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Sun J, Sepulveda JL, Komissarova EV, Hills C, Seckar TD, LeFevre NM, Simonyan H, Young C, Su G, Del Portillo A, Wang TC, Sepulveda AR. CDKN2A-p16 Deletion and Activated KRAS G12D Drive Barrett's-Like Gland Hyperplasia-Metaplasia and Synergize in the Development of Dysplasia Precancer Lesions. Cell Mol Gastroenterol Hepatol 2024; 17:769-784. [PMID: 38296052 PMCID: PMC10966774 DOI: 10.1016/j.jcmgh.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND & AIMS Barrett's esophagus is the precursor of esophageal dysplasia and esophageal adenocarcinoma. CDKN2A-p16 deletions were reported in 34%-74% of patients with Barrett's esophagus who progressed to dysplasia and esophageal adenocarcinoma, suggesting that p16 loss may drive neoplastic progression. KRAS activation frequently occurs in esophageal adenocarcinoma and precancer lesions. LGR5+ stem cells in the squamocolumnar-junction (SCJ) of mouse stomach contribute as Barrett's esophagus progenitors. We aimed to determine the functional effects of p16 loss and KRAS activation in Barrett's-like metaplasia and dysplasia development. METHODS We established mouse models with conditional knockout of CDKN2A-p16 (p16KO) and/or activated KRASG12D expression targeting SCJ LGR5+ cells in interleukin 1b transgenic mice and characterized histologic alterations (mucous-gland hyperplasia/metaplasia, inflammation, and dysplasia) in mouse SCJ. Gene expression was determined by microarray, RNA sequencing, and immunohistochemistry of SCJ tissues and cultured 3-dimensional organoids. RESULTS p16KO mice exhibited increased mucous-gland hyperplasia/metaplasia versus control mice (P = .0051). Combined p16KO+KRASG12D resulted in more frequent dysplasia and higher dysplasia scores (P = .0036), with 82% of p16KO+KRASG12D mice developing high-grade dysplasia. SCJ transcriptome analysis showed several activated pathways in p16KO versus control mice (apoptosis, tumor necrosis factor-α/nuclear factor-kB, proteasome degradation, p53 signaling, MAPK, KRAS, and G1-to-S transition). CONCLUSIONS p16 deletion in LGR5+ cell precursors triggers increased SCJ mucous-gland hyperplasia/metaplasia. KRASG12D synergizes with p16 deletion resulting in higher grades of SCJ glandular dysplasia, mimicking Barrett's high-grade dysplasia. These genetically modified mouse models establish a functional role of p16 and activated KRAS in the progression of Barrett's-like lesions to dysplasia in mice, representing an in vivo model of esophageal adenocarcinoma precancer. Derived 3-dimensional organoid models further provide in vitro modeling opportunities of esophageal precancer stages.
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Affiliation(s)
- Jing Sun
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Jorge L Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Elena V Komissarova
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Caitlin Hills
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Tyler D Seckar
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Narine M LeFevre
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Hayk Simonyan
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Colin Young
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Gloria Su
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Timothy C Wang
- Division of Digestive and Liver diseases, Department of Medicine, Columbia University, New York, New York
| | - Antonia R Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC.
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Porzucek AJ, Proctor AM, Klinkhammer KE, Tritsch SR, Robertson MA, Bashor JP, Villani J, Sepulveda JL, Mores CN. Development of an Accessible and Scalable Quantitative Polymerase Chain Reaction Assay for Monkeypox Virus Detection. J Infect Dis 2023; 227:1084-1087. [PMID: 36221256 DOI: 10.1093/infdis/jiac414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 11/14/2022] Open
Abstract
During the 2022 monkeypox (MPX) outbreak, testing has been limited and results delayed, allowing ongoing transmission. Gold-standard quantitative polymerase chain reaction (qPCR) diagnostics are difficult to obtain. This research adapted the June 2022 CDC MPX qPCR assay for broad implementation. Validated using MPX stocks in a matrix with multiple sample types, MPX was detected with cycle threshold (Ct) values 17.46-35.59 and titer equivalents 8.01 × 106 to 2.45 × 100 plaque-forming unit (PFU)/mL. The detection limit was 3.59 PFU/mL. Sensitivity and specificity were both 100%. This qPCR assay can be quickly and broadly implemented in research and public health laboratories to increase diagnostic capacity amid the growing MPX outbreak.
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Affiliation(s)
- Abigail J Porzucek
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Abigale M Proctor
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Katharina E Klinkhammer
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Sarah R Tritsch
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Molly A Robertson
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Jonathan P Bashor
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Jack Villani
- George Washington University Public Health Laboratory, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, USA
| | - Jorge L Sepulveda
- George Washington University Public Health Laboratory, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, USA
| | - Christopher N Mores
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
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Satlin MJ, Zucker J, Baer BR, Rajan M, Hupert N, Schang LM, Pinheiro LC, Shen Y, Sobieszczyk ME, Westblade LF, Goyal P, Wells MT, Sepulveda JL, Safford MM. Changes in SARS-CoV-2 viral load and mortality during the initial wave of the pandemic in New York City. PLoS One 2021; 16:e0257979. [PMID: 34797838 PMCID: PMC8604305 DOI: 10.1371/journal.pone.0257979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Public health interventions such as social distancing and mask wearing decrease the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is unclear whether they decrease the viral load of infected patients and whether changes in viral load impact mortality from coronavirus disease 2019 (COVID-19). We evaluated 6923 patients with COVID-19 at six New York City hospitals from March 15-May 14, 2020, corresponding with the implementation of public health interventions in March. We assessed changes in cycle threshold (CT) values from reverse transcription-polymerase chain reaction tests and in-hospital mortality and modeled the impact of viral load on mortality. Mean CT values increased between March and May, with the proportion of patients with high viral load decreasing from 47.7% to 7.8%. In-hospital mortality increased from 14.9% in March to 28.4% in early April, and then decreased to 8.7% by May. Patients with high viral loads had increased mortality compared to those with low viral loads (adjusted odds ratio 2.34). If viral load had not declined, an estimated 69 additional deaths would have occurred (5.8% higher mortality). SARS-CoV-2 viral load steadily declined among hospitalized patients in the setting of public health interventions, and this correlated with decreases in mortality.
