As a trauma, critical care, and acute care surgeon my research focuses on better understanding immune mechanisms in critical illness. Currently I am studying the use of Deep RNA Seqencing (>100 million reads) in sepsis. We look at multiple distinct data sets from this single blood draw to study things such as gene expression, alternative RNA splicing, antibody formation, and pathogens in critical illness as they relates to potential biomarkers and therapeutic interventions.
| Duan C, Buerer L, Wang J, Kaplan S, Sabalewski G, Jay GD, Monaghan SF, Arena AE, Fairbrother WG. "Efficient Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Exhaled Breath." The Journal of molecular diagnostics : JMD, vol. 23, no. 12, 2021, pp. 1661-1670. |
| Tindal, Elizabeth W., Armstead, Brandon E., Monaghan, Sean F., Heffernan, Daithi S., Ayala, Alfred. "Emerging therapeutic targets for sepsis." Expert Opinion on Therapeutic Targets, vol. 25, no. 3, 2021, pp. 175-189. |
| Cohen M, Monaghan SF. "Hemorrhagic shock and fluid dynamics." Physiological reports, vol. 9, no. 6, 2021, pp. e14813. |
| Kheirbek T, Jikaria N, Murray B, Martin TJ, Lueckel SN, Stephen AH, Monaghan SF, Adams CA. "Unjustified Administration in Liberal Use of Tranexamic Acid in Trauma Resuscitation." Journal of Surgical Research, vol. 258, 2021, pp. 125-131. |
| Fredericks AM, Wang LJ, Fairbrother WG, Ayala A, Monaghan SF. "Alternative RNA splicing and alternative transcription start/end in acute respiratory distress syndrome." Intensive care medicine, 2020. |
| Wakeley, Michelle E., Gray, Chyna C., Monaghan, Sean F., Heffernan, Daithi S., Ayala, Alfred. "Check Point Inhibitors and Their Role in Immunosuppression in Sepsis." Critical Care Clinics, vol. 36, no. 1, 2020, pp. 69-88. |
| Wakeley ME, Shubin NJ, Monaghan SF, Gray CC, Ayala A, Heffernan DS. "Herpes Virus Entry Mediator (HVEM): A Novel Potential Mediator of Trauma-Induced Immunosuppression." Journal of Surgical Research, vol. 245, 2020, pp. 610-618. |
| Hall BM, Geraci TC, Machan JT, Milman S, Adams CA, Cioffi W, Ng T, Monaghan S. "Lack of Lymphocyte Recovery After Esophagectomy Predicts Overall and Recurrence-Free Survival." Journal of Surgical Research, vol. 246, 2020, pp. 379-383. |
| Kheirbek T, Monaghan SF, Benoit E, Lueckel SN, Adams CA Jr. "Advances in the Management of Bleeding Trauma Patients." Rhode Island medical journal (2013), vol. 102, no. 8, 2019, pp. 30-33. |
| Stephen AH, Monaghan SF, Lueckel SN, Adams CA Jr. "Anticoagulation and Trauma." Rhode Island medical journal (2013), vol. 102, no. 8, 2019, pp. 23-26. |
| Stephen AH, Shah M, Sim JT, Soipe A, Lueckel SN, Kheirbek T, Heffernan DS, Monaghan SF, Adams CA Jr. "Dismal outcomes following damage control laparotomy in injured older adults, a cohort study." The American Journal of Surgery, vol. 218, no. 1, 2019, pp. 82-86. |
| Benoit E, Stephen AH, Monaghan SF, Lueckel SN, Adams CA Jr. "Geriatric Trauma." Rhode Island medical journal (2013), vol. 102, no. 8, 2019, pp. 19-22. |
| Connolly MD, Monaghan SF, Heffernan D, Lueckel SN, Adams CA Jr. "Practice Makes Perfect: The Evolution of Blunt Chest Trauma." Rhode Island medical journal (2013), vol. 102, no. 8, 2019, pp. 27-29. |
| Lueckel SN, Stephen AH, Monaghan SF, Binder W, Adams CA Jr. "Predicting Outcomes in Acute Traumatic Brain Injury (TBI)." Rhode Island medical journal (2013), vol. 102, no. 8, 2019, pp. 34-36. |
| Fallon, Eleanor A, Biron-Girard, Bethany M, Chung, Chun-Shiang, Lomas-Neira, Joanne, Heffernan, Daithi S, Monaghan, Sean F, Ayala, Alfred. "A novel role for coinhibitory receptors/checkpoint proteins in the immunopathology of sepsis." Journal of Leukocyte Biology, vol. 103, no. 6, 2018, pp. 1151-1164. |
