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Ahmed S, Odumade OA, van Zalm P, Fatou B, Hansen R, Martin CR, Angelidou A, Steen H. Proteomics-Based Mapping of Bronchopulmonary Dysplasia-Associated Changes in Noninvasively Accessible Oral Secretions. J Pediatr 2024; 270:113774. [PMID: 37839510 PMCID: PMC11014893 DOI: 10.1016/j.jpeds.2023.113774] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
OBJECTIVE To determine if oral secretions (OS) can be used as a noninvasively collected body fluid, in lieu of tracheal aspirates (TA), to track respiratory status and predict bronchopulmonary dysplasia (BPD) development in infants born <32 weeks. STUDY DESIGN This was a retrospective, single center cohort study that included data and convenience samples from week-of-life (WoL) 3 from 2 independent preterm infant cohorts. Using previously banked samples, we applied our sample-sparing, high-throughput proteomics technology to compare OS and TA proteomes in infants born <32 weeks admitted to the Neonatal Intensive Care Unit (NICU) (Cohort 1; n = 23 infants). In a separate similar cohort, we mapped the BPD-associated changes in the OS proteome (Cohort 2; n = 17 infants including 8 with BPD). RESULTS In samples collected during the first month of life, we identified 607 proteins unique to OS, 327 proteins unique to TA, and 687 overlapping proteins belonging to pathways involved in immune effector processes, neutrophil degranulation, leukocyte mediated immunity, and metabolic processes. Furthermore, we identified 37 OS proteins that showed significantly differential abundance between BPD cases and controls: 13 were associated with metabolic and immune dysregulation, 10 of which (eg, SERPINC1, CSTA, BPI) have been linked to BPD or other prematurity-related lung disease based on blood or TA investigations, but not OS. CONCLUSIONS OS are a noninvasive, easily accessible alternative to TA and amenable to high-throughput proteomic analysis in preterm newborns. OS samples hold promise to yield actionable biomarkers of BPD development, particularly for prospective categorization and timely tailored treatment of at-risk infants with novel therapies.
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Affiliation(s)
- Saima Ahmed
- Department of Pathology, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Oludare A Odumade
- Harvard Medical School, Boston, MA; Division of Neonatology, Boston Children's Hospital and Harvard Medical School, Boston, MA; Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Patrick van Zalm
- Department of Pathology, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Benoit Fatou
- Department of Pathology, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA; Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Rachel Hansen
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Asimenia Angelidou
- Harvard Medical School, Boston, MA; Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Hanno Steen
- Department of Pathology, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA; Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
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Bhamidimarri PM, Fuentes D, Salameh L, Mahboub B, Hamoudi R. Assessing the impact of storage conditions on RNA from human saliva and its application to the identification of mRNA biomarkers for asthma. Front Mol Biosci 2024; 11:1363897. [PMID: 38948078 PMCID: PMC11211611 DOI: 10.3389/fmolb.2024.1363897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction: Human saliva was used to develop non-invasive liquid biopsy biomarkers to establish saliva as an alternate to blood and plasma in translational research. The present study focused on understanding the impact of sample storage conditions on the extraction of RNA from saliva and the RNA yield, to be applied in clinical diagnosis. In this study, genes related to asthma were used to test the method developed. Methods: Salivary RNA was extracted from three subjects using the Qiazol® based method and quantified by both spectrophotometric (NanoDrop) and fluorometric (Qubit®) methods. RNA integrity was measured using a bioanalyzer. Quantitative PCR was used to monitor the impact of storage conditions on the expression of housekeeping genes: GAPDH and β-actin, and the asthma related genes: POSTN and FBN2. In addition, an independent cohort of 38 asthmatics and 10 healthy controls were used to validate the expression of POSTN and FBN2 as mRNA salivary biomarkers. Results: Approximately 2 µg of total RNA was obtained from the saliva stored at 40°C without any preservative for 2 weeks showing consistent gene expression with RNA stored at room temperature (RT) for 48 h with RNAlater. Although saliva stored with RNAlater showed a substantial increase in the yield (110 to 234 ng/μL), a similar Cq (15.6 ± 1.4) for the 18s rRNA gene from saliva without preservative showed that the RNA was stable enough. Gene expression analysis from the degraded RNA can be performed by designing the assay using a smaller fragment size spanning a single exon as described below in the case of the POSTN and FBN2 genes in the asthma cohort. Conclusion: This study showed that samples stored at room temperature up to a temperature of 40°C without any preservative for 2 weeks yielded relatively stable RNA. The methodology developed can be employed to transport samples from the point of collection to the laboratory, under non-stringent storage conditions enabling the execution of gene expression studies in a cost effective and efficient manner.
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Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - David Fuentes
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Rashid Hospital, Dubai, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- Centre of Excellence for Precision Medicine, Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates
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Mubarak G, Zahir FR. Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine. J Pers Med 2022; 12:199. [PMID: 35207687 PMCID: PMC8877836 DOI: 10.3390/jpm12020199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/07/2022] Open
Abstract
With the advent of genome-wide screening methods-beginning with microarray technologies and moving onto next generation sequencing methods-the era of precision and personalized medicine was born. Genomics led the way, and its contributions are well recognized. However, "other-omics" fields have rapidly emerged and are becoming as important toward defining disease causes and exploring therapeutic benefits. In this review, we focus on the impacts of transcriptomics, and its extension-epitranscriptomics-on personalized and precision medicine efforts. There has been an explosion of transcriptomic studies particularly in the last decade, along with a growing number of recent epitranscriptomic studies in several disease areas. Here, we summarize and overview major efforts for cancer, cardiovascular disease, and neurodevelopmental disorders (including autism spectrum disorder and intellectual disability) for transcriptomics/epitranscriptomics in precision and personalized medicine. We show that leading advances are being made in both diagnostics, and in investigative and landscaping disease pathophysiological studies. As transcriptomics/epitranscriptomics screens become more widespread, it is certain that they will yield vital and transformative precision and personalized medicine contributions in ways that will significantly further genomics gains.
