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Brandwein M, Fuks G, Israel A, Hodak E, Sabbah F, Steinberg D, Bentwich Z, Shental N, Meshner S. Biogeographical Landscape of the Human Face Skin Microbiome Viewed in High Definition. Acta Derm Venereol 2021; 101:adv00603. [PMID: 34515801 PMCID: PMC9455318 DOI: 10.2340/00015555-3929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The bacterial community that colonizes the human face imparts physiochemical and physiological effects on the facial skin. These skin-microbe interactions impact dermatological, cosmetic and skincare applications due to the centrality of the human face in daily interactions. However, fine-scale characterization of the human face skin microbiome is lacking. Using 16S rRNA sequencing and 3D cartography, this study plotted and characterized the facial skin microbiome in high-definition, based on 1,649 samples from 12 individuals. Analysis yielded a number of novel insights, including that of the relative uniformity of skin microbiome composition within skin sites, site localization of certain microbes, and the interpersonal variability of the skin microbiome. The results show that high-resolution topographical mapping of the skin microbiome is a powerful tool for studying the human skin microbiome. Despite a decade of skin microbiome research, there is still much to be discovered.
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Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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2
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Mishra A, Lai GC, Yao LJ, Aung TT, Shental N, Rotter-Maskowitz A, Shepherdson E, Singh GSN, Pai R, Shanti A, Wong RMM, Lee A, Khyriem C, Dutertre CA, Chakarov S, Srinivasan KG, Shadan NB, Zhang XM, Khalilnezhad S, Cottier F, Tan ASM, Low G, Chen P, Fan Y, Hor PX, Lee AKM, Choolani M, Vermijlen D, Sharma A, Fuks G, Straussman R, Pavelka N, Malleret B, McGovern N, Albani S, Chan JKY, Ginhoux F. Microbial exposure during early human development primes fetal immune cells. Cell 2021; 184:3394-3409.e20. [PMID: 34077752 PMCID: PMC8240556 DOI: 10.1016/j.cell.2021.04.039] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/09/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
The human fetal immune system begins to develop early during gestation; however, factors responsible for fetal immune-priming remain elusive. We explored potential exposure to microbial agents in utero and their contribution toward activation of memory T cells in fetal tissues. We profiled microbes across fetal organs using 16S rRNA gene sequencing and detected low but consistent microbial signal in fetal gut, skin, placenta, and lungs in the 2nd trimester of gestation. We identified several live bacterial strains including Staphylococcus and Lactobacillus in fetal tissues, which induced in vitro activation of memory T cells in fetal mesenteric lymph node, supporting the role of microbial exposure in fetal immune-priming. Finally, using SEM and RNA-ISH, we visualized discrete localization of bacteria-like structures and eubacterial-RNA within 14th weeks fetal gut lumen. These findings indicate selective presence of live microbes in fetal organs during the 2nd trimester of gestation and have broader implications toward the establishment of immune competency and priming before birth.
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Affiliation(s)
- Archita Mishra
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Ghee Chuan Lai
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Leong Jing Yao
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Thet Tun Aung
- Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Ra'anana 4353701, Israel
| | - Aviva Rotter-Maskowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Edwin Shepherdson
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Gurmit Singh Naranjan Singh
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Rhea Pai
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Adhika Shanti
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Regina Men Men Wong
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Andrea Lee
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Costerwell Khyriem
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Charles Antoine Dutertre
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Svetoslav Chakarov
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - K G Srinivasan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Xiao-Meng Zhang
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Shabnam Khalilnezhad
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Fabien Cottier
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Alrina Shin Min Tan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Gillian Low
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Phyllis Chen
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Yiping Fan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Pei Xiang Hor
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Avery Khoo May Lee
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228, Singpore
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Institute for Medical Immunology, ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Ankur Sharma
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore; Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia; Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Naomi McGovern
- Department of Pathology and Centre for Trophoblast Research, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore.
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; OBGYN-Academic Clinical Program, Duke-NUS, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore 119077, Singapore.
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China.
