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Wang Z, Neelamraju Y, Meydan C, Dunham N, Gandara J, Lee T, Prajapati S, Rapaport F, Sheridan C, Zumbo P, Becker M, Bullinger L, Carroll M, D’Andrea R, Dillon R, Levine R, Mason CE, Melnick A, Neuberg D, Bekiranov S, Zang C, Garrett-Bakelman FE. Abstract 3155: Gene expression profiles reveal distinct regulatory activities of transcription factors GATA1 and TAL1 upon AML relapse. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3155] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
The purpose of this study is to identify key regulatory pathways that potentially drive abnormal gene expression program in relapsed Acute Myeloid Leukemia (AML) patients, by integrative computational analyses on multi-omics molecular profiles. Relapsed AML remains a clinical challenge. Epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML. However, what specific transcriptional programs and potential regulatory mechanisms contribute to disease relapse are not yet well understood. To characterize the global transcriptional landscapes in relapsed AML, we integrated genomics data from two cohorts of matched diagnosis and relapse patient specimens. We identified 5,416 differentially expressed genes (DEGs) between diagnosis and relapse in Cohort I. Unsupervised clustering yielded three distinct DEG groups: group A, B and C genes that were predominantly (88%) down-regulated, divergently regulated, or predominantly (65%) up-regulated, respectively, upon relapse. The expression pattern of all DEGs separated the patients into two clusters, most robustly by Group B genes. Interestingly, the majority of DEGs did not associate with changes in gene promoter methylation. Similar patterns were observed in Cohort II. We used Binding Analysis for Regulation of Transcription (BART) to identify transcriptional regulators (TRs) that potentially regulated the DEGs not associated with DNA methylation changes, and assessed the differential expression of identified TRs during disease progression. PU.1 was identified as a potential TR for Group A genes and was down-regulated upon relapse. GATA1 and TAL1 were identified as regulating Group B genes and were up-regulated in patient cluster1 and down-regulated in cluster2, consistent with the expression pattern of Group B genes. RBBP5 was a top predicted TR for Group C genes and was up-regulated upon relapse. We next validated the potential functionality of those predicted factors. In NSG mice transplanted with a human AML specimen, TAL1 and GATA1 were downregulated in AML cells collected four weeks after chemotherapy treatment, and were inferred as TRs for the down-regulated genes, similar to the patient data. PU.1 was inferred as regulating the up-regulated genes. Furthermore, we found that the level of differential expression of TAL1, GATA1, and PU.1 in each patient specimen associated with the correlation of DEG profiles between the patient specimen and TR perturbation in human-derived hematopoietic cell lines. Our results support the possibility that in some AML patients, TRs with roles in hematopoiesis and leukemia might contribute to disease relapse. Further mechanistic studies deciphering the molecular and phenotypic events facilitated by these TRs will yield significant insight into disease biology and possible therapeutic targeting approaches in relapsed AML.
Citation Format: Zhenjia Wang, Yaseswini Neelamraju, Cem Meydan, Nicholas Dunham, Jorge Gandara, Tak Lee, Subhash Prajapati, Franck Rapaport, Caroline Sheridan, Paul Zumbo, Michael Becker, Lars Bullinger, Martin Carroll, Richard D’Andrea, Richard Dillon, Ross Levine, Christopher E. Mason, Ari Melnick, Donna Neuberg, Stefan Bekiranov, Chongzhi Zang, Francine E. Garrett-Bakelman. Gene expression profiles reveal distinct regulatory activities of transcription factors GATA1 and TAL1 upon AML relapse [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3155.
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Affiliation(s)
| | | | | | | | | | - Tak Lee
- 2Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | - Richard D’Andrea
- 7University of South Australia and SA Pathology, Adelaide, Australia
| | | | - Ross Levine
- 3Memorial Sloan Kettering Cancer Center, New York, NY
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2
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Botero D, Senior J, Velasquez J, Gandara J, Zapata A, Holguin E, Jaramillo C, Ferreira J, Munoz E. Validation of the CARPREG II risk stratification model and the WHOm scale in pregnant women with heart disease. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.2900] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The physiological changes of pregnancy imply a state of haemodynamic stress, which increases the risk of maternal-fetal complications in women with cardiac pathology. Risk stratification models allow clinical decisions to be guided and optimal diagnostic, follow-up and management strategies to be established according to each estimated category in order to reduce adverse outcomes.
