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Sender R, Weiss Y, Navon Y, Milo I, Azulay N, Keren L, Fuchs S, Ben-Zvi D, Noor E, Milo R. The total mass, number, and distribution of immune cells in the human body. Proc Natl Acad Sci U S A 2023; 120:e2308511120. [PMID: 37871201 PMCID: PMC10623016 DOI: 10.1073/pnas.2308511120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 05/21/2023] [Accepted: 09/11/2023] [Indexed: 10/25/2023] Open
Abstract
The immune system is a complex network of cells with critical functions in health and disease. However, a comprehensive census of the cells comprising the immune system is lacking. Here, we estimated the abundance of the primary immune cell types throughout all tissues in the human body. We conducted a literature survey and integrated data from multiplexed imaging and methylome-based deconvolution. We also considered cellular mass to determine the distribution of immune cells in terms of both number and total mass. Our results indicate that the immune system of a reference 73 kg man consists of 1.8 × 1012 cells (95% CI 1.5-2.3 × 1012), weighing 1.2 kg (95% CI 0.8-1.9). Lymphocytes constitute 40% of the total number of immune cells and 15% of the mass and are mainly located in the lymph nodes and spleen. Neutrophils account for similar proportions of both the number and total mass of immune cells, with most neutrophils residing in the bone marrow. Macrophages, present in most tissues, account for 10% of immune cells but contribute nearly 50% of the total cellular mass due to their large size. The quantification of immune cells within the human body presented here can serve to understand the immune function better and facilitate quantitative modeling of this vital system.
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Affiliation(s)
- Ron Sender
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yarden Weiss
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Navon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idan Milo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nofar Azulay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shai Fuchs
- Pediatric Endocrine and Diabetes Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Danny Ben-Zvi
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Amitay Y, Bussi Y, Feinstein B, Bagon S, Milo I, Keren L. CellSighter: a neural network to classify cells in highly multiplexed images. Nat Commun 2023; 14:4302. [PMID: 37463931 PMCID: PMC10354029 DOI: 10.1038/s41467-023-40066-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/08/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Multiplexed imaging enables measurement of multiple proteins in situ, offering an unprecedented opportunity to chart various cell types and states in tissues. However, cell classification, the task of identifying the type of individual cells, remains challenging, labor-intensive, and limiting to throughput. Here, we present CellSighter, a deep-learning based pipeline to accelerate cell classification in multiplexed images. Given a small training set of expert-labeled images, CellSighter outputs the label probabilities for all cells in new images. CellSighter achieves over 80% accuracy for major cell types across imaging platforms, which approaches inter-observer concordance. Ablation studies and simulations show that CellSighter is able to generalize its training data and learn features of protein expression levels, as well as spatial features such as subcellular expression patterns. CellSighter's design reduces overfitting, and it can be trained with only thousands or even hundreds of labeled examples. CellSighter also outputs a prediction confidence, allowing downstream experts control over the results. Altogether, CellSighter drastically reduces hands-on time for cell classification in multiplexed images, while improving accuracy and consistency across datasets.
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Affiliation(s)
- Yael Amitay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Mathematics and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Bussi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Mathematics and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Ben Feinstein
- Department of Mathematics and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Shai Bagon
- Department of Mathematics and Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Milo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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3
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Greenbaum S, Averbukh I, Soon E, Rizzuto G, Baranski A, Greenwald NF, Kagel A, Bosse M, Jaswa EG, Khair Z, Kwok S, Warshawsky S, Piyadasa H, Goldston M, Spence A, Miller G, Schwartz M, Graf W, Van Valen D, Winn VD, Hollmann T, Keren L, van de Rijn M, Angelo M. A spatially resolved timeline of the human maternal-fetal interface. Nature 2023; 619:595-605. [PMID: 37468587 PMCID: PMC10356615 DOI: 10.1038/s41586-023-06298-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 09/03/2021] [Accepted: 06/08/2023] [Indexed: 07/21/2023]
Abstract
Beginning in the first trimester, fetally derived extravillous trophoblasts (EVTs) invade the uterus and remodel its spiral arteries, transforming them into large, dilated blood vessels. Several mechanisms have been proposed to explain how EVTs coordinate with the maternal decidua to promote a tissue microenvironment conducive to spiral artery remodelling (SAR)1-3. However, it remains a matter of debate regarding which immune and stromal cells participate in these interactions and how this evolves with respect to gestational age. Here we used a multiomics approach, combining the strengths of spatial proteomics and transcriptomics, to construct a spatiotemporal atlas of the human maternal-fetal interface in the first half of pregnancy. We used multiplexed ion beam imaging by time-of-flight and a 37-plex antibody panel to analyse around 500,000 cells and 588 arteries within intact decidua from 66 individuals between 6 and 20 weeks of gestation, integrating this dataset with co-registered transcriptomics profiles. Gestational age substantially influenced the frequency of maternal immune and stromal cells, with tolerogenic subsets expressing CD206, CD163, TIM-3, galectin-9 and IDO-1 becoming increasingly enriched and colocalized at later time points. By contrast, SAR progression preferentially correlated with EVT invasion and was transcriptionally defined by 78 gene ontology pathways exhibiting distinct monotonic and biphasic trends. Last, we developed an integrated model of SAR whereby invasion is accompanied by the upregulation of pro-angiogenic, immunoregulatory EVT programmes that promote interactions with the vascular endothelium while avoiding the activation of maternal immune cells.