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3
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Kalaora S, Nagler A, Nejman D, Alon M, Barbolin C, Barnea E, Ketelaars SLC, Cheng K, Vervier K, Shental N, Bussi Y, Rotkopf R, Levy R, Benedek G, Trabish S, Dadosh T, Levin-Zaidman S, Geller LT, Wang K, Greenberg P, Yagel G, Peri A, Fuks G, Bhardwaj N, Reuben A, Hermida L, Johnson SB, Galloway-Peña JR, Shropshire WC, Bernatchez C, Haymaker C, Arora R, Roitman L, Eilam R, Weinberger A, Lotan-Pompan M, Lotem M, Admon A, Levin Y, Lawley TD, Adams DJ, Levesque MP, Besser MJ, Schachter J, Golani O, Segal E, Geva-Zatorsky N, Ruppin E, Kvistborg P, Peterson SN, Wargo JA, Straussman R, Samuels Y. Identification of bacteria-derived HLA-bound peptides in melanoma. Nature 2021; 592:138-143. [PMID: 33731925 PMCID: PMC9717498 DOI: 10.1038/s41586-021-03368-8] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/17/2021] [Indexed: 01/31/2023]
Abstract
A variety of species of bacteria are known to colonize human tumours1-11, proliferate within them and modulate immune function, which ultimately affects the survival of patients with cancer and their responses to treatment12-14. However, it is not known whether antigens derived from intracellular bacteria are presented by the human leukocyte antigen class I and II (HLA-I and HLA-II, respectively) molecules of tumour cells, or whether such antigens elicit a tumour-infiltrating T cell immune response. Here we used 16S rRNA gene sequencing and HLA peptidomics to identify a peptide repertoire derived from intracellular bacteria that was presented on HLA-I and HLA-II molecules in melanoma tumours. Our analysis of 17 melanoma metastases (derived from 9 patients) revealed 248 and 35 unique HLA-I and HLA-II peptides, respectively, that were derived from 41 species of bacteria. We identified recurrent bacterial peptides in tumours from different patients, as well as in different tumours from the same patient. Our study reveals that peptides derived from intracellular bacteria can be presented by tumour cells and elicit immune reactivity, and thus provides insight into a mechanism by which bacteria influence activation of the immune system and responses to therapy.
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Affiliation(s)
- Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Nagler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chaya Barbolin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eilon Barnea
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Steven L C Ketelaars
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Raanana, Israel
| | - Yuval Bussi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Benedek
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Sophie Trabish
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Levin-Zaidman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Leore T Geller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Kun Wang
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Polina Greenberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Yagel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Neerupma Bhardwaj
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leandro Hermida
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sarah B Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lior Roitman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Lotem
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Arie Admon
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Mitchell P Levesque
- Faculty of Medicine, University of Zurich Hospital, University of Zurich, Zurich, Switzerland
| | - Michal J Besser
- The Ella Lemelbaum Institute for Immuno Oncology and Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jacob Schachter
- The Ella Lemelbaum Institute for Immuno Oncology and Melanoma, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Geva-Zatorsky
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- MaRS Centre, Canadian Institute for Advanced Research (CIFAR) Azrieli Global Scholar, Toronto, Ontario, Canada
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Scott N Peterson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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4
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Benor G, Fuks G, Chin S, Rueda OM, Mukherjee S, Arandkar S, Aylon Y, Caldas C, Domany E, Oren M. Transcriptional profiling reveals a subset of human breast tumors that retain wt TP53 but display mutant p53-associated features. Mol Oncol 2020; 14:1640-1652. [PMID: 32484602 PMCID: PMC7400784 DOI: 10.1002/1878-0261.12736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 11/25/2022] Open
Abstract
TP53 gene mutations are very common in human cancer. While such mutations abrogate the tumor suppressive activities of the wild-type (wt) p53 protein, some of them also endow the mutant (mut) protein with oncogenic gain of function (GOF), facilitating cancer progression. Yet, p53 may acquire altered functionality even without being mutated; in particular, experiments with cultured cells revealed that wtp53 can be rewired to adopt mut-like features in response to growth factors or cancer-mimicking genetic manipulations. To assess whether such rewiring also occurs in human tumors, we interrogated gene expression profiles and pathway deregulation patterns in the METABRIC breast cancer (BC) dataset as a function of TP53 gene mutation status. Harnessing the power of machine learning, we optimized a gene expression classifier for ER+Her2- patients that distinguishes tumors carrying TP53 mutations from those retaining wt TP53. Interestingly, a small subset of wt TP53 tumors displayed gene expression and pathway deregulation patterns markedly similar to those of TP53-mutated tumors. Moreover, similar to TP53-mutated tumors, these 'pseudomutant' cases displayed a signature for enhanced proliferation and had worse prognosis than typical wtp53 tumors. Notably, these tumors revealed upregulation of genes which, in BC cell lines, were reported to be positively regulated by p53 GOF mutants. Thus, such tumors may benefit from mut p53-associated activities without having to accrue TP53 mutations.
