A): Better assessor of coronary heart disease risk in south Indian population. Indian J Clin Biochem 2012; 19:53-9. [PMID: 23105457 DOI: 10.1007/bf02894258] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an attempt to search for risk factors which can explain the increasing prevalence of coronary heart disease (CHD) in Indian population, we conducted a case-control study to assess the association of Lipoprotein (a)(Lp(a)) with CHD. One hundred and fifty one consecutive patients with clinical and angiographic evidence of CHD and forty-nine healthy controls were drawn for the study. Triglycerides, very low density cholesterol (VLDL-C), total cholesterol (total-C)/high density cholesterol (HDL-C) ratio, low density cholesterol (LDL-C)/HDL cholesterol ratio and Lp(a) were found to be higher in patients than controls. In female sex and in those with family history of CHD, higher total and LDL cholesterol levels were observed to be associated with higher Lp(a) levels. Lp(a) levels were also found to be higher in triple vessel disease than other vessel disease patients. Significant difference in Lp(a) levels were observed between normal coronaries vs. single and triple vessel disease(P<0.05) and also between single vs. double and triple vessel disease (P<0.01).Lp(a) levels correlated positively with vessel severity(P<0.005). Lp(a) levels >25 mg/dl were associated with coronary heart disease (Odds ratio 1.98 P<0.05 95% CI 0.007-1.18). Our findings suggest a cut-off level of 25mg/dl for determination of risk of CHD. Studies from different areas involving larger sample size are needed to confirm the findings of the present study.
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Affiliation(s)
- D Rajasekhar
- Department of Cardiology, Sri Venkatesware Institute of Medical Sciences, 517507 Tirupati, India
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Lin CP, Lin WT, Leu HB, Wu TC, Chen JW. Differential mononuclear cell activity and endothelial inflammation in coronary artery disease and cardiac syndrome X. Int J Cardiol 2003; 89:53-62. [PMID: 12727005 DOI: 10.1016/s0167-5273(02)00428-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Circulating mononuclear cells could be activated with endothelial inflammation in patients with coronary artery disease (CAD). In some patients with normal coronary angiograms, myocardial ischemia could also present with coronary microvascular dysfunction (cardiac syndrome X). This study was undertaken to investigate whether mononuclear cell activation and endothelial inflammation can present in syndrome X patients. METHODS We evaluated the biochemical parameters, circulating soluble adhesion molecules, circulating superoxide free radicals, and mononuclear cell activity in 32 patients with syndrome X, 34 with angiographically documented CAD, and 17 age- and gender-matched healthy control subjects. RESULTS Compared to that in control subjects, plasma high-density lipoprotein was reduced (P<0.001) and insulin to glucose ratio increased (P=0.02) in CAD patients. Circulating level of soluble intracellular adhesion molecule-1 was significantly higher in both syndrome X and CAD patients than in control subjects (P<0.01), whereas the levels of soluble vascular cell adhesion molecule (P=0.02) and von Willebrand factor (P=0.01) were increased in CAD patients only. The peak (P<0.001) and total counts of superoxide free radicals in whole blood (P<0.001) was significantly higher in syndrome X patients than in the other two groups. However, phorbol-12-myristate-13-acetate-induced superoxide free radical generation of mononuclear cells was increased in CAD (10.5+/-4.6%, P=0.01) but not in syndrome X patients (8.7+/-2.0%) as compared with control subjects (7.7+/-0.5%). CONCLUSIONS The results indicated that the activity of mononuclear cells was increased with significant endothelial inflammation and injury in CAD patients. In syndrome X patients, though circulating superoxide free radicals were increased, there was minimal endothelial inflammation without mononuclear cell activation. The relatively preserved lipid and metabolic profiles might contribute to less vascular inflammation in syndrome X patients.
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Affiliation(s)
- Chih-Pei Lin
- Department of Pathology, Taipei Veterans General Hospital, 201 Shih-Pai Road Section 2, Taipei, Taiwan 11217, ROC
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Stalikas CD, Konidari CN. Analysis of malondialdehyde in biological matrices by capillary gas chromatography with electron-capture detection and mass spectrometry. Anal Biochem 2001; 290:108-15. [PMID: 11180944 DOI: 10.1006/abio.2000.4951] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A gas chromatographic method is described for the quantification of free and total malondialdehyde (MDA) in biological materials. The procedure involves derivatization of the analyte with 2,4,6-trichlorophenylhydrazine, extraction with n-hexane, and separation of the cyclic derivatization product on a OV-5 gas chromatographic column. Concentration of the derivatization reagent, pH, reaction time, and temperature were investigated to determine the optimal derivatization conditions. Under these conditions, the method allows for the selective detection of free and total MDA at femtomole levels in several biological materials without any interferences. The procedure yields relative standard deviation values for the intra- and interassays in the range 3.3 and 3.9%, respectively, for the electron-capture and mass-selective (SIM mode) detection systems. Recoveries of MDA from spiked matrices reached 96%. The present method offers the advantage of the alternative use of either electron-capture or mass-selective detection. Furthermore it avoids overestimation of MDA since it employs mild conditions for sample processing and there is no need for preventing protein separation for the assessment of free MDA.
