1
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Mantel I, Fein MR, Donlin LT. Emerging synovial cell states in rheumatoid arthritis as potential therapeutic targets. Curr Opin Rheumatol 2023; 35:249-254. [PMID: 37040654 PMCID: PMC10219846 DOI: 10.1097/bor.0000000000000940] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
PURPOSE OF REVIEW To summarize recently discovered novel cell states in rheumatoid arthritis (RA) synovium that could have important implications for disease treatment. RECENT FINDINGS The use of multiomic technologies, including single-cell and spatial transcriptomics and mass cytometry, has led to the discovery of several novel cell states, which could have important implications for the treatment of RA. These cells can be found in patient blood, synovial fluid, or synovial tissue and span several immune cell subsets as well as stromal cell types. These diverse cell states may represent the targets of current or future therapeutics, while their fluctuations may inform the ideal timing for therapy. Future efforts are needed to implicate how each cell state functions in the pathophysiologic network within affected joints and how medications perturb each cell state and ultimately the tissue. SUMMARY Multiomic molecular technologies have afforded the discovery of numerous novel cellular states in RA synovium; the next challenge will be to link these states to pathophysiology and treatment response.
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Affiliation(s)
- Ian Mantel
- Weill Cornell Medicine Graduate School
- Hospital for Special Surgery Research Institute, New York, New York, USA
| | - Miriam R Fein
- Hospital for Special Surgery Research Institute, New York, New York, USA
| | - Laura T Donlin
- Weill Cornell Medicine Graduate School
- Hospital for Special Surgery Research Institute, New York, New York, USA
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2
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DNAzymes, Novel Therapeutic Agents in Cancer Therapy: A Review of Concepts to Applications. J Nucleic Acids 2021; 2021:9365081. [PMID: 34760318 PMCID: PMC8575636 DOI: 10.1155/2021/9365081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022] Open
Abstract
The past few decades have witnessed a rapid evolution in cancer drug research which is aimed at developing active biological interventions to regulate cancer-specific molecular targets. Nucleic acid-based therapeutics, including ribozymes, antisense oligonucleotides, small interference RNA (siRNA), aptamer, and DNAzymes, have emerged as promising candidates regulating cancer-specific genes at either the transcriptional or posttranscriptional level. Gene-specific catalytic DNA molecules, or DNAzymes, have shown promise as a therapeutic intervention against cancer in various in vitro and in vivo models, expediting towards clinical applications. DNAzymes are single-stranded catalytic DNA that has not been observed in nature, and they are synthesized through in vitro selection processes from a large pool of random DNA libraries. The intrinsic properties of DNAzymes like small molecular weight, higher stability, excellent programmability, diversity, and low cost have brought them to the forefront of the nucleic acid-based therapeutic arsenal available for cancers. In recent years, considerable efforts have been undertaken to assess a variety of DNAzymes against different cancers. However, their therapeutic application is constrained by the low delivery efficiency, cellular uptake, and target detection within the tumour microenvironment. Thus, there is a pursuit to identify efficient delivery methods in vivo before the full potential of DNAzymes in cancer therapy is realized. In this light, a review of the recent advances in the use of DNAzymes against cancers in preclinical and clinical settings is valuable to understand its potential as effective cancer therapy. We have thus sought to firstly provide a brief overview of construction and recent improvements in the design of DNAzymes. Secondly, this review stipulates the efficacy, safety, and tolerability of DNAzymes developed against major hallmarks of cancers tested in preclinical and clinical settings. Lastly, the recent advances in DNAzyme delivery systems along with the challenges and prospects for the clinical application of DNAzymes as cancer therapy are also discussed.