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Affiliation(s)
- Michael J. Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
| | - Jason Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Benjamin R. Baer
- Department of Statistics and Data Science, Cornell University, Ithaca, New York, United States of America
| | - Mangala Rajan
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Nathaniel Hupert
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, United States of America
- Cornell Institute for Disease and Disaster Preparedness, New York, New York, United States of America
| | - Luis M. Schang
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Laura C. Pinheiro
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, CUNY Graduate School of Public Health and Health Policy, New York, New York, United States of America
| | - Magdalena E. Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Parag Goyal
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Martin T. Wells
- Department of Statistics and Data Science, Cornell University, Ithaca, New York, United States of America
- Division of Biostatistics and Epidemiology, Weill Cornell Medicine, New York, New York, United States of America
| | - Jorge L. Sepulveda
- Department of Pathology, George Washington University, Washington, DC, United States of America
| | - Monika M. Safford
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
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Yang HS, Hou Y, Zhang H, Chadburn A, Westblade LF, Fedeli R, Steel PAD, Racine-Brzostek SE, Velu P, Sepulveda JL, Satlin MJ, Cushing MM, Kaushal R, Zhao Z, Wang F. Machine Learning Highlights Downtrending of COVID-19 Patients with a Distinct Laboratory Profile. Health Data Sci 2021; 2021:7574903. [PMID: 36405356 PMCID: PMC9629663 DOI: 10.34133/2021/7574903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/07/2021] [Indexed: 06/16/2023]
Abstract
BACKGROUND New York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2-confirmed cases in 2020. A change in the pattern of laboratory test results in COVID-19 patients over this time has not been reported or correlated with patient outcome. METHODS We performed a retrospective study of routine laboratory and SARS-CoV-2 RT-PCR test results from 5,785 patients evaluated in a NYC hospital emergency department from March to June employing machine learning analysis. RESULTS A COVID-19 high-risk laboratory test result profile (COVID19-HRP), consisting of 21 routine blood tests, was identified to characterize the SARS-CoV-2 patients. Approximately half of the SARS-CoV-2 positive patients had the distinct COVID19-HRP that separated them from SARS-CoV-2 negative patients. SARS-CoV-2 patients with the COVID19-HRP had higher SARS-CoV-2 viral loads, determined by cycle threshold values from the RT-PCR, and poorer clinical outcome compared to other positive patients without the COVID12-HRP. Furthermore, the percentage of SARS-CoV-2 patients with the COVID19-HRP has significantly decreased from March/April to May/June. Notably, viral load in the SARS-CoV-2 patients declined, and their laboratory profile became less distinguishable from SARS-CoV-2 negative patients in the later phase. CONCLUSIONS Our longitudinal analysis illustrates the temporal change of laboratory test result profile in SARS-CoV-2 patients and the COVID-19 evolvement in a US epicenter. This analysis could become an important tool in COVID-19 population disease severity tracking and prediction. In addition, this analysis may play an important role in prioritizing high-risk patients, assisting in patient triaging and optimizing the usage of resources.
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Affiliation(s)
- He S. Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Yu Hou
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Hao Zhang
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Richard Fedeli
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Peter A. D. Steel
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sabrina E. Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Jorge L. Sepulveda
- Department of Pathology, School of Medicine and Health Sciences, George Washington University, Washington DC, USA
| | - Michael J. Satlin
- Division of Infectious Disease, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa M. Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Rainu Kaushal
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Fei Wang
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
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Sepulveda JL, Abdulbaki R, Sands Z, Codoy M, Mendoza S, Isaacson N, Kochar O, Keiser J, Haile-Mariam T, Meltzer AC, Mores CN, Sepulveda AR. Performance of the Abbott ID NOW rapid SARS-CoV-2 amplification assay in relation to nasopharyngeal viral RNA loads. J Clin Virol 2021; 140:104843. [PMID: 33979738 PMCID: PMC8091002 DOI: 10.1016/j.jcv.2021.104843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, United State; Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Rami Abdulbaki
- Department of Pathology, George Washington University School of Medicine and Health Sciences, United State; Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Zachary Sands
- Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Maria Codoy
- Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Salome Mendoza
- Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Nancy Isaacson
- Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Olga Kochar
- Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - John Keiser
- Department of Pathology, George Washington University School of Medicine and Health Sciences, United State; Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States
| | - Tenagne Haile-Mariam
- Department of Emergency Medicine, George Washington University School of Medicine and Health Sciences, United States
| | - Andrew C Meltzer
- Department of Emergency Medicine, George Washington University School of Medicine and Health Sciences, United States
| | - Christopher N Mores
- Department of Global Health, George Washington University, Milken Institute School of Public Health, United States
| | - Antonia R Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, United State; Department of Pathology and Laboratory Medicine, George Washington University Hospital, United States.
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6
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Miller EH, Zucker J, Castor D, Annavajhala MK, Sepulveda JL, Green DA, Whittier S, Scherer M, Medrano N, Sobieszczyk ME, Yin MT, Kuhn L, Uhlemann AC. Pretest Symptom Duration and Cycle Threshold Values for Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-Transcription Polymerase Chain Reaction Predict Coronavirus Disease 2019 Mortality. Open Forum Infect Dis 2021; 8:ofab003. [PMID: 33604401 PMCID: PMC7798567 DOI: 10.1093/ofid/ofab003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/02/2021] [Indexed: 12/13/2022] Open
Abstract
Background The relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and patient symptom duration in both in- and outpatients, and the impact of these factors on patient outcomes, are currently unknown. Understanding these associations is important to clinicians caring for patients with coronavirus disease 2019 (COVID-19). Methods We conducted an observational study between March 10 and May 30, 2020 at a large quaternary academic medical center in New York City. Patient characteristics, laboratory values, and clinical outcomes were abstracted from the electronic medical records. Of all patients tested for SARS-CoV-2 during this time (N = 16 384), there were 5467 patients with positive tests, 4254 of which had available cycle threshold (Ct) values and were included in further analysis. Univariable and multivariable logistic regression models were used to test associations between Ct values, duration of symptoms before testing, patient characteristics, and mortality. The primary outcome is defined as death or discharge to hospice. Results Lower Ct values at diagnosis (ie, higher viral load) were associated with significantly higher mortality among both in- and outpatients. It is interesting to note that patients with a shorter time since the onset of symptoms to testing had a worse prognosis, with those presenting less than 3 days from symptom onset having 2-fold increased odds of death. After adjusting for time since symptom onset and other clinical covariates, Ct values remained a strong predictor of mortality. Conclusions Severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction Ct value and duration of symptoms are strongly associated with mortality. These 2 factors add useful information for clinicians to risk stratify patients presenting with COVID-19.
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Affiliation(s)
- Emily Happy Miller
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Jason Zucker
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Delivette Castor
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Medini K Annavajhala
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Daniel A Green
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Susan Whittier
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Matthew Scherer
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Nicola Medrano
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Magdalena E Sobieszczyk
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Michael T Yin
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, New York, USA
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7
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DeSimone RA, Costa VA, Kane K, Sepulveda JL, Ellsworth GB, Gulick RM, Zucker J, Sobieszcyk ME, Schwartz J, Cushing MM. Blood component utilization in COVID-19 patients in New York City: Transfusions do not follow the curve. Transfusion 2020; 61:692-698. [PMID: 33215718 PMCID: PMC7753518 DOI: 10.1111/trf.16202] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022]
Abstract
Background Blood suppliers and transfusion services have worked diligently to maintain an adequate blood supply during the COVID‐19 pandemic. Our experience has shown that some COVID‐19 inpatients require transfusion support; understanding this need is critical to blood product inventory management. Study Design and Methods Hospital‐wide and COVID‐19 specific inpatient blood product utilization data were collected retrospectively for our networkʼs two tertiary academic medical centers over a 9‐week period (March 1, 2020‐May 2, 2020), when most inpatients had COVID‐19. Utilization data were merged with a COVID‐19 patient database to investigate clinical demographic characteristics of transfused COVID‐19 inpatients relative to non‐transfused ones. Results Overall, 11 041 COVID‐19 patients were admitted and 364 received blood product transfusions for an overall transfusion rate of 3.3%. COVID‐19 patients received 1746 blood components in total, the majority of which were red blood cells. COVID‐19 patientsʼ weekly transfusion rate increased as the pandemic progressed, possibly reflecting their increased severity of illness. Transfusion was significantly associated with several indicators of severe disease, including mortality, intubation, thrombosis, longer hospital admission, lower hemoglobin and platelet nadirs, and longer prothrombin and activated partial thromboplastin times. As the pandemic progressed, institutional adherence to transfusion guidelines improved for RBC transfusions compared to prior year trends but did not improve for platelets or plasma. Conclusion There is a need to closely monitor the blood product inventory and demand throughout the COVID‐19 pandemic as patientsʼ transfusion needs may increase over time. Daily or weekly trending of patientsʼ clinical status and laboratory values may assist blood banks in inventory management.
