1
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024:10.1038/s41592-024-02191-z. [PMID: 38366243 DOI: 10.1038/s41592-024-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
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2
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN. bioRxiv 2023:2023.02.03.526939. [PMID: 36778387 PMCID: PMC9915700 DOI: 10.1101/2023.02.03.526939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, inter-species genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here, we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN has a unique ability to detect functionally related genes co-expressed across species, redefining differential expression for cross-species analysis. We apply SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets. We show that cell embeddings learnt in SATURN can be effectively used to transfer annotations across species and identify both homologous and species-specific cell types, even across evolutionarily remote species. Finally, we use SATURN to reannotate the five species Cell Atlas of Human Trabecular Meshwork and Aqueous Outflow Structures and find evidence of potentially divergent functions between glaucoma associated genes in humans and other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA
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3
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Navon EA, Rosen Y, Singer N, Goren O, Maor N, Eyal E, Ständer S, Yosipovitch G. 118 High unmet medical need in brachioradial pruritus: results from a large patient survey. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.128] [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: 11/19/2022]
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4
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Jones MG, Rosen Y, Yosef N. Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision. Cell Rep Methods 2022; 2:100200. [PMID: 35497495 PMCID: PMC9046453 DOI: 10.1016/j.crmeth.2022.100200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/19/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023]
Abstract
Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight from a joint analysis of these two modalities. Here, we describe "PhyloVision": an open-source software for interactively exploring data from both modalities and for identifying and interpreting heritable gene modules whose concerted expression are associated with phylogenetic relationships. PhyloVision provides a feature-rich, interactive, and shareable web-based report for investigating these modules while also supporting several other data and meta-data exploration capabilities. We demonstrate the utility of PhyloVision using a published dataset of metastatic lung adenocarcinoma cells, whose phylogeny was resolved using a CRISPR-Cas9-based lineage-tracing system. Together, we anticipate that PhyloVision and the methods it implements will be a useful resource for scalable and intuitive data exploration for any assay that simultaneously measures cell state and lineage.
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Affiliation(s)
- Matthew G. Jones
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720 USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94143, USA
- Whitehead Institute, Cambridge, MA 02142 USA
| | - Yanay Rosen
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720 USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Chan Zuckerberg Biohub Investigator, San Francisco, CA 94158 USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02114 USA
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5
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Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nat Methods 2020; 17:793-798. [PMID: 32719530 PMCID: PMC7437817 DOI: 10.1038/s41592-020-0905-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/18/2020] [Indexed: 11/10/2022]
Abstract
Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-scale single-cell and single-nucleus RNA sequencing datasets. Cumulus combines the power of cloud computing with improvements in algorithm and implementation to achieve high scalability, low cost, user-friendliness and integrated support for a comprehensive set of features. We benchmark Cumulus on the Human Cell Atlas Census of Immune Cells dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.
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Affiliation(s)
- Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Monika S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Division of Rheumatology, Allergy, and Immunology, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Timothy Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nir Hacohen
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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6
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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020; 26:1307. [PMID: 32587393 PMCID: PMC7417328 DOI: 10.1038/s41591-020-0976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Isaac Wakiro
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jingyi Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sébastien Vigneau
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara Napolitano
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Asa Karlstrom
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon Gritsch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Nomura
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Satyen H Gohil
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ofir Cohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bo Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.,Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Ludwig Center for Cancer Research at Harvard, Boston, MA, USA.,Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Rizwan Haq
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth H Stover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael R Clay
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Natalie B Collins
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikhil Wagle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020; 26:792-802. [PMID: 32405060 PMCID: PMC7220853 DOI: 10.1038/s41591-020-0844-1] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/20/2020] [Indexed: 01/20/2023]
Abstract
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.
