1
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Waliman M, Johnson RL, Natesan G, Tan S, Santella A, Hong RL, Shah PK. Automated Cell Lineage Reconstruction using Label-Free 4D Microscopy. bioRxiv 2024:2024.01.20.576449. [PMID: 38328064 PMCID: PMC10849476 DOI: 10.1101/2024.01.20.576449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Here we describe embGAN, a deep learning pipeline that addresses the challenge of automated cell detection and tracking in label-free 3D time lapse imaging. embGAN requires no manual data annotation for training, learns robust detections that exhibits a high degree of scale invariance and generalizes well to images acquired in multiple labs on multiple instruments.
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Affiliation(s)
- Matthew Waliman
- Department of Electrical and Computer Engineering, University of California, Los Angeles, California, United States of America
| | - Ryan L Johnson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United State of America
| | - Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United State of America
| | - Shiqin Tan
- Department of Computational and Systems Biology, University of California, Los Angeles, California, United States of America
| | - Anthony Santella
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ray L Hong
- Department of Biology, California State University, Northridge, California, United States of America
| | - Pavak K Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United State of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
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2
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Schvartzman JM, Forsyth G, Walch H, Chatila W, Taglialatela A, Lee BJ, Zhu X, Gershik S, Cimino FV, Santella A, Menghrajani K, Ciccia A, Koche R, Sánchez-Vega F, Zha S, Thompson CB. Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting homologous recombination. Mol Cell 2023; 83:2347-2356.e8. [PMID: 37311462 PMCID: PMC10845120 DOI: 10.1016/j.molcel.2023.05.026] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/15/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) produce 2-hydroxyglutarate (2HG), which inhibits dioxygenases that modulate chromatin dynamics. The effects of 2HG have been reported to sensitize IDH tumors to poly-(ADP-ribose) polymerase (PARP) inhibitors. However, unlike PARP-inhibitor-sensitive BRCA1/2 tumors, which exhibit impaired homologous recombination, IDH-mutant tumors have a silent mutational profile and lack signatures associated with impaired homologous recombination. Instead, 2HG-producing IDH mutations lead to a heterochromatin-dependent slowing of DNA replication accompanied by increased replication stress and DNA double-strand breaks. This replicative stress manifests as replication fork slowing, but the breaks are repaired without a significant increase in mutation burden. Faithful resolution of replicative stress in IDH-mutant cells is dependent on poly-(ADP-ribosylation). Treatment with PARP inhibitors increases DNA replication but results in incomplete DNA repair. These findings demonstrate a role for PARP in the replication of heterochromatin and further validate PARP as a therapeutic target in IDH-mutant tumors.
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Affiliation(s)
- Juan-Manuel Schvartzman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Grace Forsyth
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Human Oncology and Pathogenesis Program, and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Human Oncology and Pathogenesis Program, and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xiaolu Zhu
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Steven Gershik
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Francesco V Cimino
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anthony Santella
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, 417 E 68th St, New York, NY 10065, USA
| | - Kamal Menghrajani
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sánchez-Vega
- Department of Epidemiology and Biostatistics and Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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3
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Kang W, Santella A, Rosiek E, Pulina M, Chan E, Fan N, Tipping MJ, Barlas A, Romin Y, Manova-Todorova K. Multiplex Spatial Protein Detection by Combining Immunofluorescence with Immunohistochemistry. Methods Mol Biol 2022; 2593:233-244. [PMID: 36513935 DOI: 10.1007/978-1-0716-2811-9_15] [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] [Indexed: 12/15/2022]
Abstract
Technologies for staining and imaging multiple antigens in single tissue sections are developing rapidly due to their potential to uncover spatial relationships between proteins with cellular resolution. Detections are performed simultaneously or sequentially depending on the approach. However, several technologies can detect limited numbers of antigens or require expensive equipment and reagents. Another serious concern is the lack of flexibility. Most commercialized reagents are validated for defined antibody panels, and introducing any changes is laborious and costly. In this chapter, we describe a method where we combine, for the first time, multiplexed IF followed by sequential immunohistochemistry (IHC) with AEC chromogen on Leica Bond staining processors with paraffin tissue sections. We present data for successful detection of 10 antigens in a single tissue section with preserved tissue integrity. Our method is designed for use with any combination of antibodies of interest, with images collected using whole slide scanners. We include an image viewing and image analysis workflow using nonlinear warping to combine all staining passes in a single full-resolution image of the entire tissue section, aligned at the single cell level.