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Affiliation(s)
- Robert A DeSimone
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA
| | - Victoria A Costa
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA
| | - Kathleen Kane
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA.,Department of Pathology and Cell Biology, New York-Presbyterian Hospital-Columbia University Irving Medical Center, New York, New York, USA
| | - Jorge L Sepulveda
- Department of Pathology and Cell Biology, New York-Presbyterian Hospital-Columbia University Irving Medical Center, New York, New York, USA
| | - Grant B Ellsworth
- Division of Infectious Diseases, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA
| | - Roy M Gulick
- Division of Infectious Diseases, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA
| | - Jason Zucker
- Division of Infectious Diseases, New York-Presbyterian Hospital-Columbia University Irving Medical Center, New York, New York, USA
| | - Magdalena E Sobieszcyk
- Division of Infectious Diseases, New York-Presbyterian Hospital-Columbia University Irving Medical Center, New York, New York, USA
| | - Joseph Schwartz
- Department of Pathology and Cell Biology, New York-Presbyterian Hospital-Columbia University Irving Medical Center, New York, New York, USA
| | - Melissa M Cushing
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York, USA
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8
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Westblade LF, Brar G, Pinheiro LC, Paidoussis D, Rajan M, Martin P, Goyal P, Sepulveda JL, Zhang L, George G, Liu D, Whittier S, Plate M, Small CB, Rand JH, Cushing MM, Walsh TJ, Cooke J, Safford MM, Loda M, Satlin MJ. SARS-CoV-2 Viral Load Predicts Mortality in Patients with and without Cancer Who Are Hospitalized with COVID-19. Cancer Cell 2020; 38:661-671.e2. [PMID: 32997958 PMCID: PMC7492074 DOI: 10.1016/j.ccell.2020.09.007] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
Patients with cancer may be at increased risk of severe coronavirus disease 2019 (COVID-19), but the role of viral load on this risk is unknown. We measured SARS-CoV-2 viral load using cycle threshold (CT) values from reverse-transcription polymerase chain reaction assays applied to nasopharyngeal swab specimens in 100 patients with cancer and 2,914 without cancer who were admitted to three New York City hospitals. Overall, the in-hospital mortality rate was 38.8% among patients with a high viral load, 24.1% among patients with a medium viral load, and 15.3% among patients with a low viral load (p < 0.001). Similar findings were observed in patients with cancer (high, 45.2% mortality; medium, 28.0%; low, 12.1%; p = 0.008). Patients with hematologic malignancies had higher median viral loads (CT = 25.0) than patients without cancer (CT = 29.2; p = 0.0039). SARS-CoV-2 viral load results may offer vital prognostic information for patients with and without cancer who are hospitalized with COVID-19.
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Affiliation(s)
- Lars F Westblade
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Gagandeep Brar
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Laura C Pinheiro
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Mangala Rajan
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Peter Martin
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Parag Goyal
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Jorge L Sepulveda
- Department of Pathology, George Washington University, Washington, DC 20037, USA
| | - Lisa Zhang
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gary George
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dakai Liu
- NewYork-Presbyterian Hospital Queens, Queens, NY 11355, USA
| | - Susan Whittier
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; NewYork-Presbyterian Hospital, Columbia University Medical Center, New York, NY 10032, USA
| | - Markus Plate
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Catherine B Small
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Jacob H Rand
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Melissa M Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Thomas J Walsh
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Joseph Cooke
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital Queens, Queens, NY 11355, USA
| | - Monika M Safford
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Michael J Satlin
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA.
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9
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Byun JS, Singhal SK, Park S, Yi DI, Yan T, Caban A, Jones A, Mukhopadhyay P, Gil SM, Hewitt SM, Newman L, Davis MB, Jenkins BD, Sepulveda JL, De Siervi A, Nápoles AM, Vohra NA, Gardner K. Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival. Clin Cancer Res 2020; 26:1905-1914. [PMID: 31911546 DOI: 10.1158/1078-0432.ccr-19-0875] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/10/2019] [Accepted: 01/03/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Compared with their European American (EA) counterparts, African American (AA) women are more likely to die from breast cancer in the United States. This disparity is greatest in hormone receptor-positive subtypes. Here we uncover biological factors underlying this disparity by comparing functional expression and prognostic significance of master transcriptional regulators of luminal differentiation. EXPERIMENTAL DESIGN Data and biospecimens from 262 AA and 293 EA patients diagnosed with breast cancer from 2001 to 2010 at a major medical center were analyzed by IHC for functional biomarkers of luminal differentiation, including estrogen receptor (ESR1) and its pioneer factors, FOXA1 and GATA3. Integrated comparison of protein levels with network-level gene expression analysis uncovered predictive correlations with race and survival. RESULTS Univariate or multivariate HRs for overall survival, estimated from digital IHC scoring of nuclear antigen, show distinct differences in the magnitude and significance of these biomarkers to predict survival based on race: ESR1 [EA HR = 0.47; 95% confidence interval (CI), 0.31-0.72 and AA HR = 0.77; 95% CI, 0.48-1.18]; FOXA1 (EA HR = 0.38; 95% CI, 0.23-0.63 and AA HR = 0.53; 95% CI, 0.31-0.88), and GATA3 (EA HR = 0.36; 95% CI, 0.23-0.56; AA HR = 0.57; CI, 0.56-1.4). In addition, we identify genes in the downstream regulons of these biomarkers highly correlated with race and survival. CONCLUSIONS Even within clinically homogeneous tumor groups, regulatory networks that drive mammary luminal differentiation reveal race-specific differences in their association with clinical outcome. Understanding these biomarkers and their downstream regulons will elucidate the intrinsic mechanisms that drive racial disparities in breast cancer survival.
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Affiliation(s)
- Jung S Byun
- National Institutes of Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Sandeep K Singhal
- Columbia University Medical Center, Columbia University, New York, New York
| | - Samson Park
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Dae Ik Yi
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Tingfen Yan
- National Institutes of Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Ambar Caban
- Columbia University Medical Center, Columbia University, New York, New York
| | - Alana Jones
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Sara M Gil
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen M Hewitt
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - Jorge L Sepulveda
- Columbia University Medical Center, Columbia University, New York, New York
| | - Adriana De Siervi
- Laboratorio de Oncologıa Molecular y Nuevos Blancos Terapeuticos, Instituto de Biologıa y Medicina Experimental (IBYME), CONICET, Argentina
| | - Anna María Nápoles
- National Institutes of Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Nasreen A Vohra
- Brody School of Medicine, East Carolina University, Greenville, North Carolina
| | - Kevin Gardner
- Columbia University Medical Center, Columbia University, New York, New York.