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Affiliation(s)
- Shirley Greenbaum
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| | - Inna Averbukh
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Erin Soon
- Department of Pathology, Stanford University, Stanford, CA, USA
- Immunology Program, Stanford University, Stanford, CA, USA
| | - Gabrielle Rizzuto
- Department of Pathology, University of Californica San Francisco, San Francisco, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Adam Kagel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Eleni G Jaswa
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Shirley Kwok
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Mako Goldston
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angie Spence
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Geneva Miller
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan Schwartz
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Will Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
| | - Travis Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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4
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Abstract
The tumor microenvironment (TME) is composed of many different cellular and acellular components that together drive tumor growth, invasion, metastasis, and response to therapies. Increasing realization of the significance of the TME in cancer biology has shifted cancer research from a cancer-centric model to one that considers the TME as a whole. Recent technological advancements in spatial profiling methodologies provide a systematic view and illuminate the physical localization of the components of the TME. In this review, we provide an overview of major spatial profiling technologies. We present the types of information that can be extracted from these data and describe their applications, findings and challenges in cancer research. Finally, we provide a future perspective of how spatial profiling could be integrated into cancer research to improve patient diagnosis, prognosis, stratification to treatment and development of novel therapeutics.
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Affiliation(s)
- Ofer Elhanani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Raz Ben-Uri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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5
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Fusco L, Gazzi A, Shuck CE, Orecchioni M, Alberti D, D'Almeida SM, Rinchai D, Ahmed E, Elhanani O, Rauner M, Zavan B, Grivel JC, Keren L, Pasqual G, Bedognetti D, Ley K, Gogotsi Y, Delogu LG. Immune Profiling and Multiplexed Label-Free Detection of 2D MXenes by Mass Cytometry and High-Dimensional Imaging. Adv Mater 2022; 34:e2205154. [PMID: 36207284 PMCID: PMC10915970 DOI: 10.1002/adma.202205154] [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] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/22/2022] [Indexed: 06/16/2023]
Abstract
There is a critical unmet need to detect and image 2D materials within single cells and tissues while surveying a high degree of information from single cells. Here, a versatile multiplexed label-free single-cell detection strategy is proposed based on single-cell mass cytometry by time-of-flight (CyTOF) and ion-beam imaging by time-of-flight (MIBI-TOF). This strategy, "Label-free sINgle-cell tracKing of 2D matErials by mass cytometry and MIBI-TOF Design" (LINKED), enables nanomaterial detection and simultaneous measurement of multiple cell and tissue features. As a proof of concept, a set of 2D materials, transition metal carbides, nitrides, and carbonitrides (MXenes), is selected to ensure mass detection within the cytometry range while avoiding overlap with more than 70 currently available tags, each able to survey multiple biological parameters. First, their detection and quantification in 15 primary human immune cell subpopulations are demonstrated. Together with the detection, mass cytometry is used to capture several biological aspects of MXenes, such as their biocompatibility and cytokine production after their uptake. Through enzymatic labeling, MXenes' mediation of cell-cell interactions is simultaneously evaluated. In vivo biodistribution experiments using a mixture of MXenes in mice confirm the versatility of the detection strategy and reveal MXene accumulation in the liver, blood, spleen, lungs, and relative immune cell subtypes. Finally, MIBI-TOF is applied to detect MXenes in different organs revealing their spatial distribution. The label-free detection of 2D materials by mass cytometry at the single-cell level, on multiple cell subpopulations and in multiple organs simultaneously, will enable exciting new opportunities in biomedicine.
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Affiliation(s)
- Laura Fusco
- ImmuneNano Laboratory, Department of Biomedical Sciences, University of Padua, Padua, 35129, Italy
- A. J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104, USA
- Human Immunology Division, Translational Medicine Department, Sidra Medicine, Doha, 26999, Qatar
| | - Arianna Gazzi
- ImmuneNano Laboratory, Department of Biomedical Sciences, University of Padua, Padua, 35129, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, 34127, Italy
| | - Christopher E Shuck
- A. J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | | | - Dafne Alberti
- Laboratory of Synthetic Immunology, Oncology and Immunology Section, Department of Surgery Oncology and Gastroenterology, University of Padua, Padua, 35124, Italy
| | - Sènan Mickael D'Almeida
- Flow Cytometry Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Darawan Rinchai
- Human Immunology Division, Translational Medicine Department, Sidra Medicine, Doha, 26999, Qatar
| | - Eiman Ahmed
- Human Immunology Division, Translational Medicine Department, Sidra Medicine, Doha, 26999, Qatar
| | - Ofer Elhanani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Martina Rauner
- Department of Medicine III, Center for Healthy Aging, Technical University Dresden, 01307, Dresden, Germany
| | - Barbara Zavan
- Department of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
- Maria Cecilia Hospital, GVM Care & Research, Ravenna, 48033, Italy
| | | | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Giulia Pasqual
- Laboratory of Synthetic Immunology, Oncology and Immunology Section, Department of Surgery Oncology and Gastroenterology, University of Padua, Padua, 35124, Italy
| | - Davide Bedognetti
- Human Immunology Division, Translational Medicine Department, Sidra Medicine, Doha, 26999, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, 16132, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar
| | - Klaus Ley
- La Jolla Institute for Immunology, San Diego, CA, 92037, USA
- Immunology Center of Georgia (IMMCG), Augusta University, Augusta, GA, 30912, USA
| | - Yury Gogotsi
- A. J. Drexel Nanomaterials Institute and Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Lucia Gemma Delogu
- ImmuneNano Laboratory, Department of Biomedical Sciences, University of Padua, Padua, 35129, Italy
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6
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Keidar Haran T, Keren L. From genes to modules, from cells to ecosystems. Mol Syst Biol 2022; 18:e10726. [PMID: 35507444 PMCID: PMC9067608 DOI: 10.15252/msb.202110726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/13/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Twenty years ago, molecular biology transitioned from predominantly studying genes as isolated elements to viewing them as part of complex modules, giving rise to the field of systems biology. This transition was made possible by technological advances that allowed to simultaneously measure the expression levels of thousands of genes in a single experiment and drove a shift toward analyses identifying gene sets, modules, and pathways involved in a biological process of interest. Today we are excitingly facing a similar turning point in cell biology, where single‐cell technologies have enabled us to approach cells as cellular modules.