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Affiliation(s)
| | - Farah R. Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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Yen E, Kaneko-Tarui T, Maron JL. Technical Considerations and Protocol Optimization for Neonatal Salivary Biomarker Discovery and Analysis. Front Pediatr 2020; 8:618553. [PMID: 33575231 PMCID: PMC7870796 DOI: 10.3389/fped.2020.618553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/31/2020] [Indexed: 12/04/2022] Open
Abstract
Non-invasive techniques to monitor and diagnose neonates, particularly those born prematurely, are a long-sought out goal of Newborn Medicine. In recent years, technical advances, combined with increased assay sensitivity, have permitted the high-throughput analysis of multiple biomarkers simultaneously from a single sample source. Multiplexed transcriptomic and proteomic platforms, along with more comprehensive assays such as RNASeq, allow for interrogation of ongoing physiology and pathology in unprecedented ways. In the fragile neonatal population, saliva is an ideal biofluid to assess clinical status serially and offers many advantages over more invasively obtained blood samples. Importantly, saliva samples are amenable to analysis on emerging proteomic and transcriptomic platforms, even at quantitatively limited volumes. However, biomarker targets are often degraded in human saliva, and as a mixed source biofluid containing both human and microbial targets, saliva presents unique challenges for the investigator. Here, we provide insight into technical considerations and protocol optimizations developed in our laboratory to quantify and discover neonatal salivary biomarkers with improved reproducibility and reliability. We will detail insights learned from years of experimentation on neonatal saliva within our laboratory ranging from salivary collection techniques to processing to downstream analyses, highlighting the need for consistency in approach and a global understanding of both the potential benefits and limitations of neonatal salivary biomarker analyses. Importantly, we will highlight the need for robust and stringent research in this population to provide the field with standardized approaches and workflows to impact neonatal care successfully.
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Affiliation(s)
- Elizabeth Yen
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, United States.,Division of Newborn Medicine, Tufts Children's Hospital, Boston, MA, United States
| | - Tomoko Kaneko-Tarui
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, United States
| | - Jill L Maron
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, United States.,Division of Newborn Medicine, Tufts Children's Hospital, Boston, MA, United States
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Hassaneen M, Maron JL. Salivary Diagnostics in Pediatrics: Applicability, Translatability, and Limitations. Front Public Health 2017; 5:83. [PMID: 28473973 PMCID: PMC5397421 DOI: 10.3389/fpubh.2017.00083] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
In the last decade, technological advances, combined with an improved appreciation of the ability of saliva to inform caregivers about both oral health and systemic disease, have led to the emergence of salivary diagnostic platforms. However, the majority of these assays have targeted diseases that more commonly affect the adult population, largely neglecting infants and children who arguably could benefit the most from non-invasive assessment tools for health monitoring. Gaining access into development, infection, and disease through comprehensive "omic" analyses of saliva could significantly improve care and enhance health access. In this review, we will highlight novel applications of salivary diagnostics in pediatrics across the "omic" spectrum, including at the genomic, transcriptomic, proteomic, microbiomic, and metabolomic level. The challenges to implementing salivary platforms into care, including the effects of age, diet, and developmental stage on salivary components, will be reviewed. Ultimately, large-scale, multicenter trials must be performed to establish normative biomarker values across the age spectrum to accurately discriminate between health and disease. Only then can salivary diagnostics truly translate into pediatric care.
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Affiliation(s)
- Mona Hassaneen
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, USA
| | - Jill L. Maron
- Mother Infant Research Institute at Tufts Medical Center, Boston, MA, USA
- Division of Newborn Medicine, Floating Hospital for Children at Tufts Medical Center, Boston, MA, USA
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Maron BA, Leopold JA. Systems biology: An emerging strategy for discovering novel pathogenetic mechanisms that promote cardiovascular disease. Glob Cardiol Sci Pract 2016; 2016:e201627. [PMID: 29043273 PMCID: PMC5642838 DOI: 10.21542/gcsp.2016.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Reductionist theory proposes that analyzing complex systems according to their most fundamental components is required for problem resolution, and has served as the cornerstone of scientific methodology for more than four centuries. However, technological gains in the current scientific era now allow for the generation of large datasets that profile the proteomic, genomic, and metabolomic signatures of biological systems across a range of conditions. The accessibility of data on such a vast scale has, in turn, highlighted the limitations of reductionism, which is not conducive to analyses that consider multiple and contemporaneous interactions between intermediates within a pathway or across constructs. Systems biology has emerged as an alternative approach to analyze complex biological systems. This methodology is based on the generation of scale-free networks and, thus, provides a quantitative assessment of relationships between multiple intermediates, such as protein-protein interactions, within and between pathways of interest. In this way, systems biology is well positioned to identify novel targets implicated in the pathogenesis or treatment of diseases. In this review, the historical root and fundamental basis of systems biology, as well as the potential applications of this methodology are discussed with particular emphasis on integration of these concepts to further understanding of cardiovascular disorders such as coronary artery disease and pulmonary hypertension.
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Affiliation(s)
- Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Boston VA Healthcare System, Boston, MA, USA
| | - Jane A Leopold
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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