Objective
To validate the CARPREG II and WHOm risk prediction models in a population of pregnant women with heart disease.
Materials and methods
Validation and comparison study of a risk prediction model in a prospective cohort of pregnant women with heart disease assessed between 2016 and 2019 by a cardiobstetric team in an average income country. The CARPREG II score was established and patients were classified according to the WHOm risk scale. We assessed cardiovascular and perinatal outcomes and determined the calibration and level of discrimination of these tools.
Results
In a cohort of 328 pregnant women (27±7 years), 33% (n=110) had congenital heart disease, followed by arrhythmias in 30% (n=98), valvular pathologies in 14% (n=46) and cardiomyopathies in 9% (n=29). In 56% of the pregnancies, the route of delivery was caesarean section, 84% of these by obstetric indication. A cardiac event occurred in 15%, with left heart failure (5.3%) and arrhythmias (2.3%) being the most frequent. The frequency of maternal death of cardiac origin during the study was 1.6%. Neonatal outcomes occurred in 37% of gestations (preterm delivery (16%) and low weight for gestational age (8.4%)) and obstetric events in 12.5%: pregnancy-induced hypertension (9%) and postpartum haemorrhage (2.3%).
NYHA functional class III-IV or cyanosis (OR 12 95% CI 3.1 - 46.4) and left ventricular dysfunction (LVEF <55%) (OR 3 95% CI 1 - 10.9) were the most statistically significant risk predictors. Discrimination of both models was adequate (AUC-ROC of 0.74 95% CI 0.64 - 0.84) for the CARPREG II risk index and 0.77 for the WHOm scale (95% CI 0.69 - 0.86) (Figure 2). Calibration is also good in the study population (Hosmer- Lemeshow goodness-of-fit 0.6 and 0.1, respectively). By including in the CARPREG II model the variables ejection fraction and pulmonary artery systolic pressure in their numerical and not dichotomised form, a discrete improvement in the predictive ability of the scale is evident (AUC-ROC 0.81 95% CI 0.71–0.91).
Conclusions
The CARPREG II and WHOm risk stratification models have good ability to discriminate the risk of adverse cardiac outcomes in pregnant women with heart disease and fit our population. To improve the predictive power of CARPREG II, the variables pulmonary hypertension and left ventricular dysfunction could be used numerically and not dichotomised as in the original model.
Funding Acknowledgement
Type of funding sources: Private hospital(s). Main funding source(s): San Vicente Foundation University Hospital, Cardio-obstetric Center
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Affiliation(s)
- D Botero
- University of Antioquia, Antioquia, Medellin, Colombia
| | - J Senior
- San Vicente Fundacion, Antioquia, Medellin, Colombia
| | - J Velasquez
- San Vicente Fundacion, Antioquia, Medellin, Colombia
| | - J Gandara
- San Vicente Fundacion, Antioquia, Medellin, Colombia
| | - A Zapata
- San Vicente Fundacion, Antioquia, Medellin, Colombia
| | - E Holguin
- San Vicente Fundacion, Antioquia, Medellin, Colombia
| | - C Jaramillo
- University of Antioquia, Antioquia, Medellin, Colombia
| | - J Ferreira
- San Vicente Fundacion, Antioquia, Medellin, Colombia
| | - E Munoz
- San Vicente Fundacion, Antioquia, Medellin, Colombia
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Malaquias MJ, Pinto CM, Ramos C, Ferreira S, Gandara J, Almeida A, Cavaco S, Miranda HP, Magalhães M. Acquired hepatocerebral degeneration and hepatic encephalopathy: one or two entities? Eur J Neurol 2020; 27:2396-2404. [DOI: 10.1111/ene.14486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/13/2020] [Indexed: 12/31/2022]
Affiliation(s)
- M. J. Malaquias
- Neurology Department Centro Hospitalar Universitário do Porto Porto Portugal
| | - C. M. Pinto
- Neuroradiology Department Centro Hospitalar Universitário do Porto Porto Portugal
| | - C. Ramos
- Neuroradiology Department Centro Hospitalar Universitário do Porto Porto Portugal
| | - S. Ferreira
- Hepatic Pancreatic Transplantation Unit Centro Hospitalar Universitário do Porto Porto Portugal
| | - J. Gandara
- Hepatic Pancreatic Transplantation Unit Centro Hospitalar Universitário do Porto Porto Portugal
| | - A. Almeida
- Chemistry Science Department Faculdade de Farmácia Universidade do Porto Porto Portugal
| | - S. Cavaco
- Neuropsychology Unit Centro Hospitalar Universitário do Porto Porto Portugal
| | - H. P. Miranda
- Hepatic Pancreatic Transplantation Unit Centro Hospitalar Universitário do Porto Porto Portugal
| | - M. Magalhães
- Neurology Department Centro Hospitalar Universitário do Porto Porto Portugal