| Monaghan, Sean F., Banerjee, Debasree, Chung, Chun-Shiang, Lomas-Neira, Joanne, Cygan, Kamil J., Rhine, Christy L., Fairbrother, William G., Heffernan, Daithi S., Levy, Mitchell M., Cioffi, William G., Ayala, Alfred. "Changes in the process of alternative RNA splicing results in soluble B and T lymphocyte attenuator with biological and clinical implications in critical illness." Molecular Medicine, vol. 24, no. 1, 2018, pp. 32. |
| Rhine CL, Cygan KJ, Soemedi R, Maguire S, Murray MF, Monaghan SF, Fairbrother WG. "Hereditary cancer genes are highly susceptible to splicing mutations." PLOS Genetics, vol. 14, no. 3, 2018, pp. e1007231. |
| Lomas-Neira J, Monaghan SF, Huang X, Fallon EA, Chung CS, Ayala A. "Novel Role for PD-1:PD-L1 as Mediator of Pulmonary Vascular Endothelial Cell Functions in Pathogenesis of Indirect ARDS in Mice." Frontiers in Immunology, vol. 9, 2018, pp. 3030. |
| Lueckel, Stephanie N., Kosar, Cyrus M., Teno, Joan M., Monaghan, Sean F., Heffernan, Daithi S., Cioffi, William G., Thomas, Kali S. "Outcomes in nursing home patients with traumatic brain injury." Surgery, vol. 164, no. 1, 2018, pp. 150-154. |
| Banerjee D, Monaghan S, Zhao R, Walsh T, Palmisciano A, Phillips GS, Opal S, Levy MM. "Soluble programmed cell death protein-1 and programmed cell death ligand-1 in sepsis." Critical Care, vol. 22, no. 1, 2018, pp. 146. |
| Dickinson, Catherine M., Karlin, Daniel R., Nunez, Hector R., Cao, Shiliang A., Heffernan, Daithi S., Monaghan, Sean F., Kheirbek, Tareq, Adams, Charles A., Stephen, Andrew H. "Do Patients with Pre-Existing Psychiatric Illness Have an Increased Risk of Infection after Injury?." Surgical Infections, vol. 18, no. 5, 2017, pp. 545-549. |
| Ottinger ME, Monaghan SF, Gregg SC, Stephen AH, Connolly MD, Harrington DT, Adams CA Jr, Cioffi WG, Heffernan DS. "Trauma morning report is the ideal environment to teach and evaluate resident communication and sign-outs in the 80 hour work week." Injury, vol. 48, no. 9, 2017, pp. 2003-2009. |
| Kao MJ, Nunez H, Monaghan SF, Heffernan DS, Adams CA Jr, Lueckel SN, Stephen AH. "Trauma patients who present in a delayed fashion: a unique and challenging population." Journal of Surgical Research, vol. 208, 2017, pp. 204-210. |
| Wu, Youping, Chung, Chun-Shiang. "A Novel Role for Programmed Cell Death Receptor Ligand-1 (PD-L1) in Sepsis-Induced Intestinal Dysfunction." Molecular Medicine, vol. 22, no. 1, 2016, pp. 1. |
| Lomas-Neira JL, Heffernan DS, Ayala A, Monaghan SF. "BLOCKADE OF ENDOTHELIAL GROWTH FACTOR, ANGIOPOIETIN-2, REDUCES INDICES OF ARDS AND MORTALITY IN MICE RESULTING FROM THE DUAL-INSULTS OF HEMORRHAGIC SHOCK AND SEPSIS." Shock, vol. 45, no. 2, 2016, pp. 157-165. |
| Heffernan DS, Monaghan SF, Ayala A. "Lymphocyte integrin expression differences between SIRS and sepsis patients." Irish Journal of Medical Science (1971 -), vol. 186, no. 4, 2016, pp. 981-987. |
| Zimmerman AM, Marwaha J, Nunez H, Harrington D, Heffernan D, Monaghan S, Adams C, Stephen A. "Preoperative Myocardial Injury as a Predictor of Mortality in Emergency General Surgery: An Analysis Using the American College of Surgeons NSQIP Database." Journal of the American College of Surgeons, vol. 223, no. 2, 2016, pp. 381-6. |
| Monaghan SF, Chung CS, Chen Y, Lomas-Neira J, Fairbrother WG, Heffernan DS, Cioffi WG, Ayala A. "Soluble programmed cell death receptor-1 (sPD-1): a potential biomarker with anti-inflammatory properties in human and experimental acute respiratory distress syndrome (ARDS)." Journal of Translational Medicine, vol. 14, no. 1, 2016, pp. 312. |
| Young JS, Monaghan SF, Chung CS, Cioffi WG, Ayala A, Heffernan DS. "Divergent Invariant Natural Killer T-Cell Response to Sepsis of Abdominal vs. Non-Abdominal Origin in Human Beings." Surgical infections, vol. 16, no. 1, 2015, pp. 29-35. |