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Affiliation(s)
- Tal Keidar Haran
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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7
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McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. Nat Immunol 2022; 23:814. [PMID: 35277696 PMCID: PMC9098386 DOI: 10.1038/s41590-022-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Alea Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sanjana Gupta
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Rashmi Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratista K Ramdial
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Smriti Mehra
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Robert L Hunter
- Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Risom T, Glass DR, Averbukh I, Liu CC, Baranski A, Kagel A, McCaffrey EF, Greenwald NF, Rivero-Gutiérrez B, Strand SH, Varma S, Kong A, Keren L, Srivastava S, Zhu C, Khair Z, Veis DJ, Deschryver K, Vennam S, Maley C, Hwang ES, Marks JR, Bendall SC, Colditz GA, West RB, Angelo M. Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. Cell 2022; 185:299-310.e18. [PMID: 35063072 PMCID: PMC8792442 DOI: 10.1016/j.cell.2021.12.023] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/05/2021] [Accepted: 12/16/2021] [Indexed: 01/16/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand the changes in the tumor microenvironment (TME) accompanying transition to IBC, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) and a 37-plex antibody staining panel to interrogate 79 clinically annotated surgical resections using machine learning tools for cell segmentation, pixel-based clustering, and object morphometrics. Comparison of normal breast with patient-matched DCIS and IBC revealed coordinated transitions between four TME states that were delineated based on the location and function of myoepithelium, fibroblasts, and immune cells. Surprisingly, myoepithelial disruption was more advanced in DCIS patients that did not develop IBC, suggesting this process could be protective against recurrence. Taken together, this HTAN Breast PreCancer Atlas study offers insight into drivers of IBC relapse and emphasizes the importance of the TME in regulating these processes.
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Affiliation(s)
- Tyler Risom
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Research Pathology, Genentech, South San Francisco, CA, USA
| | - David R Glass
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Inna Averbukh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Candace C Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam Kagel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Siri H Strand
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sucheta Srivastava
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah J Veis
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Katherine Deschryver
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlo Maley
- Biodesign institute, Arizona State University, Tempe, AZ, USA
| | | | | | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Graham A Colditz
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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9
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Elhanani O, Keren L, Angelo M. High-Dimensional Tissue Profiling by Multiplexed Ion Beam Imaging. Methods Mol Biol 2021; 2386:147-156. [PMID: 34766270 DOI: 10.1007/978-1-0716-1771-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Multiplexed Ion Beam Imaging by Time of Flight (MIBI-TOF) enables high-dimensional imaging in situ of clinical specimens at single-cell resolution. In MIBI-TOF, tissue sections are stained with dozens of metal-labeled antibodies, whose abundance and location are read by secondary ionization mass spectrometry. The result is a multi-dimensional image, depicting sub-cellular expression and localization for dozens of distinct proteins in situ. Here, we describe the staining and imaging procedures of a MIBI-TOF experiment.
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Affiliation(s)
- Ofer Elhanani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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10
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Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M. Single cell biology-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:74-97. [PMID: 34605044 DOI: 10.1111/nyas.14692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
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Affiliation(s)
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California
| | - Ana I Domingos
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, United Kingdom.,The Howard Hughes Medical Institute, New York, New York
| | - Naomi Habib
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts.,Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Homaira Hamidzada
- Toronto General Hospital Research Institute, University Health Network; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, New York
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Jessica Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron Streets
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, Berkeley, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington; and Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, and Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Uri Alon
- Faculty of Sciences, Department of Human Biology, University of Haifa, Haifa, Israel
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Pfau
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts
| | - Arjun Raj
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, California.,Department of Bioengineering, Stanford University, Stanford, California.,Department of Applied Physics, Stanford University, Stanford, California
| | - Nancy R Zhang
- Graduate Group in Genomics and Computational Biology and Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine; and Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | | | | | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hernan G Garcia
- Department of Physics; Biophysics Graduate Group; Department of Molecular and Cell Biology; and Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California
| | | | - Federico Gaiti
- New York Genome Center and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, and Center for Systems Biology Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Allon M Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Samantha A Morris
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri.,Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Merrit Romeike
- Max Perutz Laboratories Vienna, University of Vienna, Vienna, Austria
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11
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Abstract
Tumor heterogeneity was traditionally considered in the genetic terms, but it has now been broadened into many more facets. These facets represent a challenge in our understanding of cancer etiology but also provide opportunity for us to understand prognosis and therapy response.