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Affiliation(s)
- C D Stalikas
- Department of Chemistry, University of Ioannina, Ioannina, 45 110, Greece
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Clark LT, Ferdinand KC, Flack JM, Gavin JR, Hall WD, Kumanyika SK, Reed JW, Saunders E, Valantine HA, Watson K, Wenger NK, Wright JT. Coronary heart disease in African Americans. HEART DISEASE (HAGERSTOWN, MD.) 2001; 3:97-108. [PMID: 11975778 DOI: 10.1097/00132580-200103000-00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
African Americans have the highest overall mortality rate from coronary heart disease (CHD) of any ethnic group in the United States, particularly out-of-hospital deaths, and especially at younger ages. Although all of the reasons for the excess CHD mortality among African Americans have not been elucidated, it is clear that there is a high prevalence of certain coronary risk factors, delay in the recognition and treatment of high-risk individuals, and limited access to cardiovascular care. The clinical spectrum of acute and chronic CHD in African Americans is similar to that in whites. However, African Americans have a higher risk of sudden cardiac death and present more often with unstable angina and non-Q-wave myocardial infarction than whites. African Americans have less obstructive coronary artery disease on angiography, but may have a similar or greater total burden of coronary atherosclerosis. Ethnic differences in the clinical manifestations of CHD may be explained largely by the inherent heterogeneity of the coronary syndromes, and the disproportionately high prevalence and severity of hypertension and type 2 diabetes in African Americans. Identification of high-risk individuals for vigorous risk factor modification-especially control of hypertension, regression of left ventricular hypertrophy, control of diabetes, treatment of dyslipidemia, and smoking cessation--is key for successful risk reduction.
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Affiliation(s)
- L T Clark
- Division of Cardiovascular Medicine, State University of New York Health Science Center, Brooklyn, New York, USA
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Desideri G, Gaspardone A, Gentile M, Santucci A, Gioffrè PA, Ferri C. Endothelial activation in patients with cardiac syndrome X. Circulation 2000; 102:2359-64. [PMID: 11067789 DOI: 10.1161/01.cir.102.19.2359] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The presence of endothelial dysfunction with increased endothelin-1 plasma concentrations in patients with cardiac syndrome X is still under debate. The aim of the present study was to evaluate the presence of endothelial dysfunction in patients with cardiac syndrome X. METHODS AND RESULTS ++Endothelin-1 levels were evaluated with a sensitive radioimmunoassay with previous purification through reverse phase HPLC in 24 patients (3 men and 21 women, mean age 54+/-7 years) with typical angina, instrumental evidence of ischemia, and normal coronary angiograms both under baseline conditions and after oral glucose load (75 g D-glucose). We also measured plasma nitrite-plus-nitrate levels, a sharp index of endothelial nitric oxide production, and circulating concentrations of the soluble fraction of the endothelial adhesion molecule vascular cell adhesion molecule-1, a well-recognized marker of early endothelial dysfunction. Fourteen healthy subjects (1 man and 13 women, mean age 47+/-15 years) served as controls. There were no significant differences in baseline plasma endothelin-1 concentrations between patients and control subjects (0.55+/-0.34 versus 0.48+/-0.22 pg/mL, P=0.503). Plasma nitrite-plus-nitrate and soluble vascular cell adhesion molecule-1 concentrations were also similar between the 2 groups. After glucose ingestion, circulating endothelin-1 concentrations were significantly higher in patients with cardiac syndrome X than in control subjects (P<0.03 at 60, 90, and 120 minutes). CONCLUSIONS Our findings show that no basal endothelial damage is present in patients with cardiac syndrome X. Nevertheless, increased responsiveness of endothelin-1 to glucose loading suggests that patients with cardiac syndrome X present an increased susceptibility to releasing endothelin-1 under stressful circumstances.
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Affiliation(s)
- G Desideri
- Department of Internal Medicine and Public Health, University of L'Aquila, L'Aquila, Italy.
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