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3
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Larroya A, Pantoja J, Codoñer-Franch P, Cenit MC. Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain. Front Pediatr 2021; 9:705859. [PMID: 34277527 PMCID: PMC8280474 DOI: 10.3389/fped.2021.705859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 01/07/2023] Open
Abstract
Mental health is determined by a complex interplay between the Neurological Exposome and the Human Genome. Multiple genetic and non-genetic (exposome) factors interact early in life, modulating the risk of developing the most common complex neurodevelopmental disorders (NDDs), with potential long-term consequences on health. To date, the understating of the precise etiology underpinning these neurological alterations, and their clinical management pose a challenge. The crucial role played by diet and gut microbiota in brain development and functioning would indicate that modulating the gut-brain axis may help protect against the onset and progression of mental-health disorders. Some nutritional deficiencies and gut microbiota alterations have been linked to NDDs, suggesting their potential pathogenic implications. In addition, certain dietary interventions have emerged as promising alternatives or adjuvant strategies for improving the management of particular NDDs, at least in particular subsets of subjects. The gut microbiota can be a key to mediating the effects of other exposome factors such as diet on mental health, and ongoing research in Psychiatry and Neuropediatrics is developing Precision Nutrition Models to classify subjects according to a diet response prediction based on specific individual features, including microbiome signatures. Here, we review current scientific evidence for the impact of early life environmental factors, including diet, on gut microbiota and neuro-development, emphasizing the potential long-term consequences on health; and also summarize the state of the art regarding the mechanisms underlying diet and gut microbiota influence on the brain-gut axis. Furthermore, we describe the evidence supporting the key role played by gut microbiota, diet and nutrition in neurodevelopment, as well as the effectiveness of certain dietary and microbiome-based interventions aimed at preventing or treating NDDs. Finally, we emphasize the need for further research to gain greater insight into the complex interplay between diet, gut microbiome and brain development. Such knowledge would help towards achieving tailored integrative treatments, including personalized nutrition.
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Affiliation(s)
- Ana Larroya
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
| | - Jorge Pantoja
- Department of Pediatrics, University Hospital De la Plana, Vila-Real, Castellón, Spain.,Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Pilar Codoñer-Franch
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain.,Department of Pediatrics, Dr. Peset University Hospital, Valencia, Spain.,Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - María Carmen Cenit
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain.,Department of Pediatrics, University Hospital De la Plana, Vila-Real, Castellón, Spain.,Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
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4
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Goda H, Kawasaki H, Masuoka Y, Kohama N, Rahman MM. Opportunities and challenges of integrating genetics education about human diversity into public health nurses' responsibilities in Japan. BMC Nurs 2019; 18:65. [PMID: 31827391 PMCID: PMC6902480 DOI: 10.1186/s12912-019-0391-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/27/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many genetic tests are now available due to evolution by the Human Genome Project. However, the growing use of genetic testing and screening may not only lead to improvements in public health and health promotion, but also trigger grave ethical, legal, and societal concerns. The involvement of community healthcare providers is expected in the future because they have direct contact with the residents through their health programs. The aims of the current study were to clarify how public health nurses perceive the relationship between genetics and professional duties and to identify opportunities and challenges of integrating genetics education into their professional duties. METHODS In 2017, data were collected through a focus group interview. Content related to the 'presence or absence of health consultation related to genetic issues as part of actual job duties' and 'training for handling genetic-related health consultations' was extracted. Entire sentences were coded and categorized based on similar semantic content. RESULTS Public health nurses had difficulties in recognizing genetic issues in public health activities. In some cases, genetic contents were included in conversation and consultation with the general public. Through the professional education and experiences, public health nurses needed specialized education, post-graduation studies and mentoring about genetics. CONCLUSIONS Public health nurses whose professional duties do not directly relate to genetics were exposed to genetics-related episodes on a regular basis without their awareness. The provision of accurate information and knowledge related to genetics by public health nurses would also provide an opportunity for clients to be informed about their latent genetic risks. Hence, there is a need for practical resources, the establishment of collaboration networks, and the development of professional organizations for public health nurses.