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12
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Patwa A, Yamashita R, Long J, Risom T, Angelo M, Keren L, Rubin DL. Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer. Commun Biol 2021; 4:852. [PMID: 34244605 PMCID: PMC8271023 DOI: 10.1038/s42003-021-02361-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/10/2021] [Indexed: 12/18/2022] Open
Abstract
Triple-negative breast cancer, the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification and treatment management. Prior literature has shown that interrogation of the tumor-immune microenvironment may be a promising approach to fill these gaps. Recently developed high-dimensional tissue imaging technology, such as multiplexed ion beam imaging, provide spatial context to protein expression in the microenvironment, allowing in-depth characterization of cellular processes. We demonstrate that profiling the functional proteins involved in cell-to-cell interactions in the microenvironment can predict recurrence and overall survival. We highlight the immunological relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying interactions involving them to recurrence and survival. Multivariate analysis reveals that our methods provide additional prognostic information compared to clinical variables. In this work, we present a computational pipeline for the examination of the tumor-immune microenvironment using multiplexed ion beam imaging that produces interpretable results, and is generalizable to other cancer types.
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Affiliation(s)
- Aalok Patwa
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Archbishop Mitty High School, San Jose, CA, USA
| | - Rikiya Yamashita
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA
| | - Jin Long
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA
| | - Tyler Risom
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel L Rubin
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA.
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13
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Bai Y, Zhu B, Rovira-Clave X, Chen H, Markovic M, Chan CN, Su TH, McIlwain DR, Estes JD, Keren L, Nolan GP, Jiang S. Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images. Front Immunol 2021; 12:652631. [PMID: 34295327 PMCID: PMC8289709 DOI: 10.3389/fimmu.2021.652631] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/09/2021] [Indexed: 01/12/2023] Open
Abstract
Multiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage of signals in densely packed tissues presents an obstacle to the assignment of high-dimensional spatial features to individual cells for accurate cell-type annotation. We devised a method to correct for lateral spillage of cell surface markers between adjacent cells termed REinforcement Dynamic Spillover EliminAtion (REDSEA). The use of REDSEA decreased contaminating signals from neighboring cells. It improved the recovery of marker signals across both isotopic (i.e., Multiplexed Ion Beam Imaging) and immunofluorescent (i.e., Cyclic Immunofluorescence) multiplexed images resulting in a marked improvement in cell-type classification.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, United States
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | | | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Maxim Markovic
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States
| | - Tung-Hung Su
- Department of Pathology, Stanford University, Stanford, CA, United States
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - David R. McIlwain
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States
| | - Leeat Keren
- Department of Pathology, Stanford University, Stanford, CA, United States
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Garry P. Nolan
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, United States
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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14
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Baranski A, Milo I, Greenbaum S, Oliveria JP, Mrdjen D, Angelo M, Keren L. MAUI (MBI Analysis User Interface)-An image processing pipeline for Multiplexed Mass Based Imaging. PLoS Comput Biol 2021; 17:e1008887. [PMID: 33872301 PMCID: PMC8084329 DOI: 10.1371/journal.pcbi.1008887] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/29/2021] [Accepted: 03/17/2021] [Indexed: 11/19/2022] Open
Abstract
Mass Based Imaging (MBI) technologies such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC) allow for the simultaneous measurement of the expression levels of 40 or more proteins in biological tissue, providing insight into cellular phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MBI Analysis User Interface (MAUI), a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. Our software streamlines these steps and accelerates processing by enabling real-time and interactive parameter tuning across multiple images. High-dimensional Imaging technologies allow to simultaneously measure the expression levels of dozens of proteins in biological tissue, providing insight into single-cell phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MAUI, a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. MAUI accelerates and automates these steps, such that reproducible, high-quality data will be the input for subsequent stages of analysis.
