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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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Heim M, Nixon IJ, Emmerson E, Callanan A. From hormone replacement therapy to regenerative scaffolds: A review of current and novel primary hypothyroidism therapeutics. Front Endocrinol (Lausanne) 2022; 13:997288. [PMID: 36277721 PMCID: PMC9581390 DOI: 10.3389/fendo.2022.997288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Primary hypothyroidism severely impacts the quality of life of patients through a decrease in the production of the thyroid hormones T3 and T4, leading to symptoms affecting cardiovascular, neurological, cognitive, and metabolic function. The incidence rate of primary hypothyroidism is expected to increase in the near future, partially due to increasing survival of patients that have undergone radiotherapy for head and neck cancer, which induces this disease in over half of those treated. The current standard of care encompasses thyroid hormone replacement therapy, traditionally in the form of synthetic T4. However, there is mounting evidence that this is unable to restore thyroid hormone signaling in all tissues due to often persistent symptoms. Additional complications are also present in the form of dosage difficulties, extensive drug interactions and poor patience compliance. The alternative therapeutic approach employed in the past is combination therapy, which consists of administration of both T3 and T4, either synthetic or in the form of desiccated thyroid extract. Here, issues are present regarding the lack of regulation concerning formulation and lack of data regarding safety and efficacy of these treatment methods. Tissue engineering and regenerative medicine have been applied in conjunction with each other to restore function of various tissues. Recently, these techniques have been adapted for thyroid tissue, primarily through the fabrication of regenerative scaffolds. Those currently under investigation are composed of either biopolymers or native decellularized extracellular matrix (dECM) in conjunction with either primary thyrocytes or stem cells which have undergone directed thyroid differentiation. Multiple of these scaffolds have successfully restored an athyroid phenotype in vivo. However, further work is needed until clinical translation can be achieved. This is proposed in the form of exploration and combination of materials used to fabricate these scaffolds, the addition of peptides which can aid restoration of tissue homeostasis and additional in vivo experimentation providing data on safety and efficacy of these implants.
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Affiliation(s)
- Maria Heim
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Nixon
- Department of ENT, Head and Neck Surgery, NHS Lothian, Edinburgh, United Kingdom
| | - Elaine Emmerson
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anthony Callanan
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Anthony Callanan,
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Ingoe LE, Hickey J, Pearce S, Rapley T, Razvi S, Wilkes S, Hrisos S. Older patients' experience of primary hypothyroidism: A qualitative study. Health Expect 2018; 21:628-635. [PMID: 29464870 PMCID: PMC5980608 DOI: 10.1111/hex.12656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Primary hypothyroidism is a common endocrine disorder, more so in an increasing UK ageing population. There is no qualitative research examining the older patient perspective of symptoms, treatment and self-management of hypothyroidism. OBJECTIVE In this study we explored the experience of hypothyroidism in older people and examined how this may influence their understanding and acceptance of diagnosis, treatment with Levothyroxine and the monitoring process. DESIGN We conducted semi-structured interviews with 18 participants aged between 80 and 93 years. Interview transcripts were analysed using a thematic approach. RESULTS The themes involved older individuals' knowledge about symptoms, confidence in diagnosis and understanding of clinical management regimen to understand hypothyroidism. Interpretation of the themes was informed by the Health Belief Model. CONCLUSION Our findings can help to inform the development of interventions by treating clinicians and support staff to engage older patients in the long-term management of this chronic condition.
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Affiliation(s)
- Lorna E Ingoe
- Department of Diabetes & Endocrinology, Queen Elizabeth Hospital, Gateshead, UK
| | | | - Simon Pearce
- Institute of Genetic Medicine, Centre for Life, Newcastle University, Newcastle upon Tyne, UK.,Endocrine Unit, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Tim Rapley
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - Salman Razvi
- Department of Diabetes & Endocrinology, Queen Elizabeth Hospital, Gateshead, UK.,Institute of Genetic Medicine, Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Scott Wilkes
- Faculty of Applied Sciences, Department of Pharmacy, Health and Wellbeing, University of Sunderland, Sunderland, UK.,Coquet Medical Group, Amble Health Centre, Amble, UK
| | - Susan Hrisos
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
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Chakera AJ, Pearce SHS, Vaidya B. Treatment for primary hypothyroidism: current approaches and future possibilities. DRUG DESIGN DEVELOPMENT AND THERAPY 2011; 6:1-11. [PMID: 22291465 PMCID: PMC3267517 DOI: 10.2147/dddt.s12894] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Primary hypothyroidism is the most common endocrine disease. Although the diagnosis and treatment of hypothyroidism is often considered simple, there are large numbers of people with this condition who are suboptimally treated. Even in those people with hypothyroidism who are biochemically euthyroid on levothyroxine replacement there is a significant proportion who report poorer quality of life. This review explores the historical and current treatment options for hypothyroidism, reasons for and potential solutions to suboptimal treatment, and future possibilities in the treatment of hypothyroidism.
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Affiliation(s)
- Ali J Chakera
- Department of Endocrinology, Royal Devon and Exeter Hospital and Peninsula Medical School, Exeter, UK
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Abstract
Abnormal thyroid function tests are common for older adults, but the clinical significance of abnormal results and the need for treatment vary. Nonthyroidal illness (eg, low T3 and T4 syndromes) needs to be ruled out before making the diagnosis of hypothyroidism. Overt hypothyroidism and myxedema coma always require treatment, but treatment of subclinical hypothyroidism is not as clear. The purpose of this review article is to summarize existing data in the elderly population on the etiology, diagnosis, and management of overt hypothyroidism and subclinical hypothyroidism.
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Affiliation(s)
- Tsui-Ming Li
- Genesis ElderCare Physician Services, Maryland, USA
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Chiovato L, Mariotti S, Pinchera A. Thyroid diseases in the elderly. BAILLIERE'S CLINICAL ENDOCRINOLOGY AND METABOLISM 1997; 11:251-70. [PMID: 9403122 DOI: 10.1016/s0950-351x(97)80272-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The ageing thyroid is associated with a number of morphological and functional changes, such as decreased serum T3 and mean thyroid-stimulating hormone concentrations, that are to some extent independent of intercurrent non-thyroidal illnesses. All thyroid diseases, including clinical and subclinical hypo- and hyperthyroidism, non-toxic nodular goitre and thyroid cancer, are encountered in the elderly, but their prevalence and clinical expression differ from those observed in younger patients. In the elderly, autoimmune hypothyroidism is particularly prevalent, hyperthyroidism is mainly characterized by cardiovascular symptoms and is frequently due to toxic nodular goitres, and differentiated thyroid carcinoma is more aggressive. The interpretation of thyroid function tests is difficult in old individuals, because of age-associated changes in thyroid function and frequent alterations secondary to non-thyroidal illnesses and/or drugs. Treatment of thyroid disease deserves special attention in old patients because of the increased risk of complications.
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Affiliation(s)
- L Chiovato
- Institute of Endocrinology, University of Pisa, Italy
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