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Affiliation(s)
- Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eugene Drokhlyansky
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Isaac Wakiro
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jingyi Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sébastien Vigneau
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara Napolitano
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mei-Ju Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Asa Karlstrom
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon Gritsch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Nomura
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Satyen H Gohil
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander M Tsankov
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Livnat Jerby-Arnon
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ofir Cohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Johanna Klughammer
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yanay Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Bo Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA, USA
- Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Columbia Center for Translational Immunology and Division of Hematology and Oncology, Columbia University Medical Center, New York, NY, USA
| | - Rizwan Haq
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Melanoma Disease Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles H Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Surgical Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Aaron N Hata
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth H Stover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael R Clay
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Natalie B Collins
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikhil Wagle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Precision Medicine of Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Affiliation(s)
- Y Rosen
- Department of Medicine, Coney Island Hospital, Brooklyn, NY, USA
| | - J Daich
- Department of Medicine, Coney Island Hospital, Brooklyn, NY, USA
| | - I Soliman
- Department of Medicine, Coney Island Hospital, Brooklyn, NY, USA
| | - E Brathwaite
- Department of Medicine, Coney Island Hospital, Brooklyn, NY, USA
| | - Y Shoenfeld
- Zabludowicz Centre for Autoimmune Diseases, Sheba Medical Centre, Tel Hashomer, Israel
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9
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Gurman P, Miranda OR, Nathan A, Washington C, Rosen Y, Elman NM. Recombinant tissue plasminogen activators (rtPA): a review. Clin Pharmacol Ther 2015; 97:274-85. [PMID: 25670034 DOI: 10.1002/cpt.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022]
Affiliation(s)
- P Gurman
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Materials Science and Bioengineering, University of Texas at Dallas, Richardson, Texas, USA
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10
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Abstract
There are conditions in clinical medicine demanding critical therapeutic decisions. These conditions necessitate accuracy, rapidity, accessibility, cost-effectiveness and mobility. New technologies have been developed in order to address these challenges. Microfluidics and Micro Electro-Mechanical Systems are two of such technologies. Microfluidics, a discipline that involves processing fluids at the microscale in etched microchannels, is being used to build lab- on-a-chip systems to run chemical and biological assays. These systems are being transformed into handheld devices designed to be used at remote settings or at the bedside. MEMS are microscale electromechanical elements integrated in lab chip systems or used as individual components. MEMS based sensors represents a highly developed field with successful commercialized products currently being incorporated into vitro,ex vivo and in vivo devices. In the present paper several examples of microfluidic devices and MEMS sensors are introduced together with some current examples of commercialized products. Future challenges and trends will be discussed.
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Affiliation(s)
- Y Rosen
- Superior NanoBioSystems LLC, 11722 Newbridge Court, Reston, VA, 20191, USA.
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11
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Rosen Y, Levy Y, Shoenfeld Y. [Pulmonary adenocarcinoma in myasthenia gravis--autoimmunity and late development of malignancy]. Harefuah 2000; 139:354-6, 406. [PMID: 11341211] [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] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
We report a 75-year-old man with myasthenia gravis for many years, who was hospitalized because of cough, fever, and dyspnea. Chest x-ray revealed a bilateral pleural effusion. Adenocarcinomatous cells were found in the pleural fluid. Computerized tomography of the chest showed widespread pulmonary dissemination of the tumor. The relationship between myasthenia gravis, an autoimmune disease involving the motor end-plate, and malignancy (thymoma) has been widely recognized. Current literature documents few reports of lung malignancies with concurrent development of myasthenia gravis. A tentative explanation, based on current research, is provided for the possible role of myasthenia gravis and the late development of lung cancer. Moreover, a model for the autoimmune phenomenon and the development of late malignancies is provided with explicit explanations. It is important to search for occult, developing malignancies in newly diagnosed autoimmune diseases.
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Affiliation(s)
- Y Rosen
- Dept. of Internal Medicine B, Sheba Medical Center, Tel Hashomer
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12
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Abstract
Venlafaxine, a structurally novel antidepressant, belongs to a new generation of antidepressants--the serotonin/noradrenaline reuptake inhibitors. In clinical trials, venlafaxine was found safe and effective in most patients. However, significant changes in vital signs (hyper- and hypotension) and cardiac conduction abnormalities were observed in a few patients, notably in elderly patients. We present a case of an elderly woman with a pre-existing history of ischaemic heart disease, who was treated with venlafaxine, and developed acute myocardial ischaemia within the first week of treatment. This is the first report of a possible association between an acute cardiovascular event and venlafaxine. The association of venlafaxine treatment with ischaemic events could be explained by its unique pharmacological and haemodynamic properties.
