Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review
Sepsis continues to be recognized as a significant global health challenge across all ages and is characterized by a complex pathophysiology. In this scoping review, PRISMA-ScR guidelines were adhered to, and a transcriptomic methodology was adopted, with the protocol registered on the Open Science...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-01-01
|
| Series: | Informatics in Medicine Unlocked |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352914823002654 |
| _version_ | 1797348659632799744 |
|---|---|
| author | Asrar Rashid Feras Al-Obeidat Hari Krishnan Kanthimathinathan Govind Benakatti Wael Hafez Raghu Ramaiah Joe Brierley Benjamin Hanisch Praveen Khilnani Christos Koutentis Berit S. Brusletto Mohammed Toufiq Zain Hussain Harish Vyas Zainab A Malik Maike Schumacher Rayaz A Malik Shriprasad Deshpande Nasir Quraishi Raziya Kadwa Amrita Sarpal M. Guftar Shaikh Javed Sharief Syed Ahmed Zaki Rajesh Phatak Akash Deep Ahmed Al-Dubai Amir Hussain |
| author_facet | Asrar Rashid Feras Al-Obeidat Hari Krishnan Kanthimathinathan Govind Benakatti Wael Hafez Raghu Ramaiah Joe Brierley Benjamin Hanisch Praveen Khilnani Christos Koutentis Berit S. Brusletto Mohammed Toufiq Zain Hussain Harish Vyas Zainab A Malik Maike Schumacher Rayaz A Malik Shriprasad Deshpande Nasir Quraishi Raziya Kadwa Amrita Sarpal M. Guftar Shaikh Javed Sharief Syed Ahmed Zaki Rajesh Phatak Akash Deep Ahmed Al-Dubai Amir Hussain |
| author_sort | Asrar Rashid |
| collection | DOAJ |
| description | Sepsis continues to be recognized as a significant global health challenge across all ages and is characterized by a complex pathophysiology. In this scoping review, PRISMA-ScR guidelines were adhered to, and a transcriptomic methodology was adopted, with the protocol registered on the Open Science Framework. We hypothesized that gene expression analysis could provide a foundation for establishing a clinical research framework for sepsis. A comprehensive search of the PubMed database was conducted with a particular focus on original research and systematic reviews of transcriptomic sepsis studies published between 2012 and 2022. Both coding and non-coding gene expression studies have been included in this review. An effort was made to enhance the understanding of sepsis at the mRNA gene expression level by applying a systems biology approach through transcriptomic analysis. Seven crucial components related to sepsis research were addressed in this study: endotyping (n = 64), biomarker (n = 409), definition (n = 0), diagnosis (n = 1098), progression (n = 124), severity (n = 451), and benchmark (n = 62). These components were classified into two groups, with one focusing on Biomarkers and Endotypes and the other oriented towards clinical aspects. Our review of the selected studies revealed a compelling association between gene transcripts and clinical sepsis, reinforcing the proposed research framework. Nevertheless, challenges have arisen from the lack of consensus in the sepsis terminology employed in research studies and the absence of a comprehensive definition of sepsis. There is a gap in the alignment between the notion of sepsis as a clinical phenomenon and that of laboratory indicators. It is potentially responsible for the variable number of patients within each category. Ideally, future studies should incorporate a transcriptomic perspective. The integration of transcriptomic data with clinical endpoints holds significant potential for advancing sepsis research, facilitating a consensus-driven approach, and enabling the precision management of sepsis. |
| first_indexed | 2024-03-08T12:09:05Z |
| format | Article |
| id | doaj.art-cc44dde4c7e94c67b131c70e3cb338e0 |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-03-08T12:09:05Z |
| publishDate | 2024-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-cc44dde4c7e94c67b131c70e3cb338e02024-01-23T04:15:44ZengElsevierInformatics in Medicine Unlocked2352-91482024-01-0144101419Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping reviewAsrar Rashid0Feras Al-Obeidat1Hari Krishnan Kanthimathinathan2Govind Benakatti3Wael Hafez4Raghu Ramaiah5Joe Brierley6Benjamin Hanisch7Praveen Khilnani8Christos Koutentis9Berit S. Brusletto10Mohammed Toufiq11Zain Hussain12Harish Vyas13Zainab A Malik14Maike Schumacher15Rayaz A Malik16Shriprasad Deshpande17Nasir Quraishi18Raziya Kadwa19Amrita Sarpal20M. Guftar Shaikh21Javed Sharief22Syed Ahmed Zaki23Rajesh Phatak24Akash Deep25Ahmed Al-Dubai26Amir Hussain27School of Computing, Edinburgh Napier University, UK; NMC Royal Hospital, Abu Dhabi, United Arab Emirates; Corresponding author. Edinburgh Napier University, Sighthill Campus, Sighthill Court, Edinburgh EH11 4BN, UK.College of Technological Innovation, Zayed University, Abu Dhabi, United Arab EmiratesBirmingham Children's Hospital, Birmingham, UKYas Clinic, Abu Dhabi, United Arab EmiratesInternal Medicine Department, The National Research Centre, Cairo, Egypt; NMC Royal Hospital, Abu Dhabi, United Arab EmiratesUniversity of Leicester NHS Trust, UKGreat Ormond Street Children's Hospital, London, UKChildren's National Hospital, Washington, DC, USAMedanta Gururam, Delhi, IndiaDepartment of Anesthesiology, SUNY Downstate Medical Center, USAThe Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, NorwayThe Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USAEdinburgh Medical School, University go Edinburgh, Edinburgh, UKNottingham University, Nottingham, UKCollege of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab EmiratesSheikh Khalifa Medical City, United Arab EmiratesInstitute of Cardiovascular Science, University of Manchester. Manchester, UK; Weill Cornell Medicine-Qatar, Doha, QatarChildren's National Hospital, Washington, DC, USACentre for Spinal Studies & Surgery, Queen's Medical Centre, The University of Nottingham, Nottingham, UKNMC Royal Hospital, Abu Dhabi, United Arab EmiratesWeill Cornell Medicine-Qatar, Doha, Qatar; Sidra Medicine, Doha, QatarDepartment of Endocrinology, Royal