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10
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Sepulveda JL. Using R and Bioconductor in Clinical Genomics and Transcriptomics. J Mol Diagn 2019; 22:3-20. [PMID: 31605800 DOI: 10.1016/j.jmoldx.2019.08.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/02/2019] [Accepted: 08/08/2019] [Indexed: 02/08/2023] Open
Abstract
Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing (NGS). Recent guidelines emphasize the need for rigorous validation and assessment of robustness, reproducibility, and quality of NGS analytic pipelines intended for clinical use. Software tools written in the R statistical language and, in particular, the set of tools available in the Bioconductor repository are widely used in research bioinformatics; and these frameworks offer several advantages for use in clinical bioinformatics, including the breath of available tools, modular nature of software packages, ease of installation, enforcement of interoperability, version control, and short learning curve. This review provides an introduction to R and Bioconductor software, its advantages and limitations for clinical bioinformatics, and illustrative examples of tools that can be used in various steps of NGS analysis.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York; Informatics Subdivision Leadership, Association for Molecular Pathology, Bethesda, Maryland.
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11
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Del Portillo A, Komissarova EV, Bokhari A, Hills C, de Gonzalez AK, Kongkarnka S, Remotti HE, Sepulveda JL, Sepulveda AR. Downregulation of Friend Leukemia Integration 1 ( FLI1) follows the stepwise progression to gastric adenocarcinoma. Oncotarget 2019; 10:3852-3864. [PMID: 31231464 PMCID: PMC6570468 DOI: 10.18632/oncotarget.26974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/04/2019] [Indexed: 12/14/2022] Open
Abstract
Gastric adenocarcinoma (GC) is a leading cause of cancer-related deaths worldwide. The transcription factor gene Friend Leukemia Integration 1 (FLI1) is methylated and downregulated in human GC tissues. Using human GC samples, we determined which cells downregulate FLI1, when FLI1 downregulation occurs, if FLI1 downregulation correlates with clinical-pathologic characteristics, and whether FLI1 plays a role in invasion and/or proliferation of cultured cells. We analyzed stomach tissues from 98 patients [8 normal mucosa, 8 intestinal metaplasia (IM), 7 dysplasia, 91 GC] by immunohistochemistry for FLI1. Epithelial cells from normal, IM, and low-grade dysplasia (LGD) showed strong nuclear FLI1 staining. GC epithelial cells showed significantly less nuclear FLI1 staining as compared to normal epithelium, IM and LGD (P=1.2×10-5, P=1.4×10-6 and P=0.006, respectively). FLI1 expression did not correlate with tumor stage or differentiation, but was associated with patient survival, depending on tumor differentiation. We tested the functional role of FLI1 by assaying proliferation and invasion in cultured GC cells. Lentiviral-transduced FLI1 overexpression in GC AGS cells inhibited invasion by 73.5% (P = 0.001) and proliferation by 31.5% (P = 0.002), as compared to controls. Our results support a combined role for FLI1 as a suppressor of invasiveness and proliferation in gastric adenocarcinoma, specifically in the transition from pre-cancer lesions and dysplasia to invasive adenocarcinoma, and suggest that FLI1 may be a prognostic biomarker of survival in gastric cancers.
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Affiliation(s)
- Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elena V Komissarova
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aqiba Bokhari
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Caitlin Hills
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne Koehne de Gonzalez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarawut Kongkarnka
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Helen E Remotti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Antonia R Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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12
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Sepulveda JL, Komissarova EV, Kongkarnka S, Friedman RA, Davison JM, Levy B, Bryk D, Jobanputra V, Del Portillo A, Falk GW, Sonett JR, Lightdale CJ, Abrams JA, Wang TC, Sepulveda AR. High-resolution genomic alterations in Barrett's metaplasia of patients who progress to esophageal dysplasia and adenocarcinoma. Int J Cancer 2019; 145:2754-2766. [PMID: 31001805 DOI: 10.1002/ijc.32351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/31/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022]
Abstract
The main risk factor for esophageal dysplasia and adenocarcinoma (DAC) is Barrett's esophagus (BE), characterized by intestinal metaplasia. The critical genomic mechanisms that lead to progression of nondysplastic BE to DAC remain poorly understood and require analyses of longitudinal patient cohorts and high-resolution assays. We tested BE tissues from 74 patients, including 42 nonprogressors from two separate groups of 21 patients each and 32 progressors (16 in a longitudinal cohort before DAC/preprogression-BE and 16 with temporally concurrent but spatially separate DAC/concurrent-BE). We interrogated genome-wide somatic copy number alterations (SCNAs) at the exon level with high-resolution SNP arrays in DNA from formalin-fixed samples histologically confirmed as nondysplastic BE. The most frequent abnormalities were SCNAs involving FHIT exon 5, CDKN2A/B or both in 88% longitudinal BE progressors to DAC vs. 24% in both nonprogressor groups (p = 0.0004). Deletions in other genomic regions were found in 56% of preprogression-BE but only in one nonprogressor-BE (p = 0.0004). SCNAs involving FHIT exon 5 and CDKN2A/B were also frequently detected in BE temporally concurrent with DAC. TP53 losses were detected in concurrent-BE but not earlier in preprogression-BE tissues of patients who developed DAC. CDKN2A/p16 immunohistochemistry showed significant loss of expression in BE of progressors vs. nonprogressors, supporting the genomic data. Our data suggest a role for CDKN2A/B and FHIT in early progression of BE to dysplasia and adenocarcinoma that warrants future mechanistic research. Alterations in CDKN2A/B and FHIT by high-resolution assays may serve as biomarkers of increased risk of progression to DAC when detected in BE tissues.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Elena V Komissarova
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Sarawut Kongkarnka
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center and Department of Biomedical Informatics, CUIMC, New York, NY
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Diana Bryk
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
| | - Gary W Falk
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Joshua R Sonett
- Division of Thoracic Surgery, Department of Surgery, CUIMC, New York, NY
| | - Charles J Lightdale
- Division of Digestive and Liver Diseases, Department of Medicine, CUIMC, New York, NY
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Department of Medicine, CUIMC, New York, NY
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Department of Medicine, CUIMC, New York, NY
| | - Antonia R Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center (CUIMC), New York, NY
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13
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Levy-Fix G, Gorman SL, Sepulveda JL, Elhadad N. When to re-order laboratory tests? Learning laboratory test shelf-life. J Biomed Inform 2018; 85:21-29. [PMID: 30036675 PMCID: PMC11073806 DOI: 10.1016/j.jbi.2018.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/15/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
Most laboratory results are valid for only a certain time period (laboratory tests shelf-life), after which they are outdated and the test needs to be re-administered. Currently, laboratory test shelf-lives are not centrally available anywhere but the implicit knowledge of doctors. In this work we propose an automated method to learn laboratory test-specific shelf-life by identifying prevalent laboratory test order patterns in electronic health records. The resulting shelf-lives performed well in the evaluation of internal validity, clinical interpretability, and external validity.