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Affiliation(s)
- I Reznik
- Abarbanel Mental Health Centre, Rabin Medical Centre-Beilinson Campus, Petah-Tikva, Israel.
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13
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Krause I, Rosen Y, Kaplan I, Milo G, Guedj D, Molad Y, Weinberger A. Recurrent aphthous stomatitis in Behçet's disease: clinical features and correlation with systemic disease expression and severity. J Oral Pathol Med 1999; 28:193-6. [PMID: 10226940 DOI: 10.1111/j.1600-0714.1999.tb02023.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Behçet's disease (BD) is a multisystem disease, in which recurrent aphthous stomatitis (RAS) is a universal finding. We studied the expression of RAS in patients with BD, and the correlation between major or minor RAS and systemic expression and severity of the disease. Thirty-five patients with BD were studied, of whom 13 (37%) had major, 21 (60%) had minor and one (3%) had herpetiform RAS. The frequency of major RAS was significantly higher compared with a control group of patients with idiopathic RAS (37% vs 9%, P < 0.05). The BD patients with major RAS had significantly more relapses of oral ulceration in a year, higher numbers of oral ulcers per relapse, and longer duration of aphthous episodes, compared with patients with minor RAS. Oral ulcers also appeared at a significantly younger age in patients with major than with minor RAS. However, the systemic expression of the disease, as well as the disease severity score, were similar in patients with major and minor RAS. The results of this study indicate that major RAS is common in patients with BD, and is associated with a more severe, repeated and prolonged oral disease. Nevertheless, the presence of major RAS in BD does not predict a more severe systemic illness.
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Affiliation(s)
- I Krause
- Department of Medicine B, Rabin Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Israel
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14
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Reznik I, Rosen Y, Rosen B. The rational antidepressant drugs selection in medically ill patients. Psychosomatics 1999; 40:269-71. [PMID: 10341543 DOI: 10.1016/s0033-3182(99)71249-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Harig B, Goldstein DJ, Rosen Y, Farman J. Colonic obstruction due to sigmoid muscular hyperplasia. Mt Sinai J Med 1999; 66:106-8. [PMID: 10100414] [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] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
We report a case of acute colonic obstruction initially presumed to be secondary to acute diverticulitis, necessitating emergent surgical intervention. Pathologic examination failed to reveal evidence of inflammation, fibrosis or neoplasia. Marked hypertrophy of the sigmoid circular muscle layer was documented and thought to be the etiology of the colonic obstruction.
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Affiliation(s)
- B Harig
- Department of Radiology, Lenox Hill Hospital, New York, NY, USA
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16
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Bahir A, Goldberg A, Mekori YA, Confino-Cohen R, Morag H, Rosen Y, Monakir D, Rigler S, Cohen AH, Horev Z, Noviski N, Mandelberg A. Continuous avoidance measures with or without acaricide in dust mite-allergic asthmatic children. Ann Allergy Asthma Immunol 1997; 78:506-12. [PMID: 9164365 DOI: 10.1016/s1081-1206(10)63239-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Improvement in the quality of life in the Western world and increased time spent indoors by children have enhanced the spread of house dust mites and increased the exposure time for sensitive children. Also, exposure to house dust mites in infancy and subsequent development of childhood asthma have been clinically linked. Recently, new acaricides have been developed. OBJECTIVE To test the efficacy of the new acaricide (esdepallethin and piperonyl butoxide--"Acardust") combined with environmental control compared with continuous house dust mite avoidance measures. METHOD Forty-six house dust mite-allergic, asthmatic children were evaluated for 6 months in a prospective, randomized, double-blind, and placebo-controlled study. Patients were randomly allocated to active and placebo acaricide treatment combined with avoidance measures, whereas only continuous avoidance measures were taken in the third group. Symptom score, medication usage, and peak flow measurements were recorded daily. The amount of house dust mite allergen in the dust vacuumed from the bedrooms was also measured. RESULTS Morning and evening peak expiratory flow rates and forced expiratory volume in one second remained unchanged throughout the study period. In all groups, the symptom scores improved significantly, whereas the amount of house dust mite allergen decreased significantly at the end of the trial. CONCLUSIONS Continuous house dust mite avoidance measures have a significant positive effect on the symptomology of children with mild or moderate asthma. "Acardust" combined with continuous house dust mite avoidance measures is not more effective than continuous house dust mite avoidance measures alone in the treatment of house dust mite-allergic, asthmatic children.