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Affiliation(s)
- Wenfei Kang
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Anthony Santella
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Rosiek
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Pulina
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ning Fan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Murray J Tipping
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Afsar Barlas
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yevgeniy Romin
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Sahu A, Kose K, Kraehenbuehl L, Byers C, Holland A, Tembo T, Santella A, Alfonso A, Li M, Cordova M, Gill M, Fox C, Gonzalez S, Kumar P, Wang AW, Kurtansky N, Chandrani P, Yin S, Mehta P, Navarrete-Dechent C, Peterson G, King K, Dusza S, Yang N, Liu S, Phillips W, Guitera P, Rossi A, Halpern A, Deng L, Pulitzer M, Marghoob A, Chen CSJ, Merghoub T, Rajadhyaksha M. In vivo tumor immune microenvironment phenotypes correlate with inflammation and vasculature to predict immunotherapy response. Nat Commun 2022; 13:5312. [PMID: 36085288 PMCID: PMC9463451 DOI: 10.1038/s41467-022-32738-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 07/09/2021] [Accepted: 08/12/2022] [Indexed: 12/03/2022] Open
Abstract
Response to immunotherapies can be variable and unpredictable. Pathology-based phenotyping of tumors into ‘hot’ and ‘cold’ is static, relying solely on T-cell infiltration in single-time single-site biopsies, resulting in suboptimal treatment response prediction. Dynamic vascular events (tumor angiogenesis, leukocyte trafficking) within tumor immune microenvironment (TiME) also influence anti-tumor immunity and treatment response. Here, we report dynamic cellular-level TiME phenotyping in vivo that combines inflammation profiles with vascular features through non-invasive reflectance confocal microscopic imaging. In skin cancer patients, we demonstrate three main TiME phenotypes that correlate with gene and protein expression, and response to toll-like receptor agonist immune-therapy. Notably, phenotypes with high inflammation associate with immunostimulatory signatures and those with high vasculature with angiogenic and endothelial anergy signatures. Moreover, phenotypes with high inflammation and low vasculature demonstrate the best treatment response. This non-invasive in vivo phenotyping approach integrating dynamic vasculature with inflammation serves as a reliable predictor of response to topical immune-therapy in patients. Standard assessment of immune infiltration of biopsies is not sufficient to accurately predict response to immunotherapy. Here, the authors show that reflectance confocal microscopy can be used to quantify dynamic vasculature and inflammatory features to better predict treatment response in skin cancers.
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Affiliation(s)
- Aditi Sahu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Kivanc Kose
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lukas Kraehenbuehl
- Parker Institute for Cancer Immunotherapy, Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Candice Byers
- Roux Institute, Northeastern University, Portland, ME, USA.,Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Aliya Holland
- Parker Institute for Cancer Immunotherapy, Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teguru Tembo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Anabel Alfonso
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Madison Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel Cordova
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa Gill
- SUNY Downstate Health Sciences University, Brooklyn, NY, USA.,Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital Solna, Stockholm, Sweden.,Faculty of Medicine and Health Sciences, University of Alcala, Madrid, Spain
| | - Christi Fox
- Caliber Imaging and Diagnostics, Rochester, NY, USA
| | - Salvador Gonzalez
- Faculty of Medicine and Health Sciences, University of Alcala, Madrid, Spain
| | - Piyush Kumar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Shen Yin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paras Mehta
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristian Navarrete-Dechent
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gary Peterson
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kimeil King
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen Dusza
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ning Yang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shuaitong Liu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Pascale Guitera
- Sydney Melanoma Diagnostic Center, Sydney, NSW, Australia.,Melanoma Institute Australia, Wollstonecraft, NSW, Australia
| | - Anthony Rossi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allan Halpern
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liang Deng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Taha Merghoub
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medicine, New York, NY, USA
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5
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Santella A, Kolotuev I, Kizilyaprak C, Bao Z. Cross-modality synthesis of EM time series and live fluorescence imaging. eLife 2022; 11:77918. [PMID: 35666127 PMCID: PMC9213002 DOI: 10.7554/elife.77918] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/05/2022] [Indexed: 11/13/2022] Open
Abstract
Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure, and function. However, systematic atlasing across modalities is limited by challenges to effective image alignment. We combine highly spatially resolved electron microscopy (EM) and highly temporally resolved time-lapse fluorescence microscopy (FM) to examine the emergence of a complex nervous system in Caenorhabditis elegans embryogenesis. We generate an EM time series at four classic developmental stages and create a landmark-based co-optimization algorithm for cross-modality image alignment, which handles developmental heterochrony among datasets to achieve accurate single-cell level alignment. Synthesis based on the EM series and time-lapse FM series carrying different cell-specific markers reveals critical dynamic behaviors across scales of identifiable individual cells in the emergence of the primary neuropil, the nerve ring, as well as a major sensory organ, the amphid. Our study paves the way for systematic cross-modality data synthesis in C. elegans and demonstrates a powerful approach that may be applied broadly.