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Affiliation(s)
- Gal Levy-Fix
- Department of Biomedical Informatics, Columbia University, 622 W. 168th Street, New York, NY, USA.
| | - Sharon Lipsky Gorman
- Department of Biomedical Informatics, Columbia University, 622 W. 168th Street, New York, NY, USA
| | - Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University, 630 W. 168th Street, New York, NY, USA
| | - Noémie Elhadad
- Department of Biomedical Informatics, Columbia University, 622 W. 168th Street, New York, NY, USA
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14
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Abstract
UNLABELLED CONTEXT : Colorectal cancer is a heterogeneous disease resulting from different molecular pathways of carcinogenesis. Recent data evaluating the histologic features and molecular basis of the serrated polyp-carcinoma pathway have significantly contributed to more comprehensive classifications of and treatment recommendations for these tumors. OBJECTIVE To integrate the most recent molecular findings in the context of histologic classifications of serrated lesions and their implications in diagnostic pathology and colorectal cancer surveillance. DATA SOURCES Published literature focused on serrated polyps and their association with colorectal cancer. CONCLUSIONS Three types of serrated polyps are currently recognized: hyperplastic polyps, sessile serrated adenomas/polyps, and traditional serrated adenomas. The BRAF V600E mutation is one of the most frequent molecular abnormalities identified in hyperplastic polyps and sessile serrated adenomas. In contrast, in traditional serrated adenomas, either BRAF V600E or KRAS mutations can be frequently identified. CpG methylation has emerged as a critical molecular mechanism in the sessile serrated pathway. CpG methylation of MLH1 often leads to reduced or lost expression in dysplastic foci and carcinomas arising in sessile serrated adenomas/polyps.
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Affiliation(s)
- Hui-Min Yang
- From the Department of Pathology and Cell Biology, Columbia University, New York, New York
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15
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Abstract
OBJECTIVE The study of utilization patterns can quantify potential overuse of laboratory tests and find new ways to reduce healthcare costs. We demonstrate the use of distributional analytics for comparing electronic health record (EHR) laboratory test orders across time to diagnose and quantify overutilization. MATERIALS AND METHODS We looked at hemoglobin A1c (HbA1c) testing across 119,000 patients and 15 years of hospital records. We examined the patterns of HbA1c ordering before and after the publication of the 2002 American Diabetes Association guidelines for HbA1c testing. We conducted analyses to answer three questions. What are the patterns of HbA1c ordering? Do HbA1c orders follow the guidelines with respect to frequency of measurement? If not, how and why do they depart from the guidelines? RESULTS The raw number of HbA1c orderings has steadily increased over time, with a specific increase in low-measurement orderings (<6.5%). There is a change in ordering pattern following the 2002 guideline (p<0.001). However, by comparing ordering distributions, we found that the changes do not reflect the guidelines and rather exhibit a new practice of rapid-repeat testing. The rapid-retesting phenomenon does not follow the 2009 guidelines for diabetes diagnosis either, illustrated by a stratified HbA1c value analysis. DISCUSSION Results suggest HbA1c test overutilization, and contributing factors include lack of care coordination, unexpected values prompting retesting, and point-of-care tests followed by confirmatory laboratory tests. CONCLUSIONS We present a method of comparing ordering distributions in an EHR across time as a useful diagnostic approach for identifying and assessing the trend of inappropriate use over time.
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Affiliation(s)
- Rimma Pivovarov
- Department of Biomedical Informatics, Columbia University, New York, USA
| | - David J Albers
- Department of Biomedical Informatics, Columbia University, New York, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, USA
| | - Jorge L Sepulveda
- Department of Pathology & Cell Biology, Columbia University, New York, USA
| | - Noémie Elhadad
- Department of Biomedical Informatics, Columbia University, New York, USA
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16
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Pivovarov R, Albers DJ, Sepulveda JL, Elhadad N. Identifying and mitigating biases in EHR laboratory tests. J Biomed Inform 2014; 51:24-34. [PMID: 24727481 DOI: 10.1016/j.jbi.2014.03.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/27/2014] [Accepted: 03/30/2014] [Indexed: 02/08/2023]
Abstract
Electronic health record (EHR) data show promise for deriving new ways of modeling human disease states. Although EHR researchers often use numerical values of laboratory tests as features in disease models, a great deal of information is contained in the context within which a laboratory test is taken. For example, the same numerical value of a creatinine test has different interpretation for a chronic kidney disease patient and a patient with acute kidney injury. We study whether EHR research studies are subject to biased results and interpretations if laboratory measurements taken in different contexts are not explicitly separated. We show that the context of a laboratory test measurement can often be captured by the way the test is measured through time. We perform three tasks to study the properties of these temporal measurement patterns. In the first task, we confirm that laboratory test measurement patterns provide additional information to the stand-alone numerical value. The second task identifies three measurement pattern motifs across a set of 70 laboratory tests performed for over 14,000 patients. Of these, one motif exhibits properties that can lead to biased research results. In the third task, we demonstrate the potential for biased results on a specific example. We conduct an association study of lipase test values to acute pancreatitis. We observe a diluted signal when using only a lipase value threshold, whereas the full association is recovered when properly accounting for lipase measurements in different contexts (leveraging the lipase measurement patterns to separate the contexts). Aggregating EHR data without separating distinct laboratory test measurement patterns can intermix patients with different diseases, leading to the confounding of signals in large-scale EHR analyses. This paper presents a methodology for leveraging measurement frequency to identify and reduce laboratory test biases.
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Affiliation(s)
- Rimma Pivovarov
- Department of Biomedical Informatics, Columbia University, 622 W. 168th Street, New York, NY, USA.
| | - David J Albers
- Department of Biomedical Informatics, Columbia University, 622 W. 168th Street, New York, NY, USA.
| | - Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University, 630 W. 168th Street, New York, NY, USA.
| | - Noémie Elhadad
- Department of Biomedical Informatics, Columbia University, 622 W. 168th Street, New York, NY, USA.
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17
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Abstract
CONTEXT Laboratory information systems (LIS) are critical components of the operation of clinical laboratories. However, the functionalities of LIS have lagged significantly behind the capacities of current hardware and software technologies, while the complexity of the information produced by clinical laboratories has been increasing over time and will soon undergo rapid expansion with the use of new, high-throughput and high-dimensionality laboratory tests. In the broadest sense, LIS are essential to manage the flow of information between health care providers, patients, and laboratories and should be designed to optimize not only laboratory operations but also personalized clinical care. OBJECTIVES To list suggestions for designing LIS with the goal of optimizing the operation of clinical laboratories while improving clinical care by intelligent management of laboratory information. DATA SOURCES Literature review, interviews with laboratory users, and personal experience and opinion. CONCLUSIONS Laboratory information systems can improve laboratory operations and improve patient care. Specific suggestions for improving the function of LIS are listed under the following sections: (1) Information Security, (2) Test Ordering, (3) Specimen Collection, Accessioning, and Processing, (4) Analytic Phase, (5) Result Entry and Validation, (6) Result Reporting, (7) Notification Management, (8) Data Mining and Cross-sectional Reports, (9) Method Validation, (10) Quality Management, (11) Administrative and Financial Issues, and (12) Other Operational Issues.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology & Cell Biology, Columbia University, New York, New York 10032, USA.