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Affiliation(s)
- Hiromi Goda
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553 Japan
| | - Hiromi Kawasaki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553 Japan
| | - Yuko Masuoka
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553 Japan
| | - Natsu Kohama
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553 Japan
| | - Md Moshiur Rahman
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553 Japan
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5
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The Interplay between miRNA-Related Variants and Age-Related Macular Degeneration: EVIDENCE of Association of MIR146A and MIR27A. Int J Mol Sci 2019; 20:ijms20071578. [PMID: 30934838 PMCID: PMC6480223 DOI: 10.3390/ijms20071578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
The complex interplay among genetic, epigenetic, and environmental variables is the basis for the multifactorial origin of age-related macular degeneration (AMD). Previous results highlighted that single nucleotide polymorphisms (SNPs) of CFH, ARMS2, IL-8, TIMP3, SLC16A8, RAD51B, VEGFA, and COL8A1 were significantly associated with the risk of AMD in the Italian population. Given these data, this study aimed to investigate the impact of SNPs in genes coding for MIR146A, MIR31, MIR23A, MIR27A, MIR20A, and MIR150 on their susceptibility to AMD. Nine-hundred and seventy-six patients with exudative AMD and 1000 controls were subjected to an epigenotyping analysis through real-time PCR and direct sequencing. Biostatistical and bioinformatic analysis was performed to evaluate the association with susceptibility to AMD. These analyses reported that the SNPs rs11671784 (MIR27A, G/A) and rs2910164 (MIR146A, C/G) were significantly associated with AMD risk. Interestingly, the bioinformatic analysis showed that MIR27A and MIR146A take part in the angiogenic and inflammatory pathways underlying AMD etiopathogenesis. Thus, polymorphisms within the pre-miRNA sequences are likely to affect their functional activity, especially the interaction with specific targets. Therefore, our study represents a step forward in the comprehension of the mechanisms leading to AMD onset and progression, which certainly include the involvement of epigenetic modifications.
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6
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Li R, Liu Y, Hou Y, Gan J, Wu P, Li C. 3D genome and its disorganization in diseases. Cell Biol Toxicol 2018; 34:351-365. [DOI: 10.1007/s10565-018-9430-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/26/2018] [Indexed: 01/25/2023]
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7
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Cascella R, Strafella C, Caputo V, Errichiello V, Zampatti S, Milano F, Potenza S, Mauriello S, Novelli G, Ricci F, Cusumano A, Giardina E. Towards the application of precision medicine in Age-Related Macular Degeneration. Prog Retin Eye Res 2017; 63:132-146. [PMID: 29197628 DOI: 10.1016/j.preteyeres.2017.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022]
Abstract
The review essentially describes genetic and non-genetic variables contributing to the onset and progression of exudative Age-related Macular Degeneration (AMD) in Italian population. In particular, AMD susceptibility within Italian population is contributed to by genetic variants, accounting for 23% of disease and non-genetic variants, accounting for 10% of AMD. Our data highlighted prominent differences concerning genetic and non-genetic contributors to AMD in our cohort with respect to worldwide populations. Among genetic variables, SNPs of CFH, ARMS2, IL-8, TIMP3, SLC16A8, RAD51B, VEGFA and COL8A1 were significantly associated with the risk of AMD in the Italian cohort. Surprisingly, other susceptibility variants described in European, American and Asiatic populations, did not reach the significance threshold in our cohort. As expected, advanced age, smoking and dietary habits were associated with the disease. In addition, we also describe a number of gene-gene and gene-phenotype interactions. In fact, AMD-associated genes may be involved in the alteration of Bruch's membrane and induction of angiogenesis, contributing to exacerbate the damage caused by aging and environmental factors. Our review provides an overview of genetic and non-genetic factors characterizing AMD susceptibility in Italian population, outlining the differences with respect to the worldwide populations. Altogether, these data reflect historical, geographic, demographic and lifestyle peculiarities of Italian population. The role of epigenetics, pharmacogenetics, comorbities and genetic counseling in the management of AMD patients have been described, in the perspective of the application of a "population-specific precision medicine" approach addressed to prevent AMD onset and improve patients' quality of life.