| Ottinger ME, Monaghan SF, Gravenstein S, Cioffi WG, Ayala A, Heffernan DS. "The geriatric cytokine response to trauma: time to consider a new threshold." Surgical Infections, vol. 15, no. 6, 2015, pp. 800-805. |
| Heffernan DS, Monaghan SF, Chung CS, Cioffi WG, Gravenstein S, Ayala A. "A divergent response of innate regulatory T-cells to sepsis in humans: circulating invariant natural killer T-cells are preserved." Human immunology, vol. 75, no. 3, 2014, pp. 277-82. |
| Huang X, Chen Y, Chung CS, Yuan Z, Monaghan SF, Wang F, Ayala A. "Identification of B7-H1 as a novel mediator of the innate immune/proinflammatory response as well as a possible myeloid cell prognostic biomarker in sepsis." The Journal of Immunology, vol. 192, no. 3, 2014, pp. 1091-9. |
| Shubin NJ, Monaghan SF, Heffernan DS, Chung CS, Ayala A. "B and T lymphocyte attenuator expression on CD4+ T-cells associates with sepsis and subsequent infections in ICU patients." Critical Care, vol. 17, no. 6, 2013, pp. R276. |
| Thakkar RK, Monaghan SF, Adams CA Jr, Stephen A, Connolly MD, Gregg S, Cioffi WG, Heffernan DS. "Empiric antibiotics pending bronchoalveolar lavage data in patients without pneumonia significantly alters the flora, but not the resistance profile, if a subsequent pneumonia develops." Journal of Surgical Research, vol. 181, no. 2, 2013, pp. 323-8. |
| Heffernan DS, Monaghan SF, Thakkar RK, Tran ML, Chung CS, Gregory SH, Cioffi WG, Ayala A. "Inflammatory mechanisms in sepsis: elevated invariant natural killer T-cell numbers in mouse and their modulatory effect on macrophage function." Shock, vol. 40, no. 2, 2013, pp. 122-8. |
| Shubin NJ, Chung CS, Heffernan DS, Irwin LR, Monaghan SF, Ayala A. "BTLA expression contributes to septic morbidity and mortality by inducing innate inflammatory cell dysfunction." Journal of Leukocyte Biology, vol. 92, no. 3, 2012, pp. 593-603. |
| Heffernan DS, Monaghan SF, Thakkar RK, Machan JT, Cioffi WG, Ayala A. "Failure to normalize lymphopenia following trauma is associated with increased mortality, independent of the leukocytosis pattern." Critical Care, vol. 16, no. 1, 2012, pp. R12. |
| Monaghan SF, Adams CA Jr, Stephen AH, Connolly MD, Gregg SC, Machan JT, Cioffi WG, Heffernan DS. "Infections after trauma are associated with subsequent cardiac injury." Journal of Trauma and Acute Care Surgery, vol. 73, no. 5, 2012, pp. 1079-84; discussion 1084-5. |
| Monaghan SF, Thakkar RK, Heffernan DS, Huang X, Chung CS, Lomas-Neira J, Cioffi WG, Ayala A. "Mechanisms of indirect acute lung injury: a novel role for the coinhibitory receptor, programmed death-1." Annals of Surgery, vol. 255, no. 1, 2012, pp. 158-64. |
| Monaghan SF, Thakkar RK, Tran ML, Huang X, Cioffi WG, Ayala A, Heffernan DS. "Programmed death 1 expression as a marker for immune and physiological dysfunction in the critically ill surgical patient." Shock, vol. 38, no. 2, 2012, pp. 117-22. |
| Monaghan SF, Blakely AM, Richardson PJ, Miner TJ, Cioffi WG, Harrington DT. "The reflective statement: a new tool to assess resident learning." Journal of Surgical Research, vol. 178, no. 2, 2012, pp. 618-22. |
| Duron VP, Monaghan SF, Connolly MD, Gregg SC, Stephen AH, Adams CA Jr, Cioffi WG, Heffernan DS. "Undiagnosed medical comorbidities in the uninsured: a significant predictor of mortality following trauma." Journal of Trauma and Acute Care Surgery, vol. 73, no. 5, 2012, pp. 1093-8; discussion 1098-9. |
| Shubin NJ, Monaghan SF, Ayala A. "Anti-inflammatory mechanisms of sepsis." Contributions to microbiology, vol. 17, 2011, pp. 108-24. |
| Heffernan DS, Vera RM, Monaghan SF, Thakkar RK, Kozloff MS, Connolly MD, Gregg SC, Machan JT, Harrington DT, Adams CA Jr, Cioffi WG. "Impact of socioethnic factors on outcomes following traumatic brain injury." The Journal of trauma, vol. 70, no. 3, 2011, pp. 527-34. |