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Affiliation(s)
- A Bahir
- Allergy and Clinical Immunology Unit, Sapir Medical Center, Kfar Saba, Israel
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17
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Abstract
Melanoma represents the second most frequent vulvar malignancy, and yet is still considered to be an uncommon neoplasm. Several varieties of melanoma exist. A patient who was diagnosed with a rare subtype of melanoma as a primary vulvar process is presented here. To date, there is only one other reported case of neurotropic desmoplastic melanoma as a primary vulvar lesion. Our management included wide local excision of the primary lesion with clinical follow-up. Microstaging of this lesion showed it to fall into the poor prognosis category as per Breslow's technique, with a thickness of 6.5 mm. Clinical follow-up has been greater than 30 months without evidence of recurrence.
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Affiliation(s)
- P R Byrne
- Department of Obstetrics and Gynecology, Winthrop University Hospital, Mineola, New York 11501, USA
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18
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Affiliation(s)
- J C Wang
- Brookdale Hospital Medical Center, Brooklyn, New York
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19
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Levendoglu H, Rosen Y. Nodular lymphoid hyperplasia of gut in HIV infection. Am J Gastroenterol 1992; 87:1200-2. [PMID: 1519583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- H Levendoglu
- Division of Gastroenterology, Brookdale Hospital Medical Center, Brooklyn, New York
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20
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Friedman D, Mooppan UM, Rosen Y, Kim H. The effect of intravesical instillations of thiotepa, mitomycin C, and adriamycin on normal urothelium: an experimental study in rats. J Urol 1991; 145:1060-3. [PMID: 1901918 DOI: 10.1016/s0022-5347(17)38535-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The effects of intravesical instillations of thiotepa, mitomycin C and adriamycin on the normal urothelium were studied in rats. Changes in the bladder wall in the form of fibroblastic atypia and submucous fibrous plaques were significant in the mitomycin C treated group. In 46% of mitomycin C treated animals there was urothelial atypia and in one animal, the atypia was severe enough to resemble carcinoma in situ. None of the rats treated with thiotepa showed intramural fibrous plaques or fibroblastic atypia and only 8% showed urothelial atypia. In the group treated by adriamycin instillation, 17% showed intramural fibrous plaques, but none showed urothelial atypia or fibroblastic atypia. The fibroblastic atypia and submucosal fibrous plaques seen in the mitomycin treated group may explain the reduced bladder capacity seen in the clinical setting.
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Affiliation(s)
- D Friedman
- Department of Urology Brookdale Hospital Medical Center, Brooklyn, New York 11212
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21
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Abstract
Intraoperative pathologic examination with frozen section (FS) was performed on 504 specimens of thyroid tissue obtained from 457 patients over a period of 9 years. After examination of permanent sections (PS) a malignant neoplasm was diagnosed in 57 specimens (11.3%); 50 (87%) of these were primary thyroid carcinoma, four (8%) metastatic carcinoma, and three (5%) malignant lymphoma. The FS diagnosis was "benign" in 448 (88.9%), "malignant" in (30) 5.9%, and "deferred" in 26 (5.2%). The sensitivity of FS diagnosis of malignancy was 53% and the specificity and positive predictive value 100%. The negative predictive value was 97.8% and overall accuracy 97.9%. The PS disclosed a malignant neoplasm in 62% of specimens in which FS diagnosis was "deferred." Sixty-eight percent of papillary carcinomas, 87% of undifferentiated carcinomas, and a single case of medullary carcinoma were diagnosed with FS examination. A FS diagnosis of malignancy was not made in any of the ten specimens containing follicular carcinoma; in all ten the neoplasms were well-differentiated and eight were encapsulated and minimally invasive. The inability to diagnose follicular carcinoma intraoperatively with FS is the most significant factor accounting for the relatively low sensitivity of FS diagnosis of malignant thyroid neoplasms.