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18
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Sepulveda JL, Tanhehco YC, Frey M, Guo L, Cropcho LJ, Gibson KM, Blair HC. Variation in human erythrocyte membrane unsaturated Fatty acids: correlation with cardiovascular disease. Arch Pathol Lab Med 2010; 134:73-80. [PMID: 20073608 DOI: 10.5858/2008-0795-oar1.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Whether cell membrane fatty acid (FA) composition is a useful indicator of vascular disease is unclear. OBJECTIVE To study variation of erythrocyte (RBC) membrane FA in samples from healthy volunteers, hospitalized patients, and cardiac troponin I-elevated patients with myocardial damage without a priori assumptions as to FA composition. DESIGN We separated FAs extracted from RBCs by gas chromatography and identified them by mass spectrometry. Fatty acids with abundance greater than 1% of total were quantified and compared: hexadecanoic (C16:0), octadecadienoic (C18:2), cis- and trans-octadecenoic (C18:1), and eicosatetraenoic (C20:4) acids. Deuterated standards established proportionality of FA recovery. The cis- and trans-C18:1 identification was verified by comparison with standards. RESULTS In troponin-positive samples, C18:2 to C18:1 ratios were increased 30% compared with healthy controls or with random patient samples. Erythrocyte trans-C18:1 had a wide variation, approximately 10-fold, in all groups but without differences between groups. Replicates showed that the wide range of RBC trans-FA load is not due to analytic variation. In healthy subjects, the RBC content of lower- molecular weight FAs (C16-C18) correlated with serum low-density lipoprotein cholesterol, but despite the established relationship between dietary trans-FA and increased low-density lipoprotein cholesterol, lipid profiles had no correlation with RBC trans-FA content. CONCLUSIONS Erythrocyte accumulation of unsaturated FA may be a useful indicator of vascular disease, whereas the wide range in trans-FAs suggests that both diet and genetic variation affect RBC trans-FA accumulation. Unsaturated FAs increase membrane fluidity and may reflect a natural response to subclinical vascular changes, which may in turn reflect increased risk of clinical disease.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology & Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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19
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Mehta JL, Sukhija R, Romeo F, Sepulveda JL. Value of CRP in coronary risk determination. Indian Heart J 2007; 59:173-177. [PMID: 19122252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Initial studies showed that C-reactive protein (CRP) may have a role in the genesis of atherosclerotic lesions and as a novel biomarkers of patients at risk of developing coronary heart disease (CHD) events. Most of these studies had methodologic limitations, and recent data contradict these findings and suggest that inflammatory markers, such as CRP, have limited usefulness in the prediction of CHD events over and above conventional risk factors. Its low predictive value creates difficulty in interpreting the CRP data in an individual patient. Current scientific literature does not support measurement of CRP in individual patients in clinical medicine. In this review, we critically appraise role of CRP in cardiovascular medicine.
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Affiliation(s)
- Jawahar L Mehta
- Division of Cardiovascular Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205-7199, USA.
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20
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Abstract
BACKGROUND Helicobacter pylori gastritis increases gastric cancer risk. Microsatellite instability-type mutations are secondary to deficient DNA mismatch repair. H. pylori gastritis is more frequent in patients with microsatellite instability-positive gastric cancers, and H. pylori organisms independently of inflammation can reduce DNA mismatch repair protein levels, raising the hypothesis that H. pylori organisms might lead to mutagenesis during infection. MATERIALS AND METHODS Mutations were detected using a green fluorescent protein reporter vector (pEGFP-CA13). Gastric cancer AGS cells transfected with pEGFP-CA13 were cocultured with H. pylori or Escherichia coli. The numbers of green fluorescent protein (GFP)-positive cells were determined, and GFP, hMSH2, and hMLH1 protein levels were measured by Western blot. The effect of H. pylori on CpG methylation status of hMLH1 was determined by methylation-specific polymerase chain reaction. RESULTS GFP levels and GFP-positive cell numbers in AGS cells cocultured with H. pylori significantly increased, as the levels of hMLH1 and hMSH2 dropped. H. pylori cocultures induced low-level CpG methylation of the hMLH1 promoter. Sequence analysis of cells cocultured with H. pylori showed an increased number of frameshift mutations and point mutations as compared to cells not cocultured with H. pylori (p = .03 and p = .001, respectively). CONCLUSIONS This is the first report showing that H. pylori bacteria may lead to accumulation of genomic mutations, independently of underlying inflammation. This is associated with reduced DNA mismatch repair, and is at least in part associated with CpG methylation of the hMLH1 promoter. These data support the notion that H. pylori-induced mutations and epigenetic alterations in gastric epithelial cells during chronic gastritis may contribute to an increased risk of gastric cancer associated with H. pylori infection.
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Affiliation(s)
- Yuan Yao
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
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21
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Clark K, Sepulveda JL. Norepinephrine inhibits migration of human bone marrow mesenchymal stem cells. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.lb115-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kenneth Clark
- PathologyUniversity of Pittsburgh200 LothropPittsburghPA15213
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22
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Abstract
PURPOSE OF REVIEW C-reactive protein, a nonspecific marker of inflammation, has recently been proposed both as a marker of low-grade inflammation involved in atherogenesis and as a predictor of disease progression. RECENT FINDINGS The physiologic functions of C-reactive protein as an anti-inflammatory scavenger molecule have begun to emerge. For example, C-reactive protein binds to damaged lipoproteins and facilitates their removal by phagocytes without full complement activation. Increased levels of C-reactive protein may result in direct effects on vascular cells, including induction of cytokines and prothrombotic factors. Several sources of biologic variation in the levels of C-reactive protein have been identified, chief among which are abdominal obesity and the metabolic syndrome. Although previous studies showed a potent independent association of C-reactive protein levels with cardiac events, the strength of association was shown to be much weaker than previously reported in recent large meta-analyses. Therapy with nonspecific anti-inflammatory agents such as statins in patients with coronary artery disease has been found to reduce adverse outcomes in association with reductions in C-reactive protein, on the basis of retrospective analysis of stored blood specimens. SUMMARY Despite a relatively strong epidemiologic association with future adverse cardiovascular events, the great majority of apparently healthy individuals with elevated C-reactive protein will not experience cardiovascular disease. Even though more than 15 000 articles in PubMed mention C-reactive protein, current knowledge is insufficient to implicate C-reactive protein as a causative factor in atherothrombosis or to enable the recommendation of C-reactive protein testing to guide preventive or therapeutic interventions in cardiovascular diseases.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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23
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Chen H, Huang XN, Yan W, Chen K, Guo L, Tummalapali L, Dedhar S, St-Arnaud R, Wu C, Sepulveda JL. Role of the integrin-linked kinase/PINCH1/alpha-parvin complex in cardiac myocyte hypertrophy. J Transl Med 2005; 85:1342-56. [PMID: 16170337 DOI: 10.1038/labinvest.3700345] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Outside-in signaling from fibronectin (FN) through integrin receptors has been shown to play an important role in promoting cardiac myocyte hypertrophy and synergizes with other hypertrophic stimuli such as the alpha-adrenergic agonist phenylephrine (PE) and mechanical strain. The integrin-linked kinase (ILK) is a critical molecule involved in cell adhesion, motility and survival in nonmyocytes such as fibroblasts and epithelial cells. Its role in cardiac myocytes is unclear. In this study, we demonstrate that (1) ILK forms a complex with PINCH1 and alpha-parvin proteins (IPAP1 complex) in neonatal rat ventricular myocytes; (2) localization of IPAP1 complex proteins to costameres in cardiac myocytes is stimulated by FN, PE and synergistically by the combination of FN and PE in an integrin beta1-dependent manner; (3) a dominant-negative mutant lacking the PINCH-binding N-terminus of ILK (ILK-C) prevents costamere association of ILK and alpha-parvin, but not PINCH1; (4) FN- and PE-induced hypertrophy, measured by increased protein/DNA ratio, beating frequency and atrial natriuretic peptide expression, is stimulated by low levels of ILK-C but repressed by high ILK-C expression; and (5) overexpression of ILK-C, as well as deletion of the ILK gene in mouse neonatal ventricular myocytes, induces marked apoptosis of cardiac myocytes. These results suggest that the IPAP1 complex plays an important role in mediating integrin-signaling pathways that regulate cardiac myocyte hypertrophy and resistance to apoptosis.