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Affiliation(s)
- Alex Baranski
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Idan Milo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shirley Greenbaum
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
| | - John-Paul Oliveria
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, Ontario, Canada
| | - Dunja Mrdjen
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Michael Angelo
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
- * E-mail: (MA); (LK)
| | - Leeat Keren
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (MA); (LK)
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15
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Risom T, Rivero B, Liu C, Baranski A, Strand S, Greenwald N, McCaffrey E, Varma S, Keren L, Srivastava S, Zhu C, Vennam S, Hwang S, Colditz G, Bendall S, West R, Angelo M. Abstract PR05: Mapping the tumor and microenvironmental evolution underlying DCIS progression through multiplexed ion beam imaging. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-pr05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ductal Carcinoma in Situ (DCIS) is a pre-invasive lesion that accounts for nearly 20% of new breast cancer diagnoses. Of these cases, about half will progress to invasive breast cancer (IBC) within ten years. However, because diagnostic criteria for delineating low risk lesions from those likely to progress to IBC have not been identified, many patients are receiving unnecessary chemotherapy and surgery that can result in therapy-related morbidity and death. With this in mind, we used Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and RNA-seq laser-capture microdissection (SMART-3SEQ) to construct a comprehensive spatial atlas describing the structure, function, and cellular composition of DCIS. MIBI-TOF and SMART-3SEQ were used to compare lesions from patients that later developed IBC with those from age- and history matched DCIS controls without recurrence. Using a 37-marker staining panel to interrogate 137 lesions, we identified 30 distinct cell populations of the epithelial, stromal, and immune lineages that were arranged in recurrent cellular microenvironments specific for DCIS or invasive disease. We observe a coordinated shift in the immune and stromal compartments as invasive disease arises, including an expansion of immune cell diversity and transition to reactive stromal phenotypes in synchronous DCIS + IBC, which was distinct from the macrophage-dominant microenvironment of recurrent IBC. Single-cell segmentation using a deep learning model was combined with pixel-level coexpression analysis to determine how thickness, continuity, and phenotype of ductal myoepithelium changes as tumors progress from a pre-invasive state. These data were incorporated into a comprehensive model which was subsequently used to identify a subset of features that correlate with disease-free survival following DCIS tumor resection. Taken together, these features represent important prognostic metrics that can be used to separate pre-invasive from indolent DCIS tumors, and allow for tailored therapy that improves patient outcomes and quality of life in this disease.
Citation Format: Tyler Risom, Belen Rivero, Candace Liu, Alex Baranski, Siri Strand, Noah Greenwald, Erin McCaffrey, Sushama Varma, Leeat Keren, Sucheta Srivastava, Chunfang Zhu, Sujay Vennam, Shelley Hwang, Graham Colditz, Sean Bendall, Robert West, Michael Angelo. Mapping the tumor and microenvironmental evolution underlying DCIS progression through multiplexed ion beam imaging [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PR05.
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16
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Abstract
Recent in situ multiplexed profiling techniques provide insight into microenvironment formation, maintenance, and transformation through a lens of localized cellular phenotype distribution. In this article, we introduce a method for recovering signatures of microenvironments from such data. We use topic models to identify characteristic cell types overrepresented in neighborhoods that serve as proxies for microenvironment. Furthermore, by assuming spatial coherence among neighboring microenvironments our model limits the number of parameters that need to be learned and permits data-driven decisions about the size of cellular neighborhoods. We apply this method to uncover anatomically known structures in mouse spleen—identifying distinct population of spleen B cells that are defined by their characteristic neighborhoods. Next, we apply the method to a dataset of triple-negative breast cancer tumors from 41 patients to study the structure of tumor-immune boundary. We uncover previously reported tumor-immune microenvironment near the tumor-immune boundary enriched for immune cells with high Indoleamine-pyrrole 2,3-dioxygenase (IDO) and Programmed death-ligand 1 (PD-L1) and a novel, immunosuppressed, microenvironment-enriched for cells expressing CD45 and FoxP3.
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Affiliation(s)
- Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Ilya Soifer
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Hugo Hilton
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Leeat Keren
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, California, USA
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17
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Affiliation(s)
- Leeat Keren
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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18
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Keren L, Bosse M, Thompson S, Risom T, Vijayaragavan K, McCaffrey E, Marquez D, Angoshtari R, Greenwald NF, Fienberg H, Wang J, Kambham N, Kirkwood D, Nolan G, Montine TJ, Galli SJ, West R, Bendall SC, Angelo M. MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Sci Adv 2019; 5:eaax5851. [PMID: 31633026 PMCID: PMC6785247 DOI: 10.1126/sciadv.aax5851] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/14/2019] [Indexed: 05/13/2023]
Abstract
Understanding tissue structure and function requires tools that quantify the expression of multiple proteins while preserving spatial information. Here, we describe MIBI-TOF (multiplexed ion beam imaging by time of flight), an instrument that uses bright ion sources and orthogonal time-of-flight mass spectrometry to image metal-tagged antibodies at subcellular resolution in clinical tissue sections. We demonstrate quantitative, full periodic table coverage across a five-log dynamic range, imaging 36 labeled antibodies simultaneously with histochemical stains and endogenous elements. We image fields of view up to 800 μm × 800 μm at resolutions down to 260 nm with sensitivities approaching single-molecule detection. We leverage these properties to interrogate intrapatient heterogeneity in tumor organization in triple-negative breast cancer, revealing regional variability in tumor cell phenotypes in contrast to a structured immune response. Given its versatility and sample back-compatibility, MIBI-TOF is positioned to leverage existing annotated, archival tissue cohorts to explore emerging questions in cancer, immunology, and neurobiology.
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Affiliation(s)
- Leeat Keren
- Department of Pathology, Stanford University, Stanford, CA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA
| | - Steve Thompson
- Department of Pathology, Stanford University, Stanford, CA
| | - Tyler Risom
- Department of Pathology, Stanford University, Stanford, CA
| | | | - Erin McCaffrey
- Department of Pathology, Stanford University, Stanford, CA
- Immunology Program, Stanford University School of Medicine, Stanford, CA
| | - Diana Marquez
- Department of Pathology, Stanford University, Stanford, CA
| | | | - Noah F. Greenwald
- Department of Pathology, Stanford University, Stanford, CA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA
| | | | - Jennifer Wang
- Department of Pathology, Stanford University, Stanford, CA
| | | | - David Kirkwood
- Department of Pathology, Stanford University, Stanford, CA
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | | | | | - Robert West
- Department of Pathology, Stanford University, Stanford, CA
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA
- Corresponding.author.