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Affiliation(s)
- Gal Benor
- Department of Physics of Complex SystemsThe Weizmann Institute of ScienceRehovotIsrael
| | - Garold Fuks
- Department of Physics of Complex SystemsThe Weizmann Institute of ScienceRehovotIsrael
| | - Suet‐Feung Chin
- Cancer Research UK Cambridge Institute and Department of OncologyLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute and Department of OncologyLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Saptaparna Mukherjee
- Department of Molecular Cell BiologyThe Weizmann Institute of ScienceRehovotIsrael
| | - Sharathchandra Arandkar
- Department of Molecular Cell BiologyThe Weizmann Institute of ScienceRehovotIsrael
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)Tata Memorial CentreKhargharIndia
| | - Yael Aylon
- Department of Molecular Cell BiologyThe Weizmann Institute of ScienceRehovotIsrael
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of OncologyLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Eytan Domany
- Department of Physics of Complex SystemsThe Weizmann Institute of ScienceRehovotIsrael
| | - Moshe Oren
- Department of Molecular Cell BiologyThe Weizmann Institute of ScienceRehovotIsrael
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5
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Nejman D, Livyatan I, Fuks G, Gavert N, Zwang Y, Geller LT, Rotter-Maskowitz A, Weiser R, Mallel G, Gigi E, Meltser A, Douglas GM, Kamer I, Gopalakrishnan V, Dadosh T, Levin-Zaidman S, Avnet S, Atlan T, Cooper ZA, Arora R, Cogdill AP, Khan MAW, Ologun G, Bussi Y, Weinberger A, Lotan-Pompan M, Golani O, Perry G, Rokah M, Bahar-Shany K, Rozeman EA, Blank CU, Ronai A, Shaoul R, Amit A, Dorfman T, Kremer R, Cohen ZR, Harnof S, Siegal T, Yehuda-Shnaidman E, Gal-Yam EN, Shapira H, Baldini N, Langille MGI, Ben-Nun A, Kaufman B, Nissan A, Golan T, Dadiani M, Levanon K, Bar J, Yust-Katz S, Barshack I, Peeper DS, Raz DJ, Segal E, Wargo JA, Sandbank J, Shental N, Straussman R. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science 2020; 368:973-980. [PMID: 32467386 DOI: 10.1126/science.aay9189] [Citation(s) in RCA: 957] [Impact Index Per Article: 239.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/22/2020] [Accepted: 04/14/2020] [Indexed: 12/15/2022]
Abstract
Bacteria were first detected in human tumors more than 100 years ago, but the characterization of the tumor microbiome has remained challenging because of its low biomass. We undertook a comprehensive analysis of the tumor microbiome, studying 1526 tumors and their adjacent normal tissues across seven cancer types, including breast, lung, ovary, pancreas, melanoma, bone, and brain tumors. We found that each tumor type has a distinct microbiome composition and that breast cancer has a particularly rich and diverse microbiome. The intratumor bacteria are mostly intracellular and are present in both cancer and immune cells. We also noted correlations between intratumor bacteria or their predicted functions with tumor types and subtypes, patients' smoking status, and the response to immunotherapy.