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Affiliation(s)
- Y Rosen
- Department of Pathology, Brookdale Hospital Medical Center, Brooklyn, New York 11212
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22
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Weintraub MS, Rosen Y, Otto R, Eisenberg S, Breslow JL. Physical exercise conditioning in the absence of weight loss reduces fasting and postprandial triglyceride-rich lipoprotein levels. Circulation 1989; 79:1007-14. [PMID: 2713969 DOI: 10.1161/01.cir.79.5.1007] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The effect of physical exercise conditioning on fasting and postprandial lipoprotein levels was studied in six normolipidemic subjects. The study consisted of two phases: a baseline stabilization phase in which subjects maintained their regular physical activity and an exercise conditioning phase in which subjects had 29 exercise sessions during a 7-week period. Each of these sessions consisted of jogging on a treadmill for 30 minutes. The subjects averaged 15.2 miles/wk. To control for possible confounding factors, such as changes in diet composition and weight loss, we placed the subjects on a metabolic diet and increased their daily caloric intake during the exercise phase. At the end of each phase of the study, a vitamin A-fat loading test was done to specifically label and follow postprandial lipoprotein levels, and a maximum oxygen consumption test was done to evaluate the subjects' physical fitness. The exercise conditioning phase significantly increased the subjects' aerobic capacity and postheparin lipoprotein lipase activity, and the phase decreased fasting triglyceride levels. Physical exercise also significantly decreased chylomicron (Sf greater than 1,000) levels by 37%. In summary, this study suggests that physical exercise conditioning reduces fasting and postprandial lipoprotein levels by increasing the catabolism of triglyceride-rich particles. Because these particles may have a role in atherogenesis, this could be a major mechanism by which exercise prevents coronary heart disease.
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Affiliation(s)
- M S Weintraub
- Laboratory of Biochemical Genetics and Metabolism, Rockefeller University, New York, NY 10021
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23
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Pepper GM, Zwickler D, Rosen Y. Fine-needle aspiration biopsy of the thyroid nodule. Results of a start-up project in a general teaching hospital setting. Arch Intern Med 1989; 149:594-6. [PMID: 2919935] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The results of the initial 102 fine-needle aspiration biopsies of the thyroid performed at a 795-bed general teaching hospital are reported. Eighty-four of the nodules (82%) were cytologically benign, 18 nodules (18%) were suspicious, and none of the nodules was diagnosed as malignant. Five nodules In the suspicious group (28%) were found to be malignant following microscopic examination of the surgical specimens. There was one false-negative result. Based on the data from 21 patients with both cytologic and histologic diagnoses, the positive predictive value of this procedure was 38% and the negative predictive value was 87% (sensitivity, 83%; specificity, 47%). Our results were comparable with those of major referral centers. Guidelines for establishing a fine-needle aspiration biopsy program at a general hospital are suggested.
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Affiliation(s)
- G M Pepper
- Department of Medicine, Brookdale Hospital Medical Center, Brooklyn, NY
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24
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Abstract
A case of renal cell carcinoma presenting with uncontrolled diabetes mellitus is reported. After a radical nephrectomy, the diabetic state completely resolved. Laboratory studies failed to reveal any endocrinopathy responsible for the diabetic state. Thus it appears that hyperglycemia and diabetes mellitus can now be included with the other paraneoplastic endocrinopathies associated with renal cell carcinoma.
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25
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Abstract
Bronchocentric granulomatosis (BG) is an uncommon inflammatory lesion of unknown etiology defined on morphologic grounds by the presence of necrotizing granulomata centered on bronchi and bronchioles. We report the typical pathologic features of BG in a patient with tuberculosis. Mycobacterial and other types of infection should be excluded by appropriate stains and cultures in all patients with BG on lung biopsy, especially those who are nonasthmatic.
