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von Felden J, Garcia-Lezana T, Dogra N, Gonzalez-Kozlova E, Ahsen ME, Craig A, Gifford S, Wunsch B, Smith JT, Kim S, Diaz JEL, Chen X, Labgaa I, Haber P, Olsen R, Han D, Restrepo P, D'Avola D, Hernandez-Meza G, Allette K, Sebra R, Saberi B, Tabrizian P, Asgharpour A, Dieterich D, Llovet JM, Cordon-Cardo C, Tewari A, Schwartz M, Stolovitzky G, Losic B, Villanueva A. Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer. Gut 2021; 71:gutjnl-2021-325036. [PMID: 34321221 PMCID: PMC8795201 DOI: 10.1136/gutjnl-2021-325036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/15/2021] [Indexed: 01/30/2023]
Abstract
OBJECTIVE Surveillance tools for early cancer detection are suboptimal, including hepatocellular carcinoma (HCC), and biomarkers are urgently needed. Extracellular vesicles (EVs) have gained increasing scientific interest due to their involvement in tumour initiation and metastasis; however, most extracellular RNA (exRNA) blood-based biomarker studies are limited to annotated genomic regions. DESIGN EVs were isolated with differential ultracentrifugation and integrated nanoscale deterministic lateral displacement arrays (nanoDLD) and quality assessed by electron microscopy, immunoblotting, nanoparticle tracking and deconvolution analysis. Genome-wide sequencing of the largely unexplored small exRNA landscape, including unannotated transcripts, identified and reproducibly quantified small RNA clusters (smRCs). Their key genomic features were delineated across biospecimens and EV isolation techniques in prostate cancer and HCC. Three independent exRNA cancer datasets with a total of 479 samples from 375 patients, including longitudinal samples, were used for this study. RESULTS ExRNA smRCs were dominated by uncharacterised, unannotated small RNA with a consensus sequence of 20 nt. An unannotated 3-smRC signature was significantly overexpressed in plasma exRNA of patients with HCC (p<0.01, n=157). An independent validation in a phase 2 biomarker case-control study revealed 86% sensitivity and 91% specificity for the detection of early HCC from controls at risk (n=209) (area under the receiver operating curve (AUC): 0.87). The 3-smRC signature was independent of alpha-fetoprotein (p<0.0001) and a composite model yielded an increased AUC of 0.93. CONCLUSION These findings directly lead to the prospect of a minimally invasive, blood-only, operator-independent clinical tool for HCC surveillance, thus highlighting the potential of unannotated smRCs for biomarker research in cancer.
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Affiliation(s)
- Johann von Felden
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Teresa Garcia-Lezana
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Navneet Dogra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mehmet Eren Ahsen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amanda Craig
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stacey Gifford
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Benjamin Wunsch
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Joshua T Smith
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Sungcheol Kim
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Jennifer E L Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Xintong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ismail Labgaa
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Visceral Surgery, Lausanne University Hospital, Lausanne, Switzerland
| | - Philipp Haber
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Reena Olsen
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dan Han
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paula Restrepo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Delia D'Avola
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Liver Unit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Clínica Universidad de Navarra, Pamplona, Spain
| | - Gabriela Hernandez-Meza
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Behnam Saberi
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Parissa Tabrizian
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Surgery, Mount Sinai School of Medicine, New York, New York, USA
| | - Amon Asgharpour
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Douglas Dieterich
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Josep M Llovet
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Liver Cancer Translational Research Laboratory, BCLC Group, IDIBAPS, CIBEREHD, Hospital Clinic, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Carlos Cordon-Cardo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ash Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Myron Schwartz
- Department of Surgery, Mount Sinai School of Medicine, New York, New York, USA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- IBM Thomas J Watson Research Center, Yorktown Heights, New York, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma'ayan A. modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Res 2020; 47:W183-W190. [PMID: 31069376 PMCID: PMC6602483 DOI: 10.1093/nar/gkz347] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 01/31/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set libraries within FishEnrichr, FlyEnrichr, WormEnrichr and YeastEnrichr are created from the Gene Ontology, mRNA expression profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific resources. Additionally, libraries were created by predicting gene function from RNA-seq co-expression data processed uniformly from the gene expression omnibus for each organism. The modEnrichr suite of tools provides the ability to convert gene lists across species using an ortholog conversion tool that automatically detects the species. For complex analyses, modEnrichr provides API access that enables submitting batch queries. In summary, modEnrichr leverages existing model organism databases and other resources to facilitate comprehensive hypothesis generation through data integration.