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Castellanos JG, Woo V, Viladomiu M, Putzel G, Lima S, Diehl GE, Marderstein AR, Gandara J, Perez AR, Withers DR, Targan SR, Shih DQ, Scherl EJ, Longman RS. Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis. Immunity 2018; 49:1077-1089.e5. [PMID: 30552020 PMCID: PMC6301104 DOI: 10.1016/j.immuni.2018.10.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [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: 03/02/2018] [Revised: 08/08/2018] [Accepted: 10/17/2018] [Indexed: 12/27/2022]
Abstract
Inflammatory bowel disease (IBD) results from a dysregulated interaction between the microbiota and a genetically susceptible host. Genetic studies have linked TNFSF15 polymorphisms and its protein TNF-like ligand 1A (TL1A) with IBD, but the functional role of TL1A is not known. Here, we found that adherent IBD-associated microbiota induced TL1A release from CX3CR1+ mononuclear phagocytes (MNPs). Using cell-specific genetic deletion models, we identified an essential role for CX3CR1+MNP-derived TL1A in driving group 3 innate lymphoid cell (ILC3) production of interleukin-22 and mucosal healing during acute colitis. In contrast to this protective role in acute colitis, TL1A-dependent expression of co-stimulatory molecule OX40L in MHCII+ ILC3s during colitis led to co-stimulation of antigen-specific T cells that was required for chronic T cell colitis. These results identify a role for ILC3s in activating intestinal T cells and reveal a central role for TL1A in promoting ILC3 barrier immunity during colitis.
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Affiliation(s)
- Jim G Castellanos
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Viola Woo
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Monica Viladomiu
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Gregory Putzel
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Svetlana Lima
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Gretchen E Diehl
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Andrew R Marderstein
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Jorge Gandara
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Alexendar R Perez
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Stephan R Targan
- F. Widjaja Foundation, Inflammatory Bowel and Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, 90048, USA
| | - David Q Shih
- F. Widjaja Foundation, Inflammatory Bowel and Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, 90048, USA
| | - Ellen J Scherl
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY, 10021, USA; Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY, 10021, USA.
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Albuquerque A, Pessegueiro Miranda H, Lopes J, Gandara J, Rodrigues S, Gaspar R, Morais R, Ramalho R, Rodrigues-Pinto E, Cardoso H, Barroca H, Dias CC, Carneiro F, Macedo G. Liver transplant recipients have a higher prevalence of anal squamous intraepithelial lesions. Br J Cancer 2017; 117:1761-1767. [PMID: 29093575 PMCID: PMC5729480 DOI: 10.1038/bjc.2017.370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022] Open
Abstract
Background: Anal squamous intraepithelial lesions (ASIL) are precancerous lesions of anal squamous cell carcinoma, with a higher prevalence in immunosuppressed patients. There are some studies in kidney transplant recipients, but there is no information regarding prevalence in liver transplantation. Our aim was to evaluate the prevalence of ASIL in this setting. Methods: Prospective case–control study involving liver transplant recipients without any other known risk factor for ASIL (n=59), which were compared with a healthy control group (n=57). All were submitted to anal cytology and high-resolution anoscopy was performed in those with abnormal results. Results: Ten (17%) of liver transplant recipients had abnormal cytological results, seven patients had atypical squamous cells of undetermined significance (ASC-US), one patient had atypical squamous cells that cannot exclude high-grade (ASC-H) and two patients had high-grade squamous intraepithelial lesions (HSIL). In the control group, one patient (2%) had an ASC-US result (P=0.005). Anal squamous intraepithelial lesions were confirmed in 7 out of 10 of liver transplant patients and 0 out of 1 in the controls (P=0.013) by high-resolution anoscopy with biopsies. Current smoking was the only risk factor for abnormal cytology (odds ratio=5.87, 95% confidence intervals=1.22–28.12, P=0.027). Conclusions: Liver transplant patients have a higher risk of ASIL. Screening should be considered, especially in smokers.