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26
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Camiel MR, Rosen Y, Farman J, Alexander L. Inoperable gastric lymphosarcoma mistaken for carcinoma: response to radiation with twenty-year survival to date. Gastrointest Radiol 1983; 8:315-7. [PMID: 6688997 DOI: 10.1007/bf01948141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
With suitable treatment, the potential for long survival with gastric lymphoma is well-documented. However, since these tumors constitute only about 1-3% of gastric malignancies, they may occur only rarely in a particular radiologist's experience. The present report of a remarkable therapeutic response is a reminder that the possibility of lymphosarcoma should be included in the differential diagnosis of every gastric neoplasm.
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27
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Pertschuk LP, Silverstein E, Friedland J, Rosen Y, Smith P. Immunofluorescent detection of angiotensin II in sarcoidosis epithelioid and giant cells. Cell Mol Biol Incl Cyto Enzymol 1981; 27:297-299. [PMID: 7028266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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28
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29
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Rosen Y. Are the case records obsolete? N Engl J Med 1980; 302:1208. [PMID: 7366670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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32
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Abstract
A prostatic leiomyoma with nuclear atypia, similar in appearance to atypia sometimes seen in uterine leiomyomas, was an incidental finding in a fifty-three-year-old man who underwent prostatectomy for hyperplasia. The smooth muscle nature of the lesion was confirmed by electron microscopic examination. This is the third lesion of this type to be reported.
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33
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Ambiavagar PC, Rosen Y. Cutaneous ciliated cyst of the chin. Probable bronchogenic cyst. Arch Dermatol 1979; 115:895-6. [PMID: 453906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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Huang CT, Heurich AE, Rosen Y, Moon S, Lyons HA. Pulmonary sarcoidosis: roentgenographic, functional, and pathologic correlations. Respiration 1979; 37:337-45. [PMID: 451366 DOI: 10.1159/000194046] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Discrepancies were observed between functional (PFT), chest roentgenographic, and open lung biopsy findings (granulomata, interstitial pneumonitis, angiitis, and fibrosis) in 81 patients with clinical diagnosis of sarcoidosis. A combination of normal PFT and Type 1 roentgenographic findings (hilar lymphadenopathy) was associated with minimal lung lesions without fibrosis. Type 1 findings alone did not preclude extensive lesions or fibrosis. Advanced roentgenographic and PFT abnormalities correlated with the presence of extensive lung lesions. The pulmonary diffusing capacity correlated best with specific and overall lung pathology, and roentgenographic types. Only this test differentiated the extent of granulomata and the roentgenographic types. Moderate degrees of other pathologic changes were not distinguished by any other PFT. Degrees of overall lung pathology correlated with an individual PFT and most significantly with overall PFT (p less than 0.001). Serial studies of PFT are a practical and valuable means for assessment of the disease process in sarcoidosis.
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35
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Abstract
An unusual, recurring, squamous papillary tumor involving and possibly arising from minor salivary gland excretory ducts in the palate is presented. Similarity to sialadenoma papilliferum and upper respiratory tract papillomatosis is noted. A paraglandular cystic mass with some resemblance to the palatal lesion, and a solitary lymph node with papillary squamous epithelial deposits was found in a radical neck dissection. We suggest that the lymph node lesion represents a metastasis which may have arisen from the palatal lesion, and therefore propose the concept of a possible malignant analogue of sialadenoma papilliferum.
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36
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Rosen Y, Athanassiades TJ, Moon S, Lyons HA. Nongranulomatous interstitial pneumonitis in sarcoidosis. Relationship to development of epithelioid granulomas. Chest 1978; 74:122-5. [PMID: 679737 DOI: 10.1378/chest.74.2.122] [Citation(s) in RCA: 89] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nongranulomatous, nonspecific interstitial pneumonitis was a predominating or prominent histopathologic finding in 62 percent of 128 granuloma-containing specimens from open lung biopsies obtained from patients with sarcoidosis. Data from this study, combined with observations by others on the evolution of experimentally induced granulomas, indicate that interstitial pneumonitis represents a very early lesion, possibly the initial lesion, in pulmonary sarcoidosis. Because of the relatively large error of sampling inherent in the currently increasing practice of obtaining small specimens for lung biopsy via the flexible fiberoptic bronchoscope, we anticipate that interstitial pneumonitis will be seen as the only histopathologic finding in these specimens with increasing frequency. It is therefore important to recognize that interstitial pneumonitis is a characteristic, although nondiagnostic, morphologic feature of pulmonary sarcoidosis.
