Acute blood RNA sequencing from SCI human patients

DOI:10.34945/F5QC7J

DATASET CITATION

Kyritsis N., Torres-Espin A., Schupp P. G., Huie J. Russell., Chou A., Duong-Fernandez X., Thomas L. H., Tsolinas R. E., Hemmerle D. D., Pascual L. U., Singh V., Pan J. Z., Talbott J. F., Whetstone W. D., Burke J. F., DiGiorgio A. M., Weinstein P. R., Manley G. T., Dhall S. S., Ferguson A. R., Oldham M. C., Bresnahan J. C., Beattie M. S. (2021) Acute blood RNA sequencing from SCI human patients. Open Data Commons for Spinal Cord Injury. ODC-SCI: 405 http://doi.org/10.34945/F5QC7J

ABSTRACT

STUDY PURPOSE: The purpose of this study is to discover, through high throughput methods, blood RNA biomarkers with the ability to diagnose accurately the severity of the spinal cord injury at the acute stage.

DATA COLLECTED: Total RNA was collected from white blood cells of 38 spinal cord injury patients, 10 healthy subjects and 10 non-CNS trauma patients. The samples were collected on average within the first 24 hours after injury. Subsequently the RNA was used for RNAseq. These subjects were enrolled in the Transforming Research and Clinical Knowledge in Spinal Cord Injury (TRACK-SCI) clinical study, and we included clinical variables such as age, sex, race, prior CNS pathology, concurrent TBI, injury severity score, AIS grade, neurological level of injury, and motor and sensory scores. Both clinical and transcriptomic data were used to generate a predictive model for the initial severity of spinal cord injury.

DATA USAGE NOTES: Analysis of our gene expression data revealed 197 genes that they are expressed in an severity-dependent manner. Furthermore, unsupervised gene co-expression network analysis was used for the discovery of 16 gene modules that are induced upon spinal cord injury. A logistic regression model using these modules displayed high accuracy in diagnosing the initial injury severity.

KEYWORDS

Spinal Cord Injury; diagnostic biomarker; RNAseq; Clinical research; blood biomarker

PROVENANCE / ORIGINATING PUBLICATIONS

• Blood RNA Profiles are Diagnostic for Severity in Human Acute Spinal Cord Injury. Nikos Kyritsis, Abel Torres-Espin, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong-Fernandez, Leigh H. Thomas, Rachel E. Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M. DiGiorgio, Philip R. Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie. bioRxiv 2020.04.15.037325; doi:10.1101/2020.04.15.037325.

Originating publication.

• Tsolinas, R. E., Burke, J. F., DiGiorgio, A. M., Thomas, L. H., Duong-Fernandez, X., Harris, M. H., Yue, J. K., Winkler, E. A., Suen, C. G., Pascual, L. U., Ferguson, A. R., Huie, J. R., Pan, J. Z., Hemmerle, D. D., Singh, V., Torres-Espin, A., Omondi, C., Kyritsis, N., Haefeli, J., Weinstein, P. R., de Almeida Neto, C. A., Kuo, Y., Taggard, D., Talbott, J. F., Whetstone, W. D., Manley, G. T., Bresnahan, J. C., Beattie, M. S., & Dhall, S. S. (2020). Transforming Research and Clinical Knowledge in Spinal Cord Injury (TRACK-SCI): an overview of initial enrollment and demographics, Neurosurgical Focus FOC, 48(5), E6. Retrieved Dec 1, 2020, from https://thejns.org/focus/view/journals/neurosurg-focus/48/5/article-pE6.xml. doi:10.3171/2020.2.FOCUS191030.

TRACK-SCI overview with description of clinical data collection.

• Kyritsis N, Torres-Espín A, Schupp PG, Huie JR, Chou A, Duong-Fernandez X, Thomas LH, Tsolinas RE, Hemmerle DD, Pascual LU, Singh V, Pan JZ, Talbott JF, Whetstone WD, Burke JF, DiGiorgio AM, Weinstein PR, Manley GT, Dhall SS, Ferguson AR, Oldham MC, Bresnahan JC, Beattie MS. Diagnostic blood RNA profiles for human acute spinal cord injury. J Exp Med. 2021 Mar 1;218(3):e20201795. doi: 10.1084/jem.20201795. PMID: 33512429.

Originating publication

DATASET INFO

Contact: Beattie Michael (michael.beattie@ucsf.edu)

Lab: TRACK-SCI

ODC-SCI Accession:405

Records in Dataset: 1015058

Fields per Record: 61

Last updated: 2021-01-22 (See changelog)

Date published: 2021-01-22

Downloads: 76

Files: 2

LICENSE

Creative Commons Attribution License (CC-BY 4.0)

FUNDING AND ACKNOWLEDGEMENTS

Department of Defense grants W81XWH-13-1-0297 (M.S.B.) and W81XWH-16-1-0497 (M.S.B.), Craig H. Neilsen Foundation UCSF SCI Center of Excellence special project award (M.S.B.), Wings for Life WFL-US-07/18 (N.K.)

CONTRIBUTORS

Kyritsis, Nikos [ORCID:0000-0001-7801-5796]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Torres-Espin, Abel [ORCID:0000-0002-9787-8738]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Schupp, Patrick G. [ORCID:0000-0001-5885-2386]

Brain Tumor Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Huie, J Russell. [ORCID:0000-0001-5594-4277]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Chou, Austin [ORCID:0000-0003-4328-5811]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Duong-Fernandez, Xuan [ORCID:0000-0001-8362-4166]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Thomas, Leigh H. [ORCID:0000-0002-7593-0240]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Tsolinas, Rachel E. [ORCID:0000-0003-3867-592X]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Hemmerle, Debra D. [ORCID:0000-0003-2796-6107]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Pascual, Lisa U. [ORCID:000-0001-6228-6217]

Orthopaedic Trauma Institure, Department of Orthopaedic Surgery, University of California San Francisco (UCSF)

Singh, Vineeta [ORCID:0000-0003-3470-3532]

Brain and Spinal Injury Center, Department of Neurology, University of California San Francisco (UCSF)

Pan, Jonathan Z. [ORCID:0000-0001-5814-3707]

Brain and Spinal Injury Center, Department of Anesthesia and Perioperative Care, University of California San Francisco (UCSF)

Talbott, Jason F. [ORCID:0000-0003-3943-5530]

Zuckerberg San Francisco General Hospital and Trauma Center, Department of Radiology and Biomedical Imaging, University of California San Francisco (UCSF)

Whetstone, William D. [ORCID:0000-0002-8568-6640]

Department of Emergency Medicine, University of California San Francisco (UCSF)

Burke, John F. [ORCID:0000-0002-6190-5116]

Department of Neurological Surgery, University of California San Francisco (UCSF)

DiGiorgio, Anthony M. [ORCID:0000-0002-5710-691X]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Weinstein, Philip R. [ORCID:0000-0003-4038-745X]

Institure for Neurodegenerative Diseases, Spine Center, Departments of Neurology and Neurological Surgery, University of California San Francisco (UCSF)

Manley, Geoffrey T. [ORCID:0000-0002-0926-3128]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Dhall, Sanjay S. [ORCID:0000-0002-6891-2722]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Ferguson, Adam R. [ORCID:0000-0001-7102-1608]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Oldham, Michael C. [ORCID:0000-0001-7633-6932]

Brain Tumor Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Bresnahan, Jacqueline C. [ORCID:0000-0003-2243-7054]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)

Beattie, Michael S. [ORCID:0000-0001-9463-3631]

Brain and Spinal Injury Center, Department of Neurological Surgery, University of California San Francisco (UCSF)