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Affiliation(s)
- Hua Chen
- Department of Pathology, New York University, New York, NY, USA
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24
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Abstract
Cell-extracellular matrix (ECM) adhesion is crucial for control of cell behavior. It connects the ECM to the intracellular cytoskeleton and transduces bidirectional signals between the extracellular and intracellular compartments. The subcellular machinery that mediates cell-ECM adhesion and signaling is complex. It consists of transmembrane proteins (e.g., integrins) and at least several dozens of membrane-proximal proteins that assemble into a network through multiple protein interactions. Furthermore, despite sharing certain common components, cell-ECM adhesions exhibit considerable heterogeneity in different types of cells (e.g., the cell-ECM adhesions in cardiac myocytes are considerably different from those in fibroblasts). Here, we will first briefly describe the general properties of the integrin-mediated cell-ECM adhesion and signal transduction. Next, we will focus on one of the recently discovered cell-ECM adhesion protein complexes consisting of PINCH, integrin-linked kinase (ILK), and Parvin and use it as an example to illustrate the molecular basis underlying the assembly and functions of cell-ECM adhesions. Finally, we will discuss in detail the structure and regulation of cell-ECM adhesion complexes in cardiac myocytes, which illustrate the importance and complexity of the cell-ECM adhesion structures in organogenesis and diseases.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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25
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Abstract
Fibronectin (FN) is an extracellular matrix protein that binds to integrin receptors and couples cardiac myocytes to the basal lamina. Cardiac FN expression is elevated in models of pressure overload, and FN causes cultured cardiac myocytes to hypertrophy by a mechanism that has not been characterized in detail. In this study, we analyzed the gene expression changes induced by FN in purified rat neonatal ventricular myocytes using the Affymetrix RAE230A microarray, to understand how FN affects gene expression in cardiac myocytes and to separate the effects contributed by cardiac nonmyocytes in vivo. Pathway analysis using z-score statistics and comparison with a mouse model of cardiac hypertrophy revealed several pathways stimulated by FN in cardiac myocytes. In addition to the known cardiac myocyte hypertrophy markers, FN significantly induced metabolic pathways including virtually all of the enzymes of cholesterol biosynthesis, fatty acid biosynthesis, and the mitochondrial electron transport chain. FN also increased the expression of genes coding for ribosomal proteins, translation factors, and the ubiquitin-proteasome pathway. Interestingly, cardiac myocytes plated on FN showed elevated expression of the fibrosis-promoting peptides connective tissue growth factor (CTGF), WNT1 inducible signaling pathway protein 2 (WISP2), and secreted acidic cysteine-rich glycoprotein (SPARC). Our data complement in vivo studies and reveal several novel genes and pathways stimulated by FN, pointing to cardiac myocyte-specific mechanisms that lead to development of the hypertrophic phenotype.
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Affiliation(s)
- Hua Chen
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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26
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Chikwava K, Lower DR, Frangiskakis SH, Sepulveda JL, Virji MA, Rao KN. Acute ethanol intoxication in a 7-month-old infant. Pediatr Dev Pathol 2004; 7:400-2. [PMID: 15383937 DOI: 10.1007/s10024-004-1017-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Accepted: 02/11/2004] [Indexed: 10/26/2022]
Affiliation(s)
- Kudakwashe Chikwava
- Department of Pathology, Division of Clinical Chemistry, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, 200 Lothrop Street, 15261, Pittsburgh, PA, USA
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27
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Sepulveda JL, Vlahopoulos S, Iyer D, Belaguli N, Schwartz RJ. Combinatorial expression of GATA4, Nkx2-5, and serum response factor directs early cardiac gene activity. J Biol Chem 2002; 277:25775-82. [PMID: 11983708 DOI: 10.1074/jbc.m203122200] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Herein, the restricted expression of serum response factors (SRF) closely overlapped with Nkx2-5 and GATA4 transcripts in early chick embryos coinciding with the earliest appearance of cardiac alpha-actin (alphaCA) transcripts and nascent myocardial cells. The combinatorial expression of SRF, a MADS box factor Nkx2-5 (a NK4 homeodomain), and/or GATA4, a dual C4 zinc finger protein, in heterologous CV1 fibroblasts and Schneider 2 insect cells demonstrated synergistic induction of alphaCA promoter activity. These three factors induced endogenous alphaCA mRNA over a 100-fold in murine embryonic stem cells. In addition, the DNA-binding defective mutant Nkx2-5pm efficiently coactivated the alphaCA promoter in the presence of SRF and GATA4 in the presence of all four SREs and was substantially weakened when individual SREs were mutated and or serially deleted. In contrast, the introduction of SRFpm, a SRF DNA-binding mutant, blocked the activation with all of the alphaCA promoter constructions. These assays indicated a dependence upon cooperative SRF binding for facilitating the recruitment of Nkx2-5 and GATA4 to the alphaCA promoter. Furthermore, the recruitment of Nkx2-5 and GATA4 by SRF was observed to strongly enhance SRF DNA binding affinity. This mechanism allowed for the formation of higher ordered alphaCA promoter DNA binding complexes, led to a model of SRF physical association with Nkx2-5 and GATA4.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology, University of Pittsburgh Medical Center, Pennsylvania 15213, USA
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28
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Cabeza-Arvelaiz Y, Thompson TC, Sepulveda JL, Chinault AC. LAPSER1: a novel candidate tumor suppressor gene from 10q24.3. Oncogene 2001; 20:6707-17. [PMID: 11709705 DOI: 10.1038/sj.onc.1204866] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2001] [Revised: 07/20/2001] [Accepted: 07/26/2001] [Indexed: 11/08/2022]
Abstract
Numerous LOH and mutation analysis studies in different tumor tissues, including prostate, indicate that there are multiple tumor suppressor genes (TSGs) present within the human chromosome 8p21-22 and 10q23-24 regions. Recently, we showed that LZTS1 (or FEZ1), a putative TSG located on 8p22, has the potential to function as a cell growth modulator. We report here the cloning, gene organization, cDNA sequence characterization and expression analysis of LAPSER1, an LZTS1-related gene. This gene maps within a subregion of human chromosome 10q24.3 that has been reported to be deleted in various cancers, including prostate tumors, as frequently as the neighboring PTEN locus. The complete LAPSER1 cDNA sequence encodes a predicted protein containing various domains resembling those typically found in transcription factors (P-Box, Q-rich and multiple leucine zippers). LAPSER1 is expressed at the highest levels in normal prostate and testis, where multiple isoforms are seen, some of which are either undetectable or differentially expressed in some prostate tumor tissues and cell lines. Over-expression of LAPSER1 cDNA strongly inhibited cell growth and colony-forming efficiencies of most cancer cells assessed. Together these data suggest that LAPSER1 is another gene involved in the regulation of cell growth whose loss of function may contribute to the development of cancer.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Cell Cycle Proteins
- Cell Division
- Cell Line
- Chromosome Mapping
- Chromosomes, Human, Pair 10
- Cloning, Molecular
- DNA Mutational Analysis
- DNA, Complementary/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Databases as Topic
- Gene Deletion
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Humans
- Loss of Heterozygosity
- Male
- Models, Genetic
- Molecular Sequence Data
- Prostate/metabolism
- Prostatic Neoplasms/metabolism
- Protein Structure, Tertiary
- Rats
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Testis/metabolism
- Tissue Distribution
- Transfection
- Tumor Suppressor Proteins
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Affiliation(s)
- Y Cabeza-Arvelaiz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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29
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Cabeza-Arvelaiz Y, Sepulveda JL, Lebovitz RM, Thompson TC, Chinault AC. Functional identification of LZTS1 as a candidate prostate tumor suppressor gene on human chromosome 8p22. Oncogene 2001; 20:4169-79. [PMID: 11464283 DOI: 10.1038/sj.onc.1204539] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2000] [Revised: 04/09/2001] [Accepted: 04/12/2001] [Indexed: 11/08/2022]
Abstract
Deletions in the 8p21-22 region of the human genome are among the most common genetic alterations in prostate carcinomas. Several studies in different tumor tissues, including prostate, indicate that there are probably multiple tumor suppressor genes (TSGs) present in this region. To identify candidate TSGs on 8p22 a YAC contig spanning this region was assembled and YAC clones retrofitted with a selectable marker (neo) were transferred into rat prostate AT6.2 cells. Two overlapping YAC clones showed greatly reduced colony-forming efficiency, indicating they may carry a TSG. Two BAC clones encompassing the overlapping region also appeared to exert suppressive effects on the growth of AT6.2 cells. Database searches for genes mapped to the critical region identified a gene known as FEZ1 (LZTS1) as a potential candidate suppressor gene. Subsequent experiments showed that over-expression of LZTS1 cDNA inhibited stable colony-forming efficiencies of AT6.2, HEK-293 and LNCaP cells. In contrast, LZTS1-transfected Rat-1 and RM1 cells were growth-stimulated. Database searches also identified additional isoforms of the LZTS1 mRNA, as well as LZTS1 protein domains reminiscent of those found in transcription factors. Together these data suggest that the LZTS1 gene is involved in the regulation of cell growth and its loss of function may contribute to the development of prostatic carcinomas, as well as other cancers.