Hospital for Children, Glasgow, UKNMC Royal Hospital, Abu Dhabi, United Arab EmiratesAll India Institute of Medical Sciences, Bibinagar, Hyderabad, IndiaPediatric Intensive Care, Burjeel Hospital, Najda, Abu Dhabi, United Arab EmiratesPediatric Intensive Care Unit, King's College Hospital, London, UKSchool of Computing, Edinburgh Napier University, UKSchool of Computing, Edinburgh Napier University, UKSepsis continues to be recognized as a significant global health challenge across all ages and is characterized by a complex pathophysiology. In this scoping review, PRISMA-ScR guidelines were adhered to, and a transcriptomic methodology was adopted, with the protocol registered on the Open Science Framework. We hypothesized that gene expression analysis could provide a foundation for establishing a clinical research framework for sepsis. A comprehensive search of the PubMed database was conducted with a particular focus on original research and systematic reviews of transcriptomic sepsis studies published between 2012 and 2022. Both coding and non-coding gene expression studies have been included in this review. An effort was made to enhance the understanding of sepsis at the mRNA gene expression level by applying a systems biology approach through transcriptomic analysis. Seven crucial components related to sepsis research were addressed in this study: endotyping (n = 64), biomarker (n = 409), definition (n = 0), diagnosis (n = 1098), progression (n = 124), severity (n = 451), and benchmark (n = 62). These components were classified into two groups, with one focusing on Biomarkers and Endotypes and the other oriented towards clinical aspects. Our review of the selected studies revealed a compelling association between gene transcripts and clinical sepsis, reinforcing the proposed research framework. Nevertheless, challenges have arisen from the lack of consensus in the sepsis terminology employed in research studies and the absence of a comprehensive definition of sepsis. There is a gap in the alignment between the notion of sepsis as a clinical phenomenon and that of laboratory indicators. It is potentially responsible for the variable number of patients within each category. Ideally, future studies should incorporate a transcriptomic perspective. The integration of transcriptomic data with clinical endpoints holds significant potential for advancing sepsis research, facilitating a consensus-driven approach, and enabling the precision management of sepsis.http://www.sciencedirect.com/science/article/pii/S2352914823002654SepsisTranscriptomicsOmicSepsis definitionBiomarkEndotype |
| spellingShingle | Asrar Rashid Feras Al-Obeidat Hari Krishnan Kanthimathinathan Govind Benakatti Wael Hafez Raghu Ramaiah Joe Brierley Benjamin Hanisch Praveen Khilnani Christos Koutentis Berit S. Brusletto Mohammed Toufiq Zain Hussain Harish Vyas Zainab A Malik Maike Schumacher Rayaz A Malik Shriprasad Deshpande Nasir Quraishi Raziya Kadwa Amrita Sarpal M. Guftar Shaikh Javed Sharief Syed Ahmed Zaki Rajesh Phatak Akash Deep Ahmed Al-Dubai Amir Hussain Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review Informatics in Medicine Unlocked Sepsis Transcriptomics Omic Sepsis definition Biomark Endotype |
| title | Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review |
| title_full | Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review |
| title_fullStr | Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review |
| title_full_unstemmed | Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review |
| title_short | Advancing sepsis clinical research: harnessing transcriptomics for an omics-based strategy - a comprehensive scoping review |
| title_sort | advancing sepsis clinical research harnessing transcriptomics for an omics based strategy a comprehensive scoping review |
| topic | Sepsis Transcriptomics Omic Sepsis definition Biomark Endotype |
| url | http://www.sciencedirect.com/science/article/pii/S2352914823002654 |
| work_keys_str_mv | AT asrarrashid advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT ferasalobeidat advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT harikrishnankanthimathinathan advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT govindbenakatti advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT waelhafez advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT raghuramaiah advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT joebrierley advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT benjaminhanisch advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT praveenkhilnani advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT christoskoutentis advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT beritsbrusletto advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT mohammedtoufiq advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT zainhussain advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT harishvyas advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT zainabamalik advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT maikeschumacher advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT rayazamalik advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT shriprasaddeshpande advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT nasirquraishi advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT raziyakadwa advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT amritasarpal advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT mguftarshaikh advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT javedsharief advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT syedahmedzaki advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT rajeshphatak advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT akashdeep advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT ahmedaldubai advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview AT amirhussain advancingsepsisclinicalresearchharnessingtranscriptomicsforanomicsbasedstrategyacomprehensivescopingreview |