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Affiliation(s)
- Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Livyatan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaara Zwang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leore T Geller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Roi Weiser
- Division of Surgery, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Giuseppe Mallel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Gigi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Arnon Meltser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Iris Kamer
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | | | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Levin-Zaidman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sofia Avnet
- Orthopaedic Pathophysiology and Regenerative Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Tehila Atlan
- Department of Bioinformatics, Jerusalem College of Technology, Jerusalem, Israel
| | - Zachary A Cooper
- Translational Medicine, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandria P Cogdill
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Md Abdul Wadud Khan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel Ologun
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuval Bussi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Perry
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Merav Rokah
- Department of Thoracic Surgery, Sheba Medical Center, Ramat Gan, Israel
| | | | - Elisa A Rozeman
- Department of Medical Oncology and Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Christian U Blank
- Department of Medical Oncology and Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anat Ronai
- Pediatric Gastroenterology Institute, Rambam Medical Center, Haifa, Israel
| | - Ron Shaoul
- Pediatric Gastroenterology Institute, Rambam Medical Center, Haifa, Israel
| | - Amnon Amit
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Obstetrics and Gynecology, Rambam Health Care Campus, Haifa, Israel
| | - Tatiana Dorfman
- Division of General Surgery, Rambam Health Care Campus, Haifa, Israel.,Ambulatory and Breast Surgery Service, Rambam Health Care Campus, Haifa, Israel
| | - Ran Kremer
- Department of Thoracic Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Zvi R Cohen
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Neurosurgery, Sheba Medical Center, Ramat Gan, Israel
| | - Sagi Harnof
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Neurosurgery, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Tali Siegal
- Neuro-Oncology Unit, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | | | | | - Hagit Shapira
- Institute of Pathology, Megalab, Maccabi Healthcare Services, Rehovot, Israel
| | - Nicola Baldini
- Orthopaedic Pathophysiology and Regenerative Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.,Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Alon Ben-Nun
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Thoracic Surgery, Sheba Medical Center, Ramat Gan, Israel
| | - Bella Kaufman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Aviram Nissan
- Department of Surgical Oncology (Surgery C), Sheba Medical Center, Ramat Gan, Israel
| | - Talia Golan
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dadiani
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Keren Levanon
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Jair Bar
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Shlomit Yust-Katz
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Neuro-Oncology Unit, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dan J Raz
- Division of Thoracic Surgery, City of Hope Medical Center, Duarte, CA, USA
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judith Sandbank
- Institute of Pathology, Megalab, Maccabi Healthcare Services, Rehovot, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Ra'anana, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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6
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Brandwein M, Fuks G, Israel A, Sabbah F, Hodak E, Szitenberg A, Harari M, Steinberg D, Bentwich Z, Shental N, Meshner S. Skin Microbiome Compositional Changes in Atopic Dermatitis Accompany Dead Sea Climatotherapy. Photochem Photobiol 2020; 96:450. [PMID: 32249480 DOI: 10.1111/php.13218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Avigail Israel
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Fareed Sabbah
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Emmilia Hodak
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Amir Szitenberg
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Marco Harari
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Droron Steinberg
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zvi Bentwich
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Shiri Meshner
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
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7
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Brandwein M, Horev A, Bogen B, Fuks G, Israel A, Shalom G, Pinsk V, Steinberg D, Bentwich Z, Shental N, Meshner S. The role of sweat in the composition of skin microbiome: lessons learned from patients with congenital insensitivity to pain with anhidrosis. J Eur Acad Dermatol Venereol 2020; 34:e183-e186. [DOI: 10.1111/jdv.16170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- M. Brandwein
- Biofilm Research Laboratory Institute of Dental Sciences Faculty of Dental Medicine The Hebrew University of Jerusalem Jerusalem Israel
- Cutaneous Microbiology Laboratory The Skin Research Institute The Dead Sea and Arava Science Center Masada Israel
| | - A. Horev
- Division of Pediatrics Soroka University Medical Center Yavne Israel
- Faculty of Health Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
| | - B. Bogen
- Department of Dermatology and Venereology Soroka University Medical Center Yavne Israel
| | - G. Fuks
- Department of Physics of Complex Systems Weizmann Institute of Science Rehovot Israel
| | - A. Israel
- Cutaneous Microbiology Laboratory The Skin Research Institute The Dead Sea and Arava Science Center Masada Israel
| | - G. Shalom