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Affiliation(s)
- Maxim V Kuleshov
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Jennifer E L Diaz
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020, New York, NY 10029, USA
| | - Zachary N Flamholz
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Alexandra B Keenan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Megan L Wojciechowicz
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Ross L Cagan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
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Velkova A, Diaz JEL, Pangilinan F, Molloy AM, Mills JL, Shane B, Sanchez E, Cunningham C, McNulty H, Cropp CD, Bailey-Wilson JE, Wilson AF, Brody LC. The FUT2 secretor variant p.Trp154Ter influences serum vitamin B12 concentration via holo-haptocorrin, but not holo-transcobalamin, and is associated with haptocorrin glycosylation. Hum Mol Genet 2017; 26:4975-4988. [PMID: 29040465 PMCID: PMC5886113 DOI: 10.1093/hmg/ddx369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/14/2022] Open
Abstract
Vitamin B12 deficiency is common in older individuals. Circulating vitamin B12 concentration can be used to diagnose deficiency, but this test has substantial false positive and false negative rates. We conducted genome-wide association studies (GWAS) in which we resolved total serum vitamin B12 into the fractions bound to transcobalamin and haptocorrin: two carrier proteins with very different biological properties. We replicated reported associations between total circulating vitamin B12 concentrations and a common null variant in FUT2. This allele determines the secretor phenotype in which blood group antigens are found in non-blood body fluids. Vitamin B12 bound to haptocorrin (holoHC) remained highly associated with FUT2 rs601338 (p.Trp154Ter). Transcobalamin bound vitamin B12 (holoTC) was not influenced by this variant. HoloTC is the bioactive the form of the vitamin and is taken up by all tissues. In contrast, holoHC is only taken up by the liver. Using holoHC from individuals with known FUT2 genotypes, we demonstrated that FUT2 rs601338 genotype influences the glycosylation of haptocorrin. We then developed an experimental model demonstrating that holoHC is transported into cultured hepatic cells (HepG2) via the asialoglycoprotein receptor (ASGR). Our data challenge current published hypotheses on the influence of genetic variation on this clinically important measure and are consistent with a model in which FUT2 rs601338 influences holoHC by altering haptocorrin glycosylation, whereas B12 bound to non-glycosylated transcobalamin (i.e. holoTC) is not affected. Our findings explain some of the observed disparity between use of total B12 or holoTC as first-line clinical tests of vitamin B12 status.
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Affiliation(s)
- Aneliya Velkova
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Jennifer E L Diaz
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Faith Pangilinan
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Anne M Molloy
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver NICHD, Bethesda, MD 20852, USA
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Erica Sanchez
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | | | - Helene McNulty
- Northern Ireland Centre for Food and Health, University of Ulster, Coleraine BT52 1SA, Northern Ireland
| | - Cheryl D Cropp
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Alexander F Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Lawrence C Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
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Diaz JEL, Ekasumara N, Menon NR, Homan E, Rajarajan P, Zamudio AR, Kim AJ, Gruener J, Poliandro E, Thomas DC, Meah YS, Soriano RP. Interpreter training for medical students: pilot implementation and assessment in a student-run clinic. BMC Med Educ 2016; 16:256. [PMID: 27687285 PMCID: PMC5043630 DOI: 10.1186/s12909-016-0760-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/29/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Trained medical interpreters are instrumental to patient satisfaction and quality of care. They are especially important in student-run clinics, where many patients have limited English proficiency. Because student-run clinics have ties to their medical schools, they have access to bilingual students who may volunteer to interpret, but are not necessarily formally trained. METHODS To study the feasibility and efficacy of leveraging medical student volunteers to improve interpretation services, we performed a pilot study at the student-run clinic at the Icahn School of Medicine at Mount Sinai. In each fall semester in 2012-2015, we implemented a 6-h course providing didactic and interactive training on medical Spanish interpreting techniques and language skills to bilingual students. We then assessed the impact of the course on interpreter abilities. RESULTS Participants' comfort levels, understanding of their roles, and understanding of terminology significantly increased after the course (p < 0.05), and these gains remained several months later (p < 0.05) and were repeated in an independent cohort. Patients and student clinicians also rated participants highly (averages above 4.5 out of 5) on these measures in real clinical encounters. CONCLUSIONS These findings suggest that a formal interpreter training course tailored for medical students in the setting of a student-run clinic is feasible and effective. This program for training qualified student interpreters can serve as a model for other settings where medical students serve as interpreters.
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Affiliation(s)
- Jennifer E. L. Diaz
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nydia Ekasumara
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nikhil R. Menon
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Edwin Homan
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Prashanth Rajarajan
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Andrés Ramírez Zamudio
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Annie J. Kim
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Jason Gruener
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Edward Poliandro
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - David C. Thomas
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Yasmin S. Meah
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Rainier P. Soriano
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY USA
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