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19
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Hausser J, Mayo A, Keren L, Alon U. Central dogma rates and the trade-off between precision and economy in gene expression. Nat Commun 2019; 10:68. [PMID: 30622246 PMCID: PMC6325141 DOI: 10.1038/s41467-018-07391-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [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: 03/07/2018] [Accepted: 10/18/2018] [Indexed: 12/31/2022] Open
Abstract
Steady-state protein abundance is set by four rates: transcription, translation, mRNA decay and protein decay. A given protein abundance can be obtained from infinitely many combinations of these rates. This raises the question of whether the natural rates for each gene result from historical accidents, or are there rules that give certain combinations a selective advantage? We address this question using high-throughput measurements in rapidly growing cells from diverse organisms to find that about half of the rate combinations do not exist: genes that combine high transcription with low translation are strongly depleted. This depletion is due to a trade-off between precision and economy: high transcription decreases stochastic fluctuations but increases transcription costs. Our theory quantitatively explains which rate combinations are missing, and predicts the curvature of the fitness function for each gene. It may guide the design of gene circuits with desired expression levels and noise.
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Affiliation(s)
- Jean Hausser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
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20
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Keren L, Bosse M, Marquez D, Angoshtari R, Jain S, Varma S, Yang SR, Kurian A, Van Valen D, West R, Bendall SC, Angelo M. A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging. Cell 2018; 174:1373-1387.e19. [PMID: 30193111 PMCID: PMC6132072 DOI: 10.1016/j.cell.2018.08.039] [Citation(s) in RCA: 563] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/13/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022]
Abstract
The immune system is critical in modulating cancer progression, but knowledge of immune composition, phenotype, and interactions with tumor is limited. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to simultaneously quantify in situ expression of 36 proteins covering identity, function, and immune regulation at sub-cellular resolution in 41 triple-negative breast cancer patients. Multi-step processing, including deep-learning-based segmentation, revealed variability in the composition of tumor-immune populations across individuals, reconciled by overall immune infiltration and enriched co-occurrence of immune subpopulations and checkpoint expression. Spatial enrichment analysis showed immune mixed and compartmentalized tumors, coinciding with expression of PD1, PD-L1, and IDO in a cell-type- and location-specific manner. Ordered immune structures along the tumor-immune border were associated with compartmentalization and linked to survival. These data demonstrate organization in the tumor-immune microenvironment that is structured in cellular composition, spatial arrangement, and regulatory-protein expression and provide a framework to apply multiplexed imaging to immune oncology.
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Affiliation(s)
- Leeat Keren
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Diana Marquez
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Roshan Angoshtari
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Samir Jain
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Soo-Ryum Yang
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Allison Kurian
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - David Van Valen
- Department of Biology, Caltech, Pasadena, CA 91125, USA; Department of Bioengineering, Caltech, Pasadena, CA 91125, USA
| | - Robert West
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford CA, 94305, USA.
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford CA, 94305, USA.
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21
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Keren L, Hausser J, Lotan-Pompan M, Vainberg Slutskin I, Alisar H, Kaminski S, Weinberger A, Alon U, Milo R, Segal E. Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness. Cell 2016; 166:1282-1294.e18. [PMID: 27545349 DOI: 10.1016/j.cell.2016.07.024] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/05/2016] [Accepted: 07/18/2016] [Indexed: 02/02/2023]
Abstract
Data of gene expression levels across individuals, cell types, and disease states is expanding, yet our understanding of how expression levels impact phenotype is limited. Here, we present a massively parallel system for assaying the effect of gene expression levels on fitness in Saccharomyces cerevisiae by systematically altering the expression level of ∼100 genes at ∼100 distinct levels spanning a 500-fold range at high resolution. We show that the relationship between expression levels and growth is gene and environment specific and provides information on the function, stoichiometry, and interactions of genes. Wild-type expression levels in some conditions are not optimal for growth, and genes whose fitness is greatly affected by small changes in expression level tend to exhibit lower cell-to-cell variability in expression. Our study addresses a fundamental gap in understanding the functional significance of gene expression regulation and offers a framework for evaluating the phenotypic effects of expression variation.