- Faculty of Health Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
- Siaal Research Center for Family Medicine and Primary Care Beer‐Sheva Israel
| | - V. Pinsk
- Division of Pediatrics Soroka University Medical Center Yavne Israel
- Faculty of Health Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
- Department of Pediatrics Samson Ashdod Assuta Medical Center Ashdod Israel
| | - D. Steinberg
- Biofilm Research Laboratory Institute of Dental Sciences Faculty of Dental Medicine The Hebrew University of Jerusalem Jerusalem Israel
| | - Z. Bentwich
- Cutaneous Microbiology Laboratory The Skin Research Institute The Dead Sea and Arava Science Center Masada Israel
| | - N. Shental
- Department of Mathematics and Computer Science Open University of Israel Raanana Israel
| | - S. Meshner
- Cutaneous Microbiology Laboratory The Skin Research Institute The Dead Sea and Arava Science Center Masada Israel
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8
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Brandwein M, Fuks G, Israel A, Sabbah F, Hodak E, Szitenberg A, Harari M, Steinberg D, Bentwich Z, Shental N, Meshner S. Skin Microbiome Compositional Changes in Atopic Dermatitis Accompany Dead Sea Climatotherapy. Photochem Photobiol 2019; 95:1446-1453. [PMID: 31074874 DOI: 10.1111/php.13119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 04/26/2019] [Indexed: 12/27/2022]
Abstract
Dead Sea climatotherapy (DSC) is a well-established therapeutic modality for the treatment of several diseases, including atopic dermatitis. Skin microbiome studies have shown that skin microbiome diversity is anticorrelated with both atopic dermatitis severity and concurrent Staphylococcus aureus overgrowth. This study aimed to determine whether DSC induces skin microbiome changes concurrent with clinical improvements in atopic dermatitis. We sampled 35 atopic dermatitis patients and ten healthy controls on both the antecubital and popliteal fossa. High-resolution microbial community profiling was attained by sequencing multiple regions of the 16S rRNA gene. Dysbiosis was observed in both lesional and nonlesional sites, which was partially attenuated following treatment. Severe AD skin underwent the most significant community shifts, and Staphylococcus epidermidis, Streptococcus mitis and Micrococcus luteus relative abundance were significantly affected by Dead Sea climatotherapy. Our study highlights the temporal shifts of the AD skin microbiome induced by Dead Sea climatotherapy and offers potential explanations for the success of climatotherapy on a variety of skin diseases, including AD.
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Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Avigail Israel
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Fareed Sabbah
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Emmilia Hodak
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Amir Szitenberg
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Marco Harari
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Droron Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zvi Bentwich
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Shiri Meshner
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
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9
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Brandwein M, Fuks G, Israel A, Nejman D, Straussman R, Hodak E, Harari M, Steinberg D, Bentwich Z, Shental N, Meshner S. Identification of a unique Staphylococcus aureus ribosomal signature in severe atopic dermatitis. Br J Dermatol 2018; 179:1222-1224. [PMID: 29962038 DOI: 10.1111/bjd.16936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M Brandwein
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, POB 12272, Jerusalem, 91120, Israel.,Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, 8693500, Israel
| | - G Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, POB 26, Rehovot, 76100, Israel
| | - A Israel
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, 8693500, Israel
| | - D Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, POB 26, Rehovot, 76100, Israel
| | - R Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, POB 26, Rehovot, 76100, Israel
| | - E Hodak
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - M Harari
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, 8693500, Israel
| | - D Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, POB 12272, Jerusalem, 91120, Israel
| | - Z Bentwich
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, 8693500, Israel
| | - N Shental
- Department of Mathematics and Computer Science, The Open University of Israel, POB 808, Raanana, 4353701, Israel
| | - S Meshner
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, 8693500, Israel
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10
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Brandwein M, Fuks G, Israel A, Al-Ashhab A, Nejman D, Straussman R, Hodak E, Harari M, Steinberg D, Bentwich Z, Shental N, Meshner S. Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy. Acta Derm Venereol 2018; 98:256-261. [PMID: 28815268 DOI: 10.2340/00015555-2769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 11/16/2022] Open
Abstract
Dead Sea climatotherapy (DSC) is a therapeutic modality for a variety of chronic skin conditions, yet there has been scarce research on the relationship between the cutaneous microbiota and disease states in response to DSC. We characterized the skin bacterial and fungal microbiome of healthy volunteers who underwent DSC. Bacterial community diversity remained similar before and after treatment, while fungal diversity was significantly reduced as a result of the treatment. Individuals showed greater inter-individual than temporal bacterial community variance, yet the opposite was true for fungal community composition. We further identified Malassezia as the genus driving temporal mycobiome variations. The results indicate that the microbiome remains stable throughout DSC, while the mycobiome undergoes dramatic community changes. The results of this study will serve as an important baseline for future investigations of microbiome and mycobiome temporal phenomena in diseased states.