| Thakkar RK, Chung CS, Chen Y, Monaghan SF, Lomas-Neira J, Heffernan DS, Cioffi WG, Ayala A. "Local tissue expression of the cell death ligand, fas ligand, plays a central role in the development of extrapulmonary acute lung injury." Shock, vol. 36, no. 2, 2011, pp. 138-43. |
| Monaghan SF, Heffernan DS, Thakkar RK, Reinert SE, Machan JT, Connolly MD, Gregg SC, Kozloff MS, Adams CA Jr, Cioffi WG. "The development of a urinary tract infection is associated with increased mortality in trauma patients." The Journal of trauma, vol. 71, no. 6, 2011, pp. 1569-74. |
| Heffernan DS, Thakkar RK, Monaghan SF, Ravindran R, Adams CA Jr, Kozloff MS, Gregg SC, Connolly MD, Machan JT, Cioffi WG. "Normal presenting vital signs are unreliable in geriatric blunt trauma victims." The Journal of trauma, vol. 69, no. 4, 2010, pp. 813-20. |
| Monaghan SF, Anjaria D, Mohr A, Livingston DH. "Necrotizing fasciitis and sepsis caused by Aeromonas hydrophila after crush injury of the lower extremity." Surgical infections, vol. 9, no. 4, 2008, pp. 459-67. |
| Monaghan SF, Swan KG. "Tube thoracostomy: the struggle to the "standard of care"." The Annals of Thoracic Surgery, vol. 86, no. 6, 2008, pp. 2019-22. |
| Deitch EA, Livingston DH, Lavery RF, Monaghan SF, Bongu A, Machiedo GW. "Hormonally active women tolerate shock-trauma better than do men: a prospective study of over 4000 trauma patients." Annals of Surgery, vol. 246, no. 3, 2007, pp. 447-53; discussion 453-5. |
1. Pathophysiologic changes present in ARDS cause alternative RNA splicing events
RNA splicing is known to be influenced by physiologic conditions such as acidosis and hypoxia, both common in ARDS. We will investigate these conditions and the splicing protein U1-70K and the impact on the pulmonary endothelial barrier. We will utilize RNA sequencing, over-expression of U1-70K isoforms, and Electric Cell-substrate Impedance Sensing (ECIS) in this work.
2. Utilize RNA sequencing data to diagnose critical illness
RNA sequencing produces large data sets, our lab usually aims for 100 million reads per sample. There is incredible information in not only the data that aligns to the genome, but also the un-mapped reads. We attempt to analyze the data in unique was to give outputs that are relevant for clinical practice. Using the RNA sequenicng data from blood samples in humans we will look at gene expression, alternative RNA splicing, antibody production, and pathogens. This data will be used to generate diagnostic and therapeutic tools
2015-2016
Brown University DEANS Award “Immune Dysfunction in Critical Illness/Injury: Role of Alternative Splicing”
Principal Investigators: Sean Monaghan, MD & Will Fairbrother, PhD
Total Costs: $80,000
2016-2018
American College of Surgeons, C. James Carrico, MD, FACS, Faculty Research Fellowship for the Study of Trauma and Critical Care “Immune Dysfunction in Critical Illness/Injury: Role of Alternative Splicing”
Principal Investigator: Sean Monaghan, MD
Total Costs: $80,000
2016-2022
National Institutes of Health (NIH) Loan Repayment Program
Principal Investigator: Sean Monaghan, MD
Total Costs: $263,241
2018
NIH-NIGMS Pilot Project from the CardioPulmonary Vascular Biology (CPVB) Centers of Biomedical Excellence (COBRE): “Alternative RNA Splicing of Endothelial Cell Adhesion Proteins (PECAM-1 and VE-Cadherin) in ARDS”
Principal Investigator: Sean Monaghan, MD
Total Support: $25,000
2018-2021
NIH-NIGMS Junior Faculty CardioPulmonary Vascular Biology (CPVB) Centers of Biomedical Excellence (COBRE): “The Role of Alternative RNA Splicing in Endothelial Cell Barrier Dysfunction in Acute Respiratory Distress Syndrome”