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37
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Abstract
A case of fibromatosis of the breast occurring in a 37-year-old woman is described. Only 15 cases of this type have been previously reported. In 5 of these cases there was also involvement of the underlying pectoral muscles, raising the possibility that some of these may have been of pectoral musculoaponeurotic origin. Two of the previously reported cases occurred in patients with Gardner's syndrome and 1 in a patient with "familial muticentric fibromatosis." It is anticipated that fibromatosis of the breast will behave in a similar fashion to fibromatosis occurring in other sites; i.e., as a local aggressive lesion which exhibits a high incidence of local recurrence following incomplete excision.
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38
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Abstract
Eight cases of phlegmonous enterocolitis which involved the small intestine exclusively in 5 patients, colon exclusively in 2, and both small intestine and colon in one are reported. Seven of the cases were studied at autopsy. The intestinal lesion was clearly the cause of death in 3 patients and was probably a secondary finding in 4 others. In one case, the cecum was involved and this segment was surgically resected. Five of the patients gave a history of alcoholism. The livers of the 7 patients studied at autopsy were all abnormal; cirrhosis was present in 4, severe fatty metamorphosis in 2, and moderate fatty metamorphosis in 1. The clinical, morphological, and bacteriological aspects of phlegmonous gastritis and phlegmonous enterocolitis are similar, and these two conditions are thought to represent the same infectious disease involving different levels of the gastrointestinal tract. In most patients the factor(s) predisposing to infection of the gastric and intestinal wall are unknown. In some patients mucosal injury of varied type and septicemia appear to have been the forerunners of the phlegmonous lesion. The possible relationships of ischemic bowel injury, alcoholism, and liver disease to phlegmonous inflammation of the gastrointestinal tract are discussed.
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39
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Cohen MM, Rosen Y, Gadoth N, Tal A. A homologous tandem translocation [45,XX,-13,-13,+t(13;13) (q12;q34)]. Cytogenet Cell Genet 1978; 20:155-9. [PMID: 648174 DOI: 10.1159/000130847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chromosomal investigation of a young girl with mental and motor retardation and congenital anomalies revealed a translocation between both members of pair No. 13. Banding analysis showed that the translocation was "tandem," leading to monosomy for segments in both the long and short arms of No. 13.
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40
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Abstract
Granulomas were found in the lungs of 21 consecutive patients with stage I sarcoidosis who underwent open lung biopsy. The extent of granulomatous disease and fibrosis was significantly less (P less than .05) than seen in open lung biopsies from larger groups of patients with stage II and stage III sarcoidosis. The results of this study support what had previously been widely suspected: that is, if sufficient lung tissue is studied microscopically, granulomas will be found in the lungs of all patients having sarcoidosis with mediastinal lymphadenopathy but not radiographically demonstrable lung abnormalities.
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Pertschuk LP, Moccia LF, Rosen Y, Lyons H, Marino CM, Rashford AA, Wollschlager CM. Acute pulmonary complications in systemic lupus erythematosus. Immunofluorescence and light microscopic study. Am J Clin Pathol 1977; 68:553-7. [PMID: 335872 DOI: 10.1093/ajcp/68.5.553] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lung tissue obtained from eight consecutive patients with systemic lupus erythematosus complicated by severe, acute pulmonary disease was studied by both light and immunofluorescence microscopy. Light microscopic examination disclosed interstitial pneumonia in four cases, cytomegalovirus pneumonitis in one case, bronchiolitis and peribronchiolitis in one case, pulmonary infarction in one case and focal atelectasis in the remaining case. Direct immunofluorescence examination revealed focally bound immunoglobulins or complement (C3) within pleural and/or pneumocyte nuclei in each specimen. Immunohistologic studies in these cases may thus suggest a diagnosis of systemic lupus erythematosus with acute pulmonary complications, despite the lack of specificity of the pathologic changes seen by light microscopy.