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Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel
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11
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Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, Shental N. Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. Microbiome 2018; 6:17. [PMID: 29373999 PMCID: PMC5787238 DOI: 10.1186/s40168-017-0396-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/25/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16-33% of the total length). Thus, many bacteria may share the same amplified region, and the resolution of profiling is inherently limited. Platforms that offer ultra-long read lengths, whole genome shotgun sequencing approaches, and computational frameworks formerly suggested by us and by others all allow different ways to circumvent this problem yet suffer various shortcomings. There is a need for a simple and low-cost 16S rRNA gene-based profiling approach that harnesses the short read length to provide a much larger coverage of the gene to allow for high resolution, even in harsh conditions of low bacterial biomass and fragmented DNA. RESULTS This manuscript suggests Short MUltiple Regions Framework (SMURF), a method to combine sequencing results from different PCR-amplified regions to provide one coherent profiling. The de facto amplicon length is the total length of all amplified regions, thus providing much higher resolution compared to current techniques. Computationally, the method solves a convex optimization problem that allows extremely fast reconstruction and requires only moderate memory. We demonstrate the increase in resolution by in silico simulations and by profiling two mock mixtures and real-world biological samples. Reanalyzing a mock mixture from the Human Microbiome Project achieved about twofold improvement in resolution when combing two independent regions. Using a custom set of six primer pairs spanning about 1200 bp (80%) of the 16S rRNA gene, we were able to achieve ~ 100-fold improvement in resolution compared to a single region, over a mock mixture of common human gut bacterial isolates. Finally, the profiling of a Drosophila melanogaster microbiome using the set of six primer pairs provided a ~ 100-fold increase in resolution and thus enabling efficient downstream analysis. CONCLUSIONS SMURF enables the identification of near full-length 16S rRNA gene sequences in microbial communities, having resolution superior compared to current techniques. It may be applied to standard sample preparation protocols with very little modifications. SMURF also paves the way to high-resolution profiling of low-biomass and fragmented DNA, e.g., in the case of formalin-fixed and paraffin-embedded samples, fossil-derived DNA, or DNA exposed to other degrading conditions. The approach is not restricted to combining amplicons of the 16S rRNA gene and may be applied to any set of amplicons, e.g., in multilocus sequence typing (MLST).
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Affiliation(s)
- Garold Fuks
- Departments of Physics of Complex Systems, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Michael Elgart
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093 USA
| | - Amit Zeisel
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, 10 Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143 USA
| | - Yoav Soen
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Noam Shental
- Department of Computer Science, The Open University of Israel, 43107 Ra’anana, Israel
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12
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Glaria A, Soulé S, Hallali N, Ojo WS, Mirjolet M, Fuks G, Cornejo A, Allouche J, Dupin JC, Martinez H, Carrey J, Chaudret B, Delpech F, Lachaize S, Nayral C. Silica coated iron nanoparticles: synthesis, interface control, magnetic and hyperthermia properties. RSC Adv 2018; 8:32146-32156. [PMID: 35547528 PMCID: PMC9085846 DOI: 10.1039/c8ra06075d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 07/17/2018] [Accepted: 09/09/2018] [Indexed: 12/02/2022] Open
Abstract
This work provides a detailed study on the synthesis and characterization of silica coated iron nanoparticles (NPs) by coupling Transmission Electronic Microscopy (TEM), X-ray Photoelectron Spectroscopy (XPS) and magnetic measurements. Remarkably, iron NPs (of 9 nm of mean diameter) have been embedded in silica without any alteration of the magnetization of the iron cores, thanks to an original protocol of silica coating in non alcoholic medium. Tuning the synthesis parameters (concentration of reactants and choice of solvent), different sizes of Fe@SiO2 composites can be obtained with different thicknesses of silica. The magnetization of these objects is fully preserved after 24 h of water exposure thanks to a thick (14 nm) silica layer, opening thus new perspectives for biomedical applications. Hyperthermia measurements have been compared between Fe and Fe@SiO2 NPs, evidencing the self-organization of the free Fe NPs when a large amplitude magnetic field is applied. This phenomenon induces an increase of heating power which is precluded when the Fe cores are immobilised in silica. High-frequency hysteresis loop measurements allowed us to observe for the first time the increase of the ferrofluid susceptibility and remanence which are the signature of the formation of Fe NPs chains. A novel method has been developed for the silica coating of iron nanoparticles while preserving the magnetic properties.![]()