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Affiliation(s)
- Leeat Keren
- Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jean Hausser
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maya Lotan-Pompan
- Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilya Vainberg Slutskin
- Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Alisar
- Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sivan Kaminski
- Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adina Weinberger
- Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Milo
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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22
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Barenholz U, Keren L, Segal E, Milo R. A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate. PLoS One 2016; 11:e0153344. [PMID: 27073913 PMCID: PMC4830519 DOI: 10.1371/journal.pone.0153344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 01/17/2016] [Accepted: 03/28/2016] [Indexed: 12/05/2022] Open
Abstract
Most proteins show changes in level across growth conditions. Many of these changes seem to be coordinated with the specific growth rate rather than the growth environment or the protein function. Although cellular growth rates, gene expression levels and gene regulation have been at the center of biological research for decades, there are only a few models giving a base line prediction of the dependence of the proteome fraction occupied by a gene with the specific growth rate. We present a simple model that predicts a widely coordinated increase in the fraction of many proteins out of the proteome, proportionally with the growth rate. The model reveals how passive redistribution of resources, due to active regulation of only a few proteins, can have proteome wide effects that are quantitatively predictable. Our model provides a potential explanation for why and how such a coordinated response of a large fraction of the proteome to the specific growth rate arises under different environmental conditions. The simplicity of our model can also be useful by serving as a baseline null hypothesis in the search for active regulation. We exemplify the usage of the model by analyzing the relationship between growth rate and proteome composition for the model microorganism E.coli as reflected in recent proteomics data sets spanning various growth conditions. We find that the fraction out of the proteome of a large number of proteins, and from different cellular processes, increases proportionally with the growth rate. Notably, ribosomal proteins, which have been previously reported to increase in fraction with growth rate, are only a small part of this group of proteins. We suggest that, although the fractions of many proteins change with the growth rate, such changes may be partially driven by a global effect, not necessarily requiring specific cellular control mechanisms.
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Affiliation(s)
- Uri Barenholz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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23
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Keren L, van Dijk D, Weingarten-Gabbay S, Davidi D, Jona G, Weinberger A, Milo R, Segal E. Noise in gene expression is coupled to growth rate. Genome Res 2015; 25:1893-902. [PMID: 26355006 PMCID: PMC4665010 DOI: 10.1101/gr.191635.115] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [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: 02/27/2015] [Accepted: 09/09/2015] [Indexed: 11/24/2022]
Abstract
Genetically identical cells exposed to the same environment display variability in gene expression (noise), with important consequences for the fidelity of cellular regulation and biological function. Although population average gene expression is tightly coupled to growth rate, the effects of changes in environmental conditions on expression variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower growth rates. Nutrient-poor conditions, which support lower growth rates, display elevated levels of noise for most promoters, regardless of their specific expression values. We present a simple model of noise in expression that results from having an asynchronous population, with cells at different cell-cycle stages, and with different partitioning of the cells between the stages at different growth rates. This model predicts non-monotonic global changes in noise at different growth rates as well as overall higher variability in expression for cell-cycle–regulated genes in all conditions. The consistency between this model and our data, as well as with noise measurements of cells growing in a chemostat at well-defined growth rates, suggests that cell-cycle heterogeneity is a major contributor to gene expression noise. Finally, we identify gene and promoter features that play a role in gene expression noise across conditions. Our results show the existence of growth-related global changes in gene expression noise and suggest their potential phenotypic implications.
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Affiliation(s)
- Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David van Dijk
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York 10027, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ghil Jona
- Biological Services Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res 2014; 24:1698-706. [PMID: 25030889 PMCID: PMC4199362 DOI: 10.1101/gr.168773.113] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genetically identical cells exhibit large variability (noise) in gene expression, with important consequences for cellular function. Although the amount of noise decreases with and is thus partly determined by the mean expression level, the extent to which different promoter sequences can deviate away from this trend is not fully known. Here, we present a high-throughput method for measuring promoter-driven noise for thousands of designed synthetic promoters in parallel. We use it to investigate how promoters encode different noise levels and find that the noise levels of promoters with similar mean expression levels can vary more than one order of magnitude, with nucleosome-disfavoring sequences resulting in lower noise and more transcription factor binding sites resulting in higher noise. We propose a kinetic model of gene expression that takes into account the nonspecific DNA binding and one-dimensional sliding along the DNA, which occurs when transcription factors search for their target sites. We show that this assumption can improve the prediction of the mean-independent component of expression noise for our designed promoter sequences, suggesting that a transcription factor target search may affect gene expression noise. Consistent with our findings in designed promoters, we find that binding-site multiplicity in native promoters is associated with higher expression noise. Overall, our results demonstrate that small changes in promoter DNA sequence can tune noise levels in a manner that is predictable and partly decoupled from effects on the mean expression levels. These insights may assist in designing promoters with desired noise levels.
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Affiliation(s)
- Eilon Sharon
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David van Dijk
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Kalma
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ohad Manor
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Yakhini
- Agilent Laboratories, Santa Clara, California 95051, USA; Computer Science Department, Technion, Haifa 32000, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel;
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25
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Abstract
A new study exploits the time-dependence of formaldehyde cross-linking in the commonly used chromatin immunoprecipitation (ChIP) assay to infer the on and off rates for site-specific chromatin interactions.
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26
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Keren L, Zackay O, Lotan-Pompan M, Barenholz U, Dekel E, Sasson V, Aidelberg G, Bren A, Zeevi D, Weinberger A, Alon U, Milo R, Segal E. Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol 2013; 9:701. [PMID: 24169404 PMCID: PMC3817408 DOI: 10.1038/msb.2013.59] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [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: 08/05/2013] [Accepted: 09/27/2013] [Indexed: 12/20/2022] Open
Abstract
Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ~900 S. cerevisiae and ~1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60-90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation-promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome-wide expression profiles across conditions. We present a parameter-free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.