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Affiliation(s)
- A Albuquerque
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - H Pessegueiro Miranda
- Liver and Pancreatic Transplant Unit Centro Hospitalar Porto, Porto, Portugal.,Abel Salazar BioMedical Sciences Institute from University of Porto, Porto, Portugal.,Institute of Public Health, University of Porto, Porto, Portugal
| | - J Lopes
- Pathology Department Centro Hospitalar São João, Porto, Portugal
| | - J Gandara
- Liver and Pancreatic Transplant Unit Centro Hospitalar Porto, Porto, Portugal.,Abel Salazar BioMedical Sciences Institute from University of Porto, Porto, Portugal
| | - S Rodrigues
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - R Gaspar
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - R Morais
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - R Ramalho
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - E Rodrigues-Pinto
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - H Cardoso
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - H Barroca
- Pathology Department Centro Hospitalar São João, Porto, Portugal
| | - C C Dias
- Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine of the University of Porto, Porto, Portugal.,Center for Health Technology and Services Research-CINTESIS, Porto, Portugal
| | - F Carneiro
- Faculty of Medicine of the University of Porto, Porto, Portugal.,Pathology Department Centro Hospitalar São João, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup) and i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - G Macedo
- Gastroenterology Department Centro Hospitalar São João, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
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Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE. Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. J Biomol Tech 2017; 28:46-55. [PMID: 28344519 DOI: 10.7171/jbt.17-2801-008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample. We extracted and sequenced genomic DNA (gDNA) from 8 environmental samples and compared the quality of the sequencing data for the MDA and their corresponding non-MDA samples. The degree of REPLI-g MDA bias was evaluated by sequence metrics, species composition, and cross-validating observed species abundance and species diversity estimates using the One Codex and MetaPhlAn taxonomic classification tools. Here, we provide evidence of the overall efficacy of REPLI-g MDA on retaining sequencing data quality and species abundance measurements while providing increased yields of high-fidelity DNA. We find that species abundance estimates are largely consistent across samples, even with REPLI-g amplification, as demonstrated by the Spearman's rank order coefficient (R2 > 0.8). However, REPLI-g MDA often produced fewer classified reads at the species, genera, and family level, resulting in decreased species diversity. We also observed some areas with the PCR "jackpot effect," with varying input DNA values for the Metagenomics Research Group (MGRG) controls at specific genomic loci. We visualize this effect in whole genome coverage plots and with sequence composition analyses and note these caveats of the MDA method. Despite overall concordance of species abundance between the amplified and unamplified samples, these results demonstrate that amplification of DNA using the REPLI-g method has some limitations. These concerns could be addressed by future improvements in the enzymes or methods for REPLI-g to be considered a >99% robust method for increasing the amount of high-fidelity DNA from low-biomass samples or at the very least, accounted for during computational analysis of MDA samples.
