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Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BJM, Metz TO. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc 2021; 16:3737-3760. [PMID: 34244696 PMCID: PMC8830262 DOI: 10.1038/s41596-021-00566-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new disease biomarkers. However, certain critical steps of study design such as cohort selection, evaluation of statistical power, sample blinding and randomization, and sample/data quality control are often neglected or underappreciated during experimental design and execution. This tutorial discusses important steps for designing and implementing a liquid-chromatography-mass-spectrometry-based biomarker discovery study. We describe the rationale, considerations and possible failures in each step of such studies, including experimental design, sample collection and processing, and data collection. We also provide guidance for major steps of data processing and final statistical analysis for meaningful biological interpretations along with highlights of several successful biomarker studies. The provided guidelines from study design to implementation to data interpretation serve as a reference for improving rigor and reproducibility of biomarker development studies.
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Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Marina Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brigitte I Frohnert
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Astrid M Suchy-Dicey
- Elson S. Floyd College of Medicine, Washington State University, Seattle, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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Beishon L, Clough RH, Kadicheeni M, Chithiramohan T, Panerai RB, Haunton VJ, Minhas JS, Robinson TG. Vascular and haemodynamic issues of brain ageing. Pflugers Arch 2021; 473:735-751. [PMID: 33439324 PMCID: PMC8076154 DOI: 10.1007/s00424-020-02508-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/17/2023]
Abstract
The population is ageing worldwide, thus increasing the burden of common age-related disorders to the individual, society and economy. Cerebrovascular diseases (stroke, dementia) contribute a significant proportion of this burden and are associated with high morbidity and mortality. Thus, understanding and promoting healthy vascular brain ageing are becoming an increasing priority for healthcare systems. In this review, we consider the effects of normal ageing on two major physiological processes responsible for vascular brain function: Cerebral autoregulation (CA) and neurovascular coupling (NVC). CA is the process by which the brain regulates cerebral blood flow (CBF) and protects against falls and surges in cerebral perfusion pressure, which risk hypoxic brain injury and pressure damage, respectively. In contrast, NVC is the process by which CBF is matched to cerebral metabolic activity, ensuring adequate local oxygenation and nutrient delivery for increased neuronal activity. Healthy ageing is associated with a number of key physiological adaptations in these processes to mitigate age-related functional and structural declines. Through multiple different paradigms assessing CA in healthy younger and older humans, generating conflicting findings, carbon dioxide studies in CA have provided the greatest understanding of intrinsic vascular anatomical factors that may mediate healthy ageing responses. In NVC, studies have found mixed results, with reduced, equivalent and increased activation of vascular responses to cognitive stimulation. In summary, vascular and haemodynamic changes occur in response to ageing and are important in distinguishing “normal” ageing from disease states and may help to develop effective therapeutic strategies to promote healthy brain ageing.
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Affiliation(s)
- Lucy Beishon
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK.
| | - Rebecca H Clough
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK
| | - Meeriam Kadicheeni
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK
| | - Tamara Chithiramohan
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK
| | - Ronney B Panerai
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK.,NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
| | - Victoria J Haunton
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK.,NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
| | - Jatinder S Minhas
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK.,NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
| | - Thompson G Robinson
- Department of Cardiovascular Sciences, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester, LE2 7LX, UK.,NIHR Leicester Biomedical Research Centre, British Heart Foundation Cardiovascular Research Centre, Glenfield Hospital, Leicester, UK
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Alvarenga ÉDSL, Silva AM, da Silva TAE, de Araújo RF, Prado Júnior RR, Mendes RF. Oral health-related quality of life in caregivers of individuals with Cerebral Palsy: a case-control study. Eur Arch Paediatr Dent 2019; 21:193-202. [PMID: 31471856 DOI: 10.1007/s40368-019-00472-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/20/2019] [Indexed: 02/07/2023]
Abstract
AIM The object of this study is to evaluate the oral health-related quality of life (OHRQoL) of caregivers of individuals with Cerebral Palsy (CP). METHODS Ninety-eight caregivers of individuals with CP (SG) and 196 caregivers of individuals without special needs (CG) completed the reduced version of the Oral Health Impact Profile (OHIP-14). In addition, a questionnaire with demographic and socioeconomic questions was used. Groups were matched according to gender, schooling and family income. Fisher's exact tests, Chi square and Mann-Whitney, and bi/multivariate logistic regression were used (p < 0.05). RESULTS The impact on OHRQoL was similar for SG and CG (OHIP-14 total score). For SG, the high negative impact was in the following OHIP domains: "Functional limitation", "Physical disability", "Psychological incapacity" and "Disadvantages". For SG, a higher number of caregivers was single, unemployed, received government financial aid. There was a statistically significant association between the number of children a caregiver has and a negative impact on OHRQoL. CONCLUSIONS Being a caregiver of children with or without CP had a negative impact of similar magnitude on ORHQoL. The negative impact on OHRQoL of caregivers of children with CP was associated with having a high number of children; the higher the number of children, the greater the negative impact on their OHRQoL.
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Affiliation(s)
- É da S L Alvarenga
- Postgraduate Program in Dentistry, Federal University of Piauí, UFPI, Campus Universitário Ministro Petrônio Portella, Bloco 5, Bairro Ininga, Teresina, PI, CEP: 64049-550, Brazil
| | - A M Silva
- Postgraduate Program in Dentistry, Federal University of Piauí, UFPI, Campus Universitário Ministro Petrônio Portella, Bloco 5, Bairro Ininga, Teresina, PI, CEP: 64049-550, Brazil.
| | - T A E da Silva
- Postgraduate Program in Dentistry, Federal University of Piauí, UFPI, Campus Universitário Ministro Petrônio Portella, Bloco 5, Bairro Ininga, Teresina, PI, CEP: 64049-550, Brazil
| | - R F de Araújo
- Postgraduate Program in Dentistry, Federal University of Piauí, UFPI, Campus Universitário Ministro Petrônio Portella, Bloco 5, Bairro Ininga, Teresina, PI, CEP: 64049-550, Brazil
| | - R R Prado Júnior
- Postgraduate Program in Dentistry, Federal University of Piauí, UFPI, Campus Universitário Ministro Petrônio Portella, Bloco 5, Bairro Ininga, Teresina, PI, CEP: 64049-550, Brazil
| | - R F Mendes
- Postgraduate Program in Dentistry, Federal University of Piauí, UFPI, Campus Universitário Ministro Petrônio Portella, Bloco 5, Bairro Ininga, Teresina, PI, CEP: 64049-550, Brazil
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Kumar B, Ravisankar A, Mohan A, Kumar D, Katyarmal D, Sachan A, Sarma K. Authors' response. Indian J Med Res 2015; 142:769. [PMID: 26831428 PMCID: PMC4774076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- B.S. Kumar
- Division of Rheumatology, Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - A. Ravisankar
- Division of Rheumatology, Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - A. Mohan
- Division of Rheumatology, Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - D.P. Kumar
- Division of Rheumatology, Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - D.T. Katyarmal
- Division of Rheumatology, Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - A. Sachan
- Department of Endocrinology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - K.V.S. Sarma
- Department of Statistics, Sri Venkateswara University, Tirupati 517 507, Andhra Pradesh, India
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