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Affiliation(s)
- Raffaella Cascella
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Via Ardeatina 354, 00142, Rome, Italy; Department of Chemical Pharmaceutical and Biomolecular Technologies, Catholic University "Our Lady of Good Counsel" Laprakë, Rruga Dritan Hoxha, 1000, Tirane, Albania
| | - Claudia Strafella
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy; Emotest Laboratory, Via Patria Montenuovo Licola 60, 80078, Pozzuoli, Italy
| | - Valerio Caputo
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy
| | - Stefania Zampatti
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Via Ardeatina 354, 00142, Rome, Italy; Neuromed IRCCS, Via Atinense, 18, 86077, Pozzilli, Italy
| | - Filippo Milano
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy
| | - Saverio Potenza
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy
| | - Silvestro Mauriello
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy
| | - Federico Ricci
- UOSD Retinal Pathology PTV Foundation "Policlinico Tor Vergata", Viale Oxford, 81, 00133, Rome, Italy
| | - Andrea Cusumano
- UOSD Retinal Pathology PTV Foundation "Policlinico Tor Vergata", Viale Oxford, 81, 00133, Rome, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Via Ardeatina 354, 00142, Rome, Italy; Department of Biomedicine and Prevention, ''Tor Vergata'' University, Via Montpellier 1, 00133, Rome, Italy.
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8
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Almassalha LM, Bauer GM, Wu W, Cherkezyan L, Zhang D, Kendra A, Gladstein S, Chandler JE, VanDerway D, Seagle BLL, Ugolkov A, Billadeau DD, O'Halloran TV, Mazar AP, Roy HK, Szleifer I, Shahabi S, Backman V. Macrogenomic engineering via modulation of the scaling of chromatin packing density. Nat Biomed Eng 2017; 1:902-913. [PMID: 29450107 DOI: 10.1038/s41551-017-0153-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many human diseases result from the dysregulation of the complex interactions between tens to thousands of genes. However, approaches for the transcriptional modulation of many genes simultaneously in a predictive manner are lacking. Here, through the combination of simulations, systems modelling and in vitro experiments, we provide a physical regulatory framework based on chromatin packing-density heterogeneity for modulating the genomic information space. Because transcriptional interactions are essentially chemical reactions, they depend largely on the local physical nanoenvironment. We show that the regulation of the chromatin nanoenvironment allows for the predictable modulation of global patterns in gene expression. In particular, we show that the rational modulation of chromatin density fluctuations can lead to a decrease in global transcriptional activity and intercellular transcriptional heterogeneity in cancer cells during chemotherapeutic responses to achieve near-complete cancer cell killing in vitro. Our findings represent a 'macrogenomic engineering' approach to modulating the physical structure of chromatin for whole-scale transcriptional modulation.
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Affiliation(s)
- Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Greta M Bauer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Wenli Wu
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Di Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Alexis Kendra
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Scott Gladstein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - John E Chandler
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - David VanDerway
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Brandon-Luke L Seagle
- Department of Obstetrics and Gynecology, Prentice Women's Hospital, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Andrey Ugolkov
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Daniel D Billadeau
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Thomas V O'Halloran
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | | | - Hemant K Roy
- Section of Gastroenterology, Boston Medical Center/Boston University School of Medicine, Boston, MA, 02118, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. .,Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
| | - Shohreh Shahabi
- Department of Obstetrics and Gynecology, Prentice Women's Hospital, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
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9
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Zidovska A. Repacking chromatin for therapy. Nat Biomed Eng 2017; 1:858-859. [PMID: 31015613 DOI: 10.1038/s41551-017-0161-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, USA.
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10
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Lewis J, Bartlett A, Atkinson P. Hidden in the Middle: Culture, Value and Reward in Bioinformatics. MINERVA 2016; 54:471-490. [PMID: 27942075 PMCID: PMC5124041 DOI: 10.1007/s11024-016-9304-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bioinformatics - the so-called shotgun marriage between biology and computer science - is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised 'outputs' in academia are often defined and rewarded by discipline. Bioinformatics, as an interdisciplinary bricolage, incorporates experts from various disciplinary cultures with their own distinct ways of working. Perceived problems of interdisciplinarity include difficulties of making explicit knowledge that is practical, theoretical, or cognitive. But successful interdisciplinary research also depends on an understanding of disciplinary cultures and value systems, often only tacitly understood by members of the communities in question. In bioinformatics, the 'parent' disciplines have different value systems; for example, what is considered worthwhile research by computer scientists can be thought of as trivial by biologists, and vice versa. This paper concentrates on the problems of reward and recognition described by scientists working in academic bioinformatics in the United Kingdom. We highlight problems that are a consequence of its cross-cultural make-up, recognising that the mismatches in knowledge in this borderland take place not just at the level of the practical, theoretical, or epistemological, but also at the cultural level too. The trend in big, interdisciplinary science is towards multiple authors on a single paper; in bioinformatics this has created hybrid or fractional scientists who find they are being positioned not just in-between established disciplines but also in-between as middle authors or, worse still, left off papers altogether.