Principal Investigator: Sean Monaghan, MD
2019-2020
Brown Physicians Inc (BPI) Research Award “The Role of Alternative RNA Splicing in Endothelial Cell Barrier Dysfunction in Acute Respiratory Distress Syndrome”
Principal Investigator: Sean Monaghan, MD
Total Support: $50,000
2021-2022
Brown Physicians Inc (BPI) Research Award “The Role of Alternative RNA Splicing in Endothelial Cell Barrier Dysfunction in Acute Respiratory Distress Syndrome”
Principal Investigator: Sean Monaghan, MD
Total Support: $50,000
2021-2026
NIH-NIGMS Improving Sepsis Care with Deep RNA Sequencing Data (R35GM142638)
Principal Investigator: Sean Monaghan, MD
Total Support: $1,982,510
| Year | Degree | Institution |
|---|---|---|
| 2007 | MD | University of Medicine/Dentistry of New Jersey |
| 2002 | BS | Boston College |
2006 Gold Humanism Honor Society, UMDNJ-New Jersey Medical School
2008 Outstanding Intern, Alpert Medical School of Brown University Department of Surgery
2009 Armand D. Versaci Research Scholar In Surgical Sciences, Alpert Medical School of Brown University Department of Surgery
2011 Dorman Award for Best Clinical Research Paper, Alpert Medical School of Brown University Department of Surgery
2011 American Association for the Surgery of Trauma (AAST) Resident Scholarship
2013 Alpha Omega Alpha Honor Society, Alpert Medical School of Brown University
2013 Dorman Award for Best Clinical Research Paper, Alpert Medical School of Brown University Department of Surgery
2014 Haffenreffer Family House Staff Excellence Award, Rhode Island Hospital
2014 Russell E. White, MD Award of Professionalism and Ethics in Surgery, Alpert Medical School of Brown University Department of Surgery
2014 Dr. Shoiab Shiekh Surgical Research Award, Alpert Medical School of Brown University Department of Surgery
2014 American Association for the Surgery of Trauma (AAST) Resident/Fellow Scholarship
2017 Outstanding Teaching Faculty, Alpert Medical School of Brown University Department of Surgery
| Name | Title |
|---|---|
| Albina, Jorge | Professor Emeritus of Surgery |
| Ayala, Alfred | Professor of Surgery (Research) |
| Banerjee, Debasree | Associate Professor of Medicine |
| Chung, Chun-Shiang | Assistant Professor Emerita (Research) of Surgery |
| Cioffi, William | Professor Emeritus of Surgery |
| Elias, Jack | Warren Alpert Foundation Professor of Translational Science, Professor of Molecular Biology, Cell Biology and Biochemistry, Professor of Medicine |
| Fairbrother, William | Professor of Biology |
| Harrington, Elizabeth | Associate Dean for Graduate Studies, Professor of Medicine |
| Heffernan, Daithi | Associate Professor of Surgery |
| Jamieson, Amanda | Esther Elizabeth Brintzenhoff Associate Professor of Molecular Microbiology and Immunology, Pathobiology Graduate Program Co-Director |
| Lefort, Craig | Associate Professor of Surgery (Research) |
| Levy, Mitchell | Professor of Medicine |
| Lisi, George | Thomas J. and Alice M. Tisch Assistant Professor of Molecular Biology, Cell Biology, and Biochemistry |
| Lomas-Neira, Joanne | Assistant Professor of Surgery (Research) |
| Lu, Qing | Associate Professor of Medicine |
| Machan, Jason | Associate Professor of Surgery (Research), Associate Professor of Orthopaedics (Research) |
| Nau, Gerard | Associate Professor of Medicine, Clinician Educator |
| Reichner, Jonathan | Professor of Surgery (Research) |
| Rounds, Sharon | Associate Dean for Translational Science, Professor of Medicine, Professor of Pathology and Laboratory Medicine |
American College of Surgeons
Association for Academic Surgery
Shock Society
Society for Critical Care Medicine
Surgical Infection Society
American Association for the Surgery of Trauma
Society of University Surgeons
RNA Society
