Decoding Injury Project (BECCAi)


Blood Diagnostics for Physiology and Trauma in the Acute Care Settings

Recent advancements in technologies allowing for the rapid analysis of DNA, RNA and protein have opened up a new frontier of discovery from a simple blood specimen. These technologies to date have mostly been focused upon cancer detection and monitoring and infectious diagnosis. It is the aim of this proposal to leverage these technologic advances into addressing unsolved diagnostic dilemmas in the acute care setting. We aim to create the infrastructure for IRB support, patient consent, clinical data accumulation, sample collection, to assess genomic and proteomic signatures from normal patients and those suffering acute clinical syndromes (trauma). We aim to define genomic and proteomic signatures that can more precisely decode injury states previously only assessable by radiologic or surgical approaches. For example, patients presenting unconscious to emergency room setting undergo costly stabilization and radiologic assessment to distinguish metabolically toxic states from traumatic brain injury (TBI). We hypothesize that a combination of brain derived protein biomarkers and or neural specific mRNAs will be present in measurable quantities in circulating blood and these could be measured on emerging rapid sample-to-answer platforms in the acute care setting. We aim to create a world leading infrastructure for discovery and validation of the next generation of diagnostic tools addressing acute care diagnostic dilemmas. We expect that this methodology will be available to all members of our faculty that have relevant clinical questions that can provide a diagnostic signature for the patient population of interest.


CNS specific biomarkers in blood that could be applied at point of care would be transformative in the diagnosis and treatment of brain trauma. We aim to identify novel nucleic acid biomarkers in plasma to differentiate traumatic brain injury from toxicologic and metabolic causes of altered mental status.  Here we propose the discovery of brain specific RNA transcripts in human plasma that are diagnostic for the type and extent of tissue injury in traumatic brain injury (TBI). Physical or ischemic tissue damage to the internal organs leads to discharge of cellular components into the circulation in trauma patients [4]. Traditionally, protein markers have been thought of as the primary source of tissue specific biomarkers. Recent studies have demonstrated a surprising amount of RNA species in plasma suggesting that RNA, including mRNA fragments, might also be detectable as biomarkers [10]. Here we show that RNAs found in plasma can be significantly correlated with severe traumatic brain injury (TBI). In order to narrow and specify the RNA transcripts most useful for diagnostic purposes, human plasma samples collected from trauma patients were subjected to RNA sequencing with high read depth (~20 million reads per sample). Our source of human plasma samples is the PROPPR blood-coagulation studies (ZSFG, Dr. Mitch Cohen). This sample collection contains nearly 1200 trauma activations with highly-annotated associated diagnostic workups and clinical outcomes. Most importantly plasma samples from all patients were stored from the initial blood draw (i.e. prior to transfusion) and possess a time stamp for the trauma event. Precisely timed CNS-perturbation human samples are rare and, with such resources, we have a unique opportunity to identify the earliest markers of the TBI and other organ specific damage. The overall goal of the project is to survey the entire trauma database and create a rich publicly available database for trauma, based on type of injury and severity, demographics, treatment and outcome derived from an ongoing prospective clinical database. For example by comparing patients who have severe traumatic brain injury (TBI) to trauma patients with toxicologic or metabolic causes of altered mental status, we will identify unique biomarkers for diagnosis and grading of the extent of TBI. Furthermore by matching unique sequence reads from human plasma to tissue specific genomic profiles of highly purified organ cell types we will identify nucleic acid biomarkers that diagnose cell type damage in trauma (i.e. identifying markers for blood brain barrier breakdown and or site-specific CNS parenchymal tissue damage.) Diagnostically specific biomarkers will be used to develop organ specific CLIA-based lab tests to guide care of the TBI and trauma patient in acute care and ICU settings.


Roland Bainton, MD, PhD

Professor In Residence
Department of Anesthesia and Perioperative Care




Arun Prakash, MD, PhD

Assistant Professor In Residence,
Department of Anesthesia and Perioperative Care




Philip Kurien, MD

Assistant Professor In Residence
Department of Anesthesia and Perioperative Care