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Affiliation(s)
- A. Glaria
- LPCNO
- Université de Toulouse
- CNRS
- INSA
- UPS
| | - S. Soulé
- Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux
- Université de Pau et des Pays de l’Adour
- Hélioparc
- F-64053 Pau
- France
| | | | - W.-S. Ojo
- LPCNO
- Université de Toulouse
- CNRS
- INSA
- UPS
| | | | - G. Fuks
- LPCNO
- Université de Toulouse
- CNRS
- INSA
- UPS
| | | | - J. Allouche
- Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux
- Université de Pau et des Pays de l’Adour
- Hélioparc
- F-64053 Pau
- France
| | - J. C. Dupin
- Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux
- Université de Pau et des Pays de l’Adour
- Hélioparc
- F-64053 Pau
- France
| | - H. Martinez
- Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux
- Université de Pau et des Pays de l’Adour
- Hélioparc
- F-64053 Pau
- France
| | - J. Carrey
- LPCNO
- Université de Toulouse
- CNRS
- INSA
- UPS
| | | | | | | | - C. Nayral
- LPCNO
- Université de Toulouse
- CNRS
- INSA
- UPS
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13
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Golan-Lavi R, Giacomelli C, Fuks G, Zeisel A, Sonntag J, Sinha S, Köstler W, Wiemann S, Korf U, Yarden Y, Domany E. Coordinated Pulses of mRNA and of Protein Translation or Degradation Produce EGF-Induced Protein Bursts. Cell Rep 2017; 18:3129-3142. [PMID: 28355565 DOI: 10.1016/j.celrep.2017.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/16/2017] [Accepted: 03/01/2017] [Indexed: 11/25/2022] Open
Abstract
Protein responses to extracellular cues are governed by gene transcription, mRNA degradation and translation, and protein degradation. In order to understand how these time-dependent processes cooperate to generate dynamic responses, we analyzed the response of human mammary cells to the epidermal growth factor (EGF). Integrating time-dependent transcript and protein data into a mathematical model, we inferred for several proteins their pre-and post-stimulus translation and degradation coefficients and found that they exhibit complex, time-dependent variation. Specifically, we identified strategies of protein production and degradation acting in concert to generate rapid, transient protein bursts in response to EGF. Remarkably, for some proteins, for which the response necessitates rapidly decreased abundance, cells exhibit a transient increase in the corresponding degradation coefficient. Our model and analysis allow inference of the kinetics of mRNA translation and protein degradation, without perturbing cells, and open a way to understanding the fundamental processes governing time-dependent protein abundance profiles.
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Affiliation(s)
- Roni Golan-Lavi
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chiara Giacomelli
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amit Zeisel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Johanna Sonntag
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Sanchari Sinha
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Wolfgang Köstler
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Eytan Domany
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel.
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14
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Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science 2017; 357:1156-1160. [PMID: 28912244 PMCID: PMC5727343 DOI: 10.1126/science.aah5043] [Citation(s) in RCA: 912] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 04/05/2017] [Accepted: 08/19/2017] [Indexed: 12/17/2022]
Abstract
Growing evidence suggests that microbes can influence the efficacy of cancer therapies. By studying colon cancer models, we found that bacteria can metabolize the chemotherapeutic drug gemcitabine (2',2'-difluorodeoxycytidine) into its inactive form, 2',2'-difluorodeoxyuridine. Metabolism was dependent on the expression of a long isoform of the bacterial enzyme cytidine deaminase (CDDL), seen primarily in Gammaproteobacteria. In a colon cancer mouse model, gemcitabine resistance was induced by intratumor Gammaproteobacteria, dependent on bacterial CDDL expression, and abrogated by cotreatment with the antibiotic ciprofloxacin. Gemcitabine is commonly used to treat pancreatic ductal adenocarcinoma (PDAC), and we hypothesized that intratumor bacteria might contribute to drug resistance of these tumors. Consistent with this possibility, we found that of the 113 human PDACs that were tested, 86 (76%) were positive for bacteria, mainly Gammaproteobacteria.