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Affiliation(s)
- Jamie Lewis
- School of Social Sciences, Cardiff University, Glamorgan Building, King Edward VIIth Avenue, Cardiff, CF10 3WT UK
| | - Andrew Bartlett
- School of Social Sciences, Cardiff University, Glamorgan Building, King Edward VIIth Avenue, Cardiff, CF10 3WT UK
| | - Paul Atkinson
- School of Social Sciences, Cardiff University, Glamorgan Building, King Edward VIIth Avenue, Cardiff, CF10 3WT UK
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11
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Mueller SC, Sommer B, Backes C, Haas J, Meder B, Meese E, Keller A. From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. J Biol Chem 2016; 291:1582-1590. [PMID: 26601959 DOI: 10.1074/jbc.m115.695247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 01/18/2023] Open
Abstract
Understanding the role of genetics in disease has become a central part of medical research. Non-synonymous single nucleotide variants (nsSNVs) in coding regions of human genes frequently lead to pathological phenotypes. Beyond single variations, the individual combination of nsSNVs may add to pathogenic processes. We developed a multiscale pipeline to systematically analyze the existence of quantitative effects of multiple nsSNVs and gene combinations in single individuals on pathogenicity. Based on this pipeline, we detected in a data set of 842 nsSNVs discovered in 76 genes related to cardiomyopathies, associated nsSNV combinations in seven genes present in at least 70% of all 639 patient samples, but not in a control cohort of healthy humans. Structural analyses of these revealed primarily an influence on the protein stability. For amino acid substitutions located at the protein surface, we generally observed a proximity to putative binding pockets. To computationally analyze cumulative effects and their impact, pathogenicity methods are currently being developed. Our approach supports this process, as shown on the example of a cardiac phenotype but can be likewise applied to other diseases such as cancer.
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Affiliation(s)
- Sabine C Mueller
- From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,; Department of Human Genetics, Saarland University, 66421 Homburg, Germany,.
| | - Björn Sommer
- the Bio-/Medical Informatics Department, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany,; Clayton School of Information Technology, Faculty of Information Technology, Monash University, Melbourne 3800, Australia
| | - Christina Backes
- From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jan Haas
- the Department of Internal Medicine III, Heidelberg University, 69120 Heidelberg, Germany, and; the DZHK (German Centre for Cardiovascular Research), 69120 Heidelberg, Germany
| | - Benjamin Meder
- the Department of Internal Medicine III, Heidelberg University, 69120 Heidelberg, Germany, and; the DZHK (German Centre for Cardiovascular Research), 69120 Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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12
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Hoyt R, Linnville S, Thaler S, Moore J. Digital Family History Data Mining with Neural Networks: A Pilot Study. PERSPECTIVES IN HEALTH INFORMATION MANAGEMENT 2016; 13:1c. [PMID: 26903781 PMCID: PMC4739442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Following the passage of the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009, electronic health records were widely adopted by eligible physicians and hospitals in the United States. Stage 2 meaningful use menu objectives include a digital family history but no stipulation as to how that information should be used. A variety of data mining techniques now exist for these data, which include artificial neural networks (ANNs) for supervised or unsupervised machine learning. In this pilot study, we applied an ANN-based simulation to a previously reported digital family history to mine the database for trends. A graphical user interface was created to display the input of multiple conditions in the parents and output as the likelihood of diabetes, hypertension, and coronary artery disease in male and female offspring. The results of this pilot study show promise in using ANNs to data mine digital family histories for clinical and research purposes.