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Affiliation(s)
- Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA;; School of Medicine, New York Medical College, Valhalla, New York, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Mustafa Hakyemezoğlu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA;; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA;; Feil Family Brain & Mind Research Institute, New York, New York, USA
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Cruz C, Pereira S, Gandara J, Ferreira S, Lopes V, Daniel J, Miranda H. Efficacy and Safety of Monotherapy With Mycophenolate Mofetil in Liver Transplantation Patients With Nephrotoxicity. Transplant Proc 2016; 48:2341-2343. [DOI: 10.1016/j.transproceed.2016.06.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Pereira S, Cruz C, Soares M, Gandara J, Ferreira S, Lopes V, Vizcaíno R, Daniel J, Miranda H. Histology Utility in Liver Graft Surveillance: What About Normal Liver Tests? Transplant Proc 2016; 48:2344-2347. [DOI: 10.1016/j.transproceed.2016.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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9
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Pereira C, Oliveira H, Lopes V, Gandara J, Ferreira S, Daniel J, Miranda H. Visceral leishmaniasis after orthotopic liver transplantation: a rare cause of infection. Transpl Infect Dis 2016; 18:251-4. [DOI: 10.1111/tid.12511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 12/10/2015] [Accepted: 12/14/2015] [Indexed: 11/28/2022]
Affiliation(s)
- C.M. Pereira
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
| | - H.M. Oliveira
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
| | - V. Lopes
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
- Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Porto Portugal
| | - J. Gandara
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
- Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Porto Portugal
| | - S. Ferreira
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
- Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Porto Portugal
| | - J. Daniel
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
- Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Porto Portugal
| | - H.P. Miranda
- Hepato-pancreatic Transplantation Unit; Centro Hospitalar do Porto; Hospital de Santo António; Porto Portugal
- Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; Porto Portugal
- Instituto de Saúde Pública; Universidade do Porto; Porto Portugal
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Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE. Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun 2016; 7:10164. [PMID: 26836631 PMCID: PMC4740774 DOI: 10.1038/ncomms10164] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [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: 04/02/2015] [Accepted: 11/10/2015] [Indexed: 01/21/2023] Open
Abstract
The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on human blood and included genes from the Wolbachia endosymbiont, which shows a simultaneous and coordinated host/commensal response to haematophagous activity. These data provide a rich genetic resource for mapping activity and density of C. lectularius across human hosts and cities, which can help track, manage and control bed bug infestations.
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Affiliation(s)
- Jeffrey A Rosenfeld
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08908, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Mercer R Brugler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA.,Biological Sciences Department, NYC College of Technology (CUNY), Brooklyn, New York 11201, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Sabrina Simon
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Biosystematics, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Russell Durrett
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, New York 10065, USA
| | - Jonathan Foox
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Kevin Shianna
- Illumina Inc. 5200 Illumina Way, San Diego, California 92122, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, New York 10065, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, New York 10065, USA
| | - Ernest T Lam
- BioNanoGenomics Inc. 9640 Towne Centre Drive Ste. 100, San Diego, California 92121, USA
| | - Alex R Hastie
- BioNanoGenomics Inc. 9640 Towne Centre Drive Ste. 100, San Diego, California 92121, USA
| | - Saki Chan
- BioNanoGenomics Inc. 9640 Towne Centre Drive Ste. 100, San Diego, California 92121, USA
| | - Han Cao
- BioNanoGenomics Inc. 9640 Towne Centre Drive Ste. 100, San Diego, California 92121, USA
| | - Michael Saghbini
- BioNanoGenomics Inc. 9640 Towne Centre Drive Ste. 100, San Diego, California 92121, USA
| | - Alex Kentsis
- Molecular Pharmacology and Chemistry Program, Department of Pediatrics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA.,Division of Pediatric Infectious Diseases, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Vladyslav Kholodovych
- High Performance and Research Computing Group, Rutgers Biomedical and Health Sciences, Newark, New Jersey 07103, USA
| | - Michael Tessler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Richard Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Louis N Sorkin
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA.,Department of Biological Sciences, Fordham University, Bronx, New York 10458, USA
| | - Mark E Siddall
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA.,The Feil Family Brain and Mind Research Institute, New York, New York 10065, USA
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11
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Henssen AG, Henaff E, Jiang E, Eisenberg AR, Carson JR, Villasante CM, Ray M, Still E, Burns M, Gandara J, Feschotte C, Mason CE, Kentsis A. Genomic DNA transposition induced by human PGBD5. eLife 2015; 4. [PMID: 26406119 PMCID: PMC4625184 DOI: 10.7554/elife.10565] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 11/13/2022] Open
Abstract
Transposons are mobile genetic elements that are found in nearly all organisms, including humans. Mobilization of DNA transposons by transposase enzymes can cause genomic rearrangements, but our knowledge of human genes derived from transposases is limited. In this study, we find that the protein encoded by human PGBD5, the most evolutionarily conserved transposable element-derived gene in vertebrates, can induce stereotypical cut-and-paste DNA transposition in human cells. Genomic integration activity of PGBD5 requires distinct aspartic acid residues in its transposase domain, and specific DNA sequences containing inverted terminal repeats with similarity to piggyBac transposons. DNA transposition catalyzed by PGBD5 in human cells occurs genome-wide, with precise transposon excision and preference for insertion at TTAA sites. The apparent conservation of DNA transposition activity by PGBD5 suggests that genomic remodeling contributes to its biological function.