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Affiliation(s)
- Y Cabeza-Arvelaiz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, TX 77030, USA
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30
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Belaguli NS, Sepulveda JL, Nigam V, Charron F, Nemer M, Schwartz RJ. Cardiac tissue enriched factors serum response factor and GATA-4 are mutual coregulators. Mol Cell Biol 2000; 20:7550-8. [PMID: 11003651 PMCID: PMC86307 DOI: 10.1128/mcb.20.20.7550-7558.2000] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2000] [Accepted: 06/12/2000] [Indexed: 11/20/2022] Open
Abstract
Combinatorial interaction among cardiac tissue-restricted enriched transcription factors may facilitate the expression of cardiac tissue-restricted genes. Here we show that the MADS box factor serum response factor (SRF) cooperates with the zinc finger protein GATA-4 to synergistically activate numerous myogenic and nonmyogenic serum response element (SRE)-dependent promoters in CV1 fibroblasts. In the absence of GATA binding sites, synergistic activation depends on binding of SRF to the proximal CArG box sequence in the cardiac and skeletal alpha-actin promoter. GATA-4's C-terminal activation domain is obligatory for synergistic coactivation with SRF, and its N-terminal domain and first zinc finger are inhibitory. SRF and GATA-4 physically associate both in vivo and in vitro through their MADS box and the second zinc finger domains as determined by protein A pullout assays and by in vivo one-hybrid transfection assays using Gal4 fusion proteins. Other cardiovascular tissue-restricted GATA factors, such as GATA-5 and GATA-6, were equivalent to GATA-4 in coactivating SRE-dependent targets. Thus, interaction between the MADS box and C4 zinc finger proteins, a novel regulatory paradigm, mediates activation of SRF-dependent gene expression.
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Affiliation(s)
- N S Belaguli
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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31
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Leung WK, Kim JJ, Wu L, Sepulveda JL, Sepulveda AR. Identification of a second MutL DNA mismatch repair complex (hPMS1 and hMLH1) in human epithelial cells. J Biol Chem 2000; 275:15728-32. [PMID: 10748105 DOI: 10.1074/jbc.m908768199] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deficiencies of MutL DNA mismatch repair-complex proteins (hMLH1, hPMS2, and hPMS1) typically result in microsatellite instability in human cancers. We examined the association patterns of MutL proteins in human epithelial cancer cell lines with (HCT-116, N87, SNU-1, and SNU-638) and without microsatellite instability (HeLa, AGS, KATO-III, and SNU-16). The analysis of hMLH1, hPMS2, and hPMS1 was performed using Northern blot, Western blot, and co-immunoprecipitation studies. Our data provide evidence that MutL proteins form two different complexes, MutL-alpha (hPMS2 and hMLH1) and MutL-beta (hPMS1 and hMLH1). Gastric and colorectal cancer cells lines with microsatellite instability lacked detectable hMLH1. Decreased levels of hMLH1 protein were associated with markedly reduced levels of hPMS2 and hPMS1 proteins, but the RNA levels of hPMS1 and hPMS2 were normal. In this study, we describe the association of hPMS1 with hMLH1 as a heterodimer, in human cells. Furthermore, normal levels of hMLH1 protein appear to be important in maintaining normal levels of hPMS1 and hPMS2 proteins.
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Affiliation(s)
- W K Leung
- Departments of Medicine and Pathology, Veterans Affairs Medical Center and Baylor College of Medicine, Houston, Texas 77030, USA
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32
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Sepulveda JL, Belaguli N, Nigam V, Chen CY, Nemer M, Schwartz RJ. GATA-4 and Nkx-2.5 coactivate Nkx-2 DNA binding targets: role for regulating early cardiac gene expression. Mol Cell Biol 1998; 18:3405-15. [PMID: 9584181 PMCID: PMC108922 DOI: 10.1128/mcb.18.6.3405] [Citation(s) in RCA: 254] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/1997] [Accepted: 03/18/1998] [Indexed: 02/07/2023] Open
Abstract
The cardiogenic homeodomain factor Nkx-2.5 and serum response factor (SRF) provide strong transcriptional coactivation of the cardiac alpha-actin (alphaCA) promoter in fibroblasts (C. Y. Chen and R. J. Schwartz, Mol. Cell. Biol. 16:6372-6384, 1996). We demonstrate here that Nkx-2.5 also cooperates with GATA-4, a dual C-4 zinc finger transcription factor expressed in early cardiac progenitor cells, to activate the alphaCA promoter and a minimal promoter, containing only multimerized Nkx-2.5 DNA binding sites (NKEs), in heterologous CV-1 fibroblasts. Transcriptional activity requires the N-terminal activation domain of Nkx-2.5 and Nkx-2.5 binding activity through its homeodomain but does not require GATA-4's activation domain. The minimal interactive regions were mapped to the homeodomain of Nkx-2.5 and the second zinc finger of GATA-4. Removal of Nkx-2.5's C-terminal inhibitory domain stimulated robust transcriptional activity, comparable to the effects of GATA-4 on wild-type Nkx-2.5, which in part facilitated Nkx-2.5 DNA binding activity. We postulate the following simple model: GATA-4 induces a conformational change in Nkx-2.5 that displaces the C-terminal inhibitory domain, thus eliciting transcriptional activation of promoters containing Nkx-2.5 DNA binding targets. Therefore, alphaCa promoter activity appears to be regulated through the combinatorial interactions of at least three cardiac tissue-enriched transcription factors, Nkx-2.5, GATA-4, and SRF.
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Affiliation(s)
- J L Sepulveda
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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