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Affiliation(s)
- Robert Hoyt
- Health Informatics Program at the College of Science, Engineering and Health at the University of West Florida in Pensacola, FL
| | - Steven Linnville
- Robert E. Mitchell Center for Prisoner of War Studies in Pensacola, FL
| | | | - Jeffrey Moore
- Robert E. Mitchell Center for Prisoner of War Studies in Pensacola, FL
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13
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Chan JPL, Thalamuthu A, Oldmeadow C, Armstrong NJ, Holliday EG, McEvoy M, Kwok JB, Assareh AA, Peel R, Hancock SJ, Reppermund S, Menant J, Trollor JN, Brodaty H, Schofield PR, Attia JR, Sachdev PS, Scott RJ, Mather KA. Genetics of hand grip strength in mid to late life. AGE (DORDRECHT, NETHERLANDS) 2015; 37:9745. [PMID: 25637336 PMCID: PMC4312310 DOI: 10.1007/s11357-015-9745-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
Hand grip strength (GS) is a predictor of mortality in older adults and is moderately to highly heritable, but no genetic variants have been consistently identified. We aimed to identify single nucleotide polymorphisms (SNPs) associated with GS in middle-aged to older adults using a genome-wide association study (GWAS). GS was measured using handheld dynamometry in community-dwelling men and women aged 55-85 from the Hunter Community Study (HCS, N = 2088) and the Sydney Memory and Ageing Study (Sydney MAS, N = 541). Genotyping was undertaken using Affymetrix microarrays with imputation to HapMap2. Analyses were performed using linear regression. No genome-wide significant results were observed in HCS nor were any of the top signals replicated in Sydney MAS. Gene-based analyses in HCS identified two significant genes (ZNF295, C2CD2), but these results were not replicated in Sydney MAS. One out of eight SNPs previously associated with GS, rs550942, located near the CNTF gene, was significantly associated with GS (p = 0.005) in the HCS cohort only. Study differences may explain the lack of consistent results between the studies, including the smaller sample size of the Sydney MAS cohort. Our modest sample size also had limited power to identify variants of small effect. Our results suggest that similar to various other complex traits, many genetic variants of small effect size may influence GS. Future GWAS using larger samples and consistent measures may prove more fruitful at identifying genetic contributors for GS in middle-aged to older adults.
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Affiliation(s)
- Jessica P. L. Chan
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
| | - Anbupalam Thalamuthu
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
| | | | - Nicola J. Armstrong
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
- />School of Mathematics and Statistics, University of Sydney, Sydney, Australia
| | - Elizabeth G. Holliday
- />Public Health Program, Hunter Medical Research Institute, Newcastle, Australia
- />Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales Australia
| | - Mark McEvoy
- />Public Health Program, Hunter Medical Research Institute, Newcastle, Australia
- />Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales Australia
| | - John B. Kwok
- />Neuroscience Research Australia, Sydney, Australia
- />School of Medical Sciences, UNSW, Sydney, Australia
| | - Amelia A. Assareh
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
| | - Rosanne Peel
- />Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales Australia
| | - Stephen J. Hancock
- />Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales Australia
| | - Simone Reppermund
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
| | | | - Julian N. Trollor
- />Department of Developmental Disability Neuropsychiatry, UNSW, Sydney, Australia
| | - Henry Brodaty
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
- />Primary Dementia Collaborative Research Centre, UNSW, Sydney, Australia
| | - Peter R. Schofield
- />Neuroscience Research Australia, Sydney, Australia
- />School of Medical Sciences, UNSW, Sydney, Australia
| | - John R. Attia
- />Public Health Program, Hunter Medical Research Institute, Newcastle, Australia
- />Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales Australia
| | - Perminder S. Sachdev
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
- />Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, Australia
| | - Rodney J. Scott
- />School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales Australia
- />Division of Molecular Medicine, Pathology North, Newcastle, Australia
- />Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
| | - Karen A. Mather
- />Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW), NPI, Euroa Centre, Barker St, Randwick, Sydney, NSW 2031 Australia
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