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Affiliation(s)
- Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ora Zackay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Barenholz
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Erez Dekel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Vered Sasson
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Aidelberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Danny Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Milo
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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27
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Abstract
The core promoter is the region in which RNA polymerase II is recruited to the DNA and acts to initiate transcription, but the extent to which the core promoter sequence determines promoter activity levels is largely unknown. Here, we identified several base content and k-mer sequence features of the yeast core promoter sequence that are highly predictive of maximal promoter activity. These features are mainly located in the region 75 bp upstream and 50 bp downstream of the main transcription start site, and their associations hold for both constitutively active promoters and promoters that are induced or repressed in specific conditions. Our results unravel several architectural features of yeast core promoters and suggest that the yeast core promoter sequence downstream of the TATA box (or of similar sequences involved in recruitment of the pre-initiation complex) is a major determinant of maximal promoter activity. We further show that human core promoters also contain features that are indicative of maximal promoter activity; thus, our results emphasize the important role of the core promoter sequence in transcriptional regulation.
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Affiliation(s)
- Shai Lubliner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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28
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Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, Zeevi D, Sharon E, Weinberger A, Segal E. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 2012; 44:743-50. [PMID: 22634752 DOI: 10.1038/ng.2305] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 05/03/2012] [Indexed: 11/09/2022]
Abstract
Understanding how precise control of gene expression is specified within regulatory DNA sequences is a key challenge with far-reaching implications. Many studies have focused on the regulatory role of transcription factor-binding sites. Here, we explore the transcriptional effects of different elements, nucleosome-disfavoring sequences and, specifically, poly(dA:dT) tracts that are highly prevalent in eukaryotic promoters. By measuring promoter activity for a large-scale promoter library, designed with systematic manipulations to the properties and spatial arrangement of poly(dA:dT) tracts, we show that these tracts significantly and causally affect transcription. We show that manipulating these elements offers a general genetic mechanism, applicable to promoters regulated by different transcription factors, for tuning expression in a predictable manner, with resolution that can be even finer than that attained by altering transcription factor sites. Overall, our results advance the understanding of the regulatory code and suggest a potential mechanism by which promoters yielding prespecified expression patterns can be designed.
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Affiliation(s)
- Tali Raveh-Sadka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
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29
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Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, Keren L, Levo M, Weinberger A, Segal E. Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res 2011; 21:2114-28. [PMID: 22009988 PMCID: PMC3227101 DOI: 10.1101/gr.119669.110] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 08/02/2011] [Indexed: 11/24/2022]
Abstract
Coordinate regulation of ribosomal protein (RP) genes is key for controlling cell growth. In yeast, it is unclear how this regulation achieves the required equimolar amounts of the different RP components, given that some RP genes exist in duplicate copies, while others have only one copy. Here, we tested whether the solution to this challenge is partly encoded within the DNA sequence of the RP promoters, by fusing 110 different RP promoters to a fluorescent gene reporter, allowing us to robustly detect differences in their promoter activities that are as small as ~10%. We found that single-copy RP promoters have significantly higher activities, suggesting that proper RP stoichiometry is indeed partly encoded within the RP promoters. Notably, we also partially uncovered how this regulation is encoded by finding that RP promoters with higher activity have more nucleosome-disfavoring sequences and characteristic spatial organizations of these sequences and of binding sites for key RP regulators. Mutations in these elements result in a significant decrease of RP promoter activity. Thus, our results suggest that intrinsic (DNA-dependent) nucleosome organization may be a key mechanism by which genomes encode biologically meaningful promoter activities. Our approach can readily be applied to uncover how transcriptional programs of other promoters are encoded.
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Affiliation(s)
- Danny Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eilon Sharon
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Shipony
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tali Raveh-Sadka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Levo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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30
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Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet 2010; 26:335-40. [PMID: 20598393 PMCID: PMC2910793 DOI: 10.1016/j.tig.2010.05.008] [Citation(s) in RCA: 265] [Impact Index Per Article: 18.9] [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: 03/14/2010] [Revised: 05/27/2010] [Accepted: 05/27/2010] [Indexed: 11/26/2022]
Abstract
The recently discovered prokaryotic immune system known as CRISPR (clustered regularly interspaced short palindromic repeats) is based on small RNAs ('spacers') that restrict phage and plasmid infection. It has been hypothesized that CRISPRs can also regulate self gene expression by utilizing spacers that target self genes. By analyzing CRISPRs from 330 organisms we found that one in every 250 spacers is self-targeting, and that such self-targeting occurs in 18% of all CRISPR-bearing organisms. However, complete lack of conservation across species, combined with abundance of degraded repeats near self-targeting spacers, suggests that self-targeting is a form of autoimmunity rather than a regulatory mechanism. We propose that accidental incorporation of self nucleic acids by CRISPR can incur an autoimmune fitness cost, and this could explain the abundance of degraded CRISPR systems across prokaryotes.
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Affiliation(s)
- Adi Stern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Omri Wurtzel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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31
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Abstract
Hepatitis occurred in five out of 12 patients with selective IgA deficiency who had been detected by immunelectrophoretic screening of 2,600 individuals. This apparent increased susceptibility to hepatitis has not been reported before, and it may be due to the defect in their local and humoral immune mechanisms.
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