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Affiliation(s)
- Anton G Henssen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Elizabeth Henaff
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Eileen Jiang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Amy R Eisenberg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Julianne R Carson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Camila M Villasante
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Mondira Ray
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Melissa Burns
- Boston Children's Hospital, Harvard Medical School, Boston, United States
| | - Jorge Gandara
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Cedric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Christopher E Mason
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Pediatrics, Memorial Sloan Kaettering Cancer Center, New York, United States.,Weill Cornell Medical College, Cornell University, New York, United States
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12
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Webster AF, Zumbo P, Fostel J, Gandara J, Hester SD, Recio L, Williams A, Wood CE, Yauk CL, Mason CE. Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues. Toxicol Sci 2015; 148:460-72. [PMID: 26361796 PMCID: PMC4659533 DOI: 10.1093/toxsci/kfv195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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] [Indexed: 11/21/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic research. However, use of FFPE samples in genomic studies has been limited by technical challenges resulting from nucleic acid degradation. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues preserved in formalin for different amounts of time using 2 DNA microarray protocols and 2 whole-transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other methods by having the highest correlations of differentially expressed genes (DEGs), and best overlap of pathways, between FRO and FFPE groups. The effect of sample time in formalin (18 h or 3 weeks) on gene expression profiles indicated that test article treatment, not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18 h and 3 week FFPE samples compared with FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of time in paraffin on genomic profiles. Ribo-depletion RNA-seq analysis of 8-, 19-, and 26-year-old control blocks resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, untranslated region, intronic, and ribosomal fractions of the transcriptome. Overall, our results indicate that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.
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Affiliation(s)
- A Francina Webster
- *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa K1S 5B6, Canada
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065
| | - Jennifer Fostel
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065
| | - Susan D Hester
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Leslie Recio
- ILS, Inc., PO Box 13501, Research Triangle Park, North Carolina 27709
| | - Andrew Williams
- *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | - Charles E Wood
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Carole L Yauk
- *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada;
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065; The Feil Family Brain and Mind Research Institute (BMRI), 413 East 69th Street, New York, New York 10021; and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, New York, New York 10065
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13
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Henssen A, Eisenberg A, Jiang E, Henaff E, Koche R, Burns M, Carson JR, Nanjangud G, Still E, Gandara J, Cifani P, Dhabaria A, Huang X, de Stanchina E, Mullen E, Steen H, Perlman E, Dome J, Antonescu C, Feschotte C, Mason CE, Kentsis A. Abstract 1103: Human tumorigenesis induced by endogenous DNA transposase. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1103] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent cancer genome surveys have revealed extremely low rates of coding gene mutations in distinct tumor subtypes, suggesting that alternative mechanisms must contribute to their pathogenesis. Transposons are mobile genetic elements that are found in all living organisms, including humans where they occupy nearly half of the genome. Their mobilization can cause structural rearrangements in normal and cancer cells. However, it remains unknown whether transposition is a cause of cellular transformation or merely a bystander effect of dysregulated gene expression. Here, we report that PGBD5, a recently characterized human gene related to the piggyBac transposase from the cabbage looper moth, is aberrantly expressed in rhabdoid tumors, medulloblastoma, acute leukemias, and some sarcomas and carcinomas. Ectopic expression of PGBD5 in non-transformed primary human cells is sufficient to induce anchorage independence in vitro and penetrant tumor formation in immunodeficient mice in vivo. PGBD5 expression is sufficient to induce genomic mobilization of engineered DNA transposons in human cells, and purified recombinant PGBD5 exhibits transposase domain-dependent endonuclease activity in vitro. Flanking-sequence exponential anchored PCR and massively parallel sequencing of DNA transposon integrations revealed distinct activity on piggyBac-like inverted terminal repeats, and preference for specific euchromatic human genomic loci. This enables mapping of structural rearrangements of endogenous human transposable elements in primary human tumor genomes, some of which target genes involved in cellular transformation. We find that PGBD5 transposase-induced cell transformation is associated with morphologic de-differentiation, induction of distinct Polycomb gene expression programs and structural chromatin remodeling, consistent with its epigenetic control. These findings reveal an unanticipated mechanism of human tumorigenesis, genomic plasticity and structural alterations of non-coding regulatory genomic loci in human cancer.