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Abstract
This is the eighth case report of an endodermal sinus tumor of the mediastinum (first case studied by electron microscopy). The ultrastructure of the tumor was found to mimic that of the normal yolk sac and was also similar to that of three previously reported cases of endodermal sinus tumor of the ovary, thus confirming the correctness of Teilum's original interpretation of the tumor as arising in germ cells and differentiating towards extraembryonic structures.
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Abstract
The inability of slowly frozen formalin-fixed tissues to reimbibe water normally on thawing accounts for the persistence of extracellular ice crystal spaces in such tissues and renders them useless for diagnostic microscopic examination. This phenomenon may be encountered by the surgical pathologist when tissues obtained for diagnosis are placed in formalin for fixation and the inadvertently frozen. The same type of ice crystal distortion was produced when formalin-fixed tissues were slowly frozen under laboratory conditions. The freezing artifact was not produced when formalin-fixed tissues were frozen in non-formalin-containing aqueous media.
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Rosen Y, Kim DS, Farman J, Dallemand S. Genip fruit: an unusual intragastric foreign body simulating a neoplasm. Am J Gastroenterol 1977; 67:497-500. [PMID: 900114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Rosen Y, Moon S, Huang CT, Gourin A, Lyons HA. Granulomatous pulmonary angiitis in sarcoidosis. Arch Pathol Lab Med 1977; 101:170-4. [PMID: 576782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The occurrence and morphologic aspects of granulomatous pulmonary angiitis were evaluated in open lung biopsy specimens from 128 patients with sarcoidosis. All of the specimens showed parenchymal granulomas characteristic of sarcoidosis, and in 88(69%), granulomatous angiitis was seen. In the speclimens that exhibited granulomatous angiitis, venous involvement was mos common, seen in 92% of the cases. In 61% of these biopsy specimens, only venous involvement was seen; in 31%, both venous and arterial involvement was present. Only 8% of the positive specimens showed arterial lesions exclusively. The extent of angiitis was quantitated. Focal segmental elastic tissue destruction, partial or complete, was a common finding. No instances of aneurysm formation, endothelial erosion, or thrombosis were observed. Occlusive narrowing of small vessels was frequent. Bronchial blood vessels were not involved.
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Rosen Y, Chen C. Infarction of the gallbladder: a complication of hypertension. Case report. Am J Gastroenterol 1977; 67:249-52. [PMID: 868844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A case of gallbladder infarction, occurring in a 34-year old man with severe hypertension is described, with uneventful recovery following cholecystectomy. In the absence of other obvious etiologic factors, the gallbladder infarction is presumed to be directly related to hypertensive vascular disease. Infarction of the gallbladder is rare; a few cases associated with hypertension have been previously reported. Other types of vascular disease including embolization, thrombosis complicating atherosclerosis and celiac angiography, polyarteritis nodosa, occlusion following torsion and cystic vein thrombosis have been reported to cause gallbladder infarction.
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Hermann G, Rosen Y. Radiologic notes. case no. 395. Ossifying lipoma. Mt Sinai J Med 1977; 44:292-5. [PMID: 405562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Rosen Y, Giannattasio CR, Boyce JG. Implantation of placental tissue in the cervix: complication of simultaneous cone biopsy and abortion. JAMA 1977; 237:767. [PMID: 576310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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50
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Rosen Y, Vaillant JG, Yermakov V. Submucosal mucous cysts at a colostomy site: relationship to colitis cystica profunda and report of a case. Dis Colon Rectum 1976; 19:453-7. [PMID: 939162 DOI: 10.1007/bf02590833] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A unique case of submucosal mucus-containing cysts of the colon occurring at a colostomy site is described. The cysts appear to have been the result of surgery eight years previously, and were due to either implantation of colonic mucosa into the submucosa or entrapment of mucosa following healing of postsurgical ulceration. Because these cysts are identical to the lesions seen in colitis cystica profunda, this case provides additional support for the hypothesis that colitis cystica profunda is an acquired disease, and illustrates that it may occur as a rare complication of colonic surgery.
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