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Affiliation(s)
- Leore T Geller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Tal Danino
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Oliver H Jonas
- Department of Radiology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Raanana, Israel
| | - Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaara Zwang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zachary A Cooper
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kevin Shee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christoph A Thaiss
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexandre Reuben
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Dennie T Frederick
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Matteo Ligorio
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Kelly Chatman
- Small Molecule Mass Spectrometry Facility, Faculty of Arts and Sciences Division of Science, Harvard University, Cambridge, MA 02138, USA
| | | | - Carrie M Mosher
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Candice Gurbatri
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA
| | | | - Michael Kim
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark W Hurd
- Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Katz
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Fleming
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David A Smith
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matt Skalak
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Jeffrey Bu
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Monia Michaud
- Harvard T. H. Chan School of Public Health, Departments of Immunology and Infectious Diseases and Genetics and Complex Diseases, Boston, MA 02115, USA
| | - Sunia A Trauger
- Small Molecule Mass Spectrometry Facility, Faculty of Arts and Sciences Division of Science, Harvard University, Cambridge, MA 02138, USA
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Talia Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Judith Sandbank
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Anna Mandinova
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Wendy S Garrett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard T. H. Chan School of Public Health, Departments of Immunology and Infectious Diseases and Genetics and Complex Diseases, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sarah P Thayer
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE 68198-6345, USA
| | - Cristina R Ferrone
- Pancreas and Biliary Surgery Program, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sangeeta N Bhatia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute (HHMI), Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Division of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
- Ludwig Center for Molecular Oncology, MIT, Cambridge, MA 02139, USA
- Marble Center for Cancer Nanomedicine, MIT, Cambridge, MA 02139, USA
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Todd R Golub
- HHMI, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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15
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Livshits A, Git A, Fuks G, Caldas C, Domany E. Pathway-based personalized analysis of breast cancer expression data. Mol Oncol 2015; 9:1471-83. [PMID: 25963740 PMCID: PMC5528809 DOI: 10.1016/j.molonc.2015.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 03/23/2015] [Accepted: 04/16/2015] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Most analyses of high throughput cancer data represent tumors by "atomistic" single-gene properties. Pathifier, a recently introduced method, characterizes a tumor in terms of "coarse grained" pathway-based variables. METHODS We applied Pathifier to study a very large dataset of 2000 breast cancer samples and 144 normal tissues. Pathifier uses known gene assignments to pathways and biological processes to calculate for each pathway and tumor a Pathway Deregulation Score (PDS). Individual samples are represented in terms of their PDSs calculated for several hundred pathways, and the samples of the data set are analyzed and stratified on the basis of their profiles over these "coarse grained", biologically meaningful variables. RESULTS We identified nine tumor subtypes; a new subclass (comprising about 7% of the samples) exhibits high deregulation in 38 PKA pathways, induced by overexpression of the gene PRKACB. Another interesting finding is that basal tumors break into two subclasses, with low and high deregulation of a cluster of immune system pathways. High deregulation corresponds to higher concentrations of Tumor Infiltrating Lymphocytes, and the patients of this basal subtype have better prognosis. The analysis used 1000 "discovery set" tumors; our results were highly reproducible on 1000 independent "validation" samples. CONCLUSIONS The coarse-grained variables that represent pathway deregulation provide a basis for relevant, novel and robust findings for breast cancer. Our analysis indicates that in breast cancer reliable prognostic signatures are most likely to be obtained by treating separately different subgroups of the patients.
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Affiliation(s)
- Anna Livshits
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anna Git
- Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2XZ, UK.
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Carlos Caldas
- Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2XZ, UK.
| | - Eytan Domany
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.
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16
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Nguyen R, Jouault N, Zanirati S, Rawiso M, Allouche L, Fuks G, Buhler E, Giuseppone N. Core-shell inversion by pH modulation in dynamic covalent micelles. Soft Matter 2014; 10:3926-3937. [PMID: 24699990 DOI: 10.1039/c4sm00072b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Dynamic covalent surfactants have been obtained by the reversible condensation of a hydrophobic aldehyde (ended by an ionic tip) with various neutral polyethylene glycol based hydrophilic amines. In water, the duality between the two hydrophilic domains (charged and neutral) leads to their segregation when the surfactants are self-assembled within micelles. Depending on the number of polyethylene glycol units, a core-shell inversion leading to a switching orientation of the ionic tips from the inside to the outside of the micelles has been demonstrated by a combination of scattering techniques. In competition experiments, when several amines of different pKas and hydrophilic polyethylene glycol chains are competing for the same aldehyde, it becomes possible to trigger this core-shell inversion by pH modulation and associated dynamic constitutional reorganization.
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Affiliation(s)
- R Nguyen
- Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France.
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17
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Meffre A, Mehdaoui B, Fuks G, Lacroix L, Lachaize S, Carrey J, Nayral C, Delpech F, Gougeon M, Respaud M, Chaudret B. R106: Nanoparticules de fer(0) pour une application en hyperthermie magnétique. Bull Cancer 2010. [DOI: 10.1016/s0007-4551(15)31025-0] [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: 11/24/2022]
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