Citation Format: Anton Henssen, Amy Eisenberg, Eileen Jiang, Elizabeth Henaff, Richard Koche, Melissa Burns, Julianne R. Carson, Gouri Nanjangud, Eric Still, Jorge Gandara, Paolo Cifani, Avantika Dhabaria, Xiaodong Huang, Elisa de Stanchina, Elizabeth Mullen, Hanno Steen, Elizabeth Perlman, Jeffrey Dome, Cristina Antonescu, Cedric Feschotte, Christopher E. Mason, Alex Kentsis. Human tumorigenesis induced by endogenous DNA transposase. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1103. doi:10.1158/1538-7445.AM2015-1103
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Affiliation(s)
- Anton Henssen
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amy Eisenberg
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eileen Jiang
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Henaff
- 2Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Richard Koche
- 3Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Burns
- 4Dana Farber Cancer Institute, Harvard University, Boston, MA
| | - Julianne R. Carson
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Eric Still
- 5Memorial-Sloan Kettering Cancer Center, New York, NY
| | - Jorge Gandara
- 2Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Paolo Cifani
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avantika Dhabaria
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaodong Huang
- 6Antitumor Assessment Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Elisa de Stanchina
- 6Antitumor Assessment Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Hanno Steen
- 7Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Elizabeth Perlman
- 8Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Jeffrey Dome
- 9Division of Oncology, Children's National Medical Center, Washington, DC
| | - Cristina Antonescu
- 10Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cedric Feschotte
- 11Department of Human Genetics University of Utah, Salt Lake City, UT
| | - Christopher E. Mason
- 2Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Alex Kentsis
- 1Molecular Pharmacology & Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
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14
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Modern Methods for Delineating Metagenomic Complexity. Cell Syst 2015; 1:6-7. [PMID: 27135684 DOI: 10.1016/j.cels.2015.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/16/2015] [Accepted: 07/16/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shanin Chowdhury
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; CUNY Hunter College, New York 10065, NY, USA
| | - Dyala Jaroudi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Collin Boyer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nick Bernstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Julia M Maritz
- Center for Genomics, New York University, New York, NY 10065, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY Center for Genomics, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | - Amber Simmons
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | - Nell Kirchberger
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Isaac Garcia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sean Dhanraj
- Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | - Tanzina Nawrin
- Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY Center for Genomics, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY Center for Genomics, USA
| | - Elizabeth M Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Walsh
- State University of New York, Downstate, Brooklyn, NY 11203, USA
| | - Gregory D O'Mullan
- School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT 05405, USA
| | - Joel T Dudley
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Anya Dunaif
- Rockefeller University, New York, NY 10065, USA
| | - Sean Ennis
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College, Dublin 12, Ireland
| | - Eoghan O'Halloran
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Tiago R Magalhaes
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College, Dublin 12, Ireland
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Theodore R Muth
- Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | | | | | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | | | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jane M Carlton
- Center for Genomics, New York University, New York, NY 10065, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA.
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15
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst 2015; 1:97-97.e3. [PMID: 27135689 DOI: 10.1016/j.cels.2015.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Pereira M, Ferreira I, Gandara J, Ferreira S, Lopes V, Coelho A, Vizcaino R, Marinho A, Daniel J, Miranda H. Seventh-Day Syndrome: A Catastrophic Event After Liver Transplantation: Case Report. Transplant Proc 2015; 47:1055-8. [DOI: 10.1016/j.transproceed.2015.03.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst 2015; 1:72-87. [PMID: 26594662 PMCID: PMC4651444 DOI: 10.1016/j.cels.2015.01.001] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [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] [Indexed: 01/08/2023]
Abstract
The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
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Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shanin Chowdhury
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Hunter College, New York, NY 10065, USA
| | - Dyala Jaroudi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Collin Boyer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nick Bernstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Julia M Maritz
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Amber Simmons
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | - Nell Kirchberger
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Isaac Garcia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sean Dhanraj
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Tanzina Nawrin
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Elizabeth M Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Walsh
- State University of New York, Downstate, Brooklyn, NY 11203, USA
| | - Gregory D O'Mullan
- School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT 05405, USA
| | - Joel T Dudley
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anya Dunaif
- Rockefeller University, New York, NY 10065, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Eoghan O'Halloran
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland
| | - Tiago R Magalhaes
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Theodore R Muth
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | | | | | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jane M Carlton
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA
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Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol 2014; 32:915-925. [PMID: 25150835 DOI: 10.1038/nbt.2972] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/01/2014] [Indexed: 01/17/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) greatly expands the potential for genomics discoveries, but the wide variety of platforms, protocols and performance capabilitites has created the need for comprehensive reference data. Here we describe the Association of Biomolecular Resource Facilities next-generation sequencing (ABRF-NGS) study on RNA-seq. We carried out replicate experiments across 15 laboratory sites using reference RNA standards to test four protocols (poly-A-selected, ribo-depleted, size-selected and degraded) on five sequencing platforms (Illumina HiSeq, Life Technologies PGM and Proton, Pacific Biosciences RS and Roche 454). The results show high intraplatform (Spearman rank R > 0.86) and inter-platform (R > 0.83) concordance for expression measures across the deep-count platforms, but highly variable efficiency and cost for splice junction and variant detection between all platforms. For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA depletion enables effective analysis of degraded RNA samples. This study provides a broad foundation for cross-platform standardization, evaluation and improvement of RNA-seq.
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Affiliation(s)
- Sheng Li
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Scott W Tighe
- Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Charles M Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Deborah Grove
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Agnes Viale
- Memorial Sloan-Kettering Cancer Institute, New York, New York, USA
| | - Chris Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois, USA
| | - Peter A Schweitzer
- Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Yuan Gao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Dewey Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joe Boland
- NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA
| | | | - Ryan Kim
- Genome Center, University of California, Davis, Davis, California, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Nadereh Jafari
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Natàlia Garcia-Reyero
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi, USA
| | | | | | - Jeffrey Rosenfeld
- Division of High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA
| | - Todd Smith
- PerkinElmer Inc., Seattle, Washington, USA
| | - Jason G Underwood
- University of Washington, Department of Genome Sciences. Seattle, Washington, USA
| | - May Wang
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | | | - George S Grills
- Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
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Garcia A, Suarez M, Gandara J, Pereiro J, Pardo F, Diz P. Introduction of paracoccidioidomycosis into Spain by a galician retorne from Venezuela. Med Oral 1997; 2:39-43. [PMID: 11507456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- A. Garcia
- Facultad de Medicina y Odontologia. Universidad de Santiago de Compostela. Spain
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20
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Amador D, Pedraza A, Gandara J, Burns W, Kabacoff R, Roth L. Accuracy of the classification of patients with dementia versus memory loss-without-dementia. Arch Clin Neuropsychol 1995. [DOI: 10.1093/arclin/10.4.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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De Neef P, Gandara J. Experience with indeterminate mammograms. West J Med 1991; 154:36-9. [PMID: 2024508 PMCID: PMC1002672] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Most radiologists recommend follow-up mammography in 3 to 6 months for asymptomatic patients with mammographic lesions that do not appear suspicious enough to warrant immediate biopsy. In this retrospective cohort study, the medical records of 776 patients were audited 24 to 35 months after mammography to estimate the frequency of indeterminate lesions, the probability of malignancy, and the rate of patients' compliance with recommendations. Almost 2% of patients retested after an indeterminate mammogram were found to have breast cancer (95% confidence limits 0.2% and 5.9%). Only 26% of the patients retested during the audit period had the test within the suggested upper limit of 6 months. We conclude that timely follow-up after an indeterminate mammogram is advisable and that for the population we studied, compliance with this recommendation is low.
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Affiliation(s)
- P De Neef
- Department of Family Medicine, University of Washington School of Medicine, Seattle 98195
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