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Affiliation(s)
- Anthony Santella
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | | | - Zhirong Bao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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6
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Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler W, Shroff H, Colón-Ramos DA. Differential adhesion regulates neurite placement via a retrograde zippering mechanism. eLife 2021; 10:71171. [PMID: 34783657 PMCID: PMC8843091 DOI: 10.7554/elife.71171] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Received: 06/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of the C. elegans brain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificity in vivo in developing neuropil bundles.
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Affiliation(s)
- Titas Sengupta
- Yale University School of Medicine, New Haven, United States
| | - Noelle L Koonce
- Yale University School of Medicine, New Haven, United States
| | | | - Mark W Moyle
- Yale University School of Medicine, New Haven, United States
| | | | - Sarah E Emerson
- Yale University School of Medicine, New Haven, United States
| | - Xiaofei Han
- National Institutes of Health, Bethesda, United States
| | - Lin Shao
- Yale University School of Medicine, New Haven, United States
| | - Yicong Wu
- National Institutes of Health, Bethesda, United States
| | - Anthony Santella
- Developmental Biology Program, Molecular Cytology Core, Sloan-Kettering Institute, New York, United States
| | - Li Fan
- Helen and Robert Appel Alzheimer's Disease Institute, Weill Cornell Medicine, New York, United States
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - William Mohler
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Hari Shroff
- National Institutes of Health, Bethesda, United States
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7
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Sahu A, Gill M, Cordova M, Santella A, Kose K, Tembo T, Alfonso A, Chandrani P, Fox C, Gonzalez S, Kurtansky N, Pulitzer M, Phillips W, Li M, King K, Dusza S, Liu S, Yang N, Jilani H, Mehta P, Marghoob A, Halpern A, Rossi A, Deng L, Chen CSJ, Rajadhyaksha M. Abstract 2814: Dynamic imaging of tumor-immune microenvironment (TiME) and microvasculature identifies ‘hot' and ‘cold' tumor phenotypes in vivo in patients. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2814] [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
Investigating the dynamic crosstalk between the tumor-immune microenvironment (TiME) and microvasculature in vivo in patients can lead to important insights into the underlying biology, help identify tumor phenotypes and reveal attractive druggable targets.
Dynamic non-invasive label-free imaging of TiME and microvasculature in real-time directly in patients using reflectance confocal microscopy (RCM) was investigated on 60 skin cancer patients (basal cell carcinoma, BCC; squamous cell carcinoma, SCC), followed by automated and machine-learning based quantification of TiME and microvasculature features such as vascular density, leukocyte trafficking and immune cell density. Manual (two readers) and histopathological evaluation (dermatopathologist) of these features was also performed. Molecular correlation of imaging features and phenotypes was performed using anti-CD3/anti-CD20 IHC staining for tertiary lymphoid structures (TLS) and total lymphocyte density (n=33), flow cytometry for immune cells (n=3), and differential RNA expression (n=14). Correlation of RCM features and phenotypes at baseline (before treatment) with treatment response was also evaluated on 9 cancer lesions undergoing topical immunotherapy imiquimod. High agreement for feature presence on RCM and Histology, and manual and automated RCM features was observed. Unsupervised clustering on total TiME and microvasculature features on RCM using principal component analysis (PCA) indicates four distinct tumor phenotypes (PCA 1). The phenotype with high inflammation, high trafficking and higher density of vessels or the denoted ‘hot' phenotype correlated with higher activated CD8+ Granzyme B+ cells (67% of total CD8+cells). The clustering pattern on RCM was compared to TLS and lymphocyte density (PCA 2) and gene expression following CIBERSORT analysis (PCA 3). The clustering in RCM correlated better with gene expression (PCA 1 and 3, 100% agreement) than TLS and lymphocyte density (PCA 1 and 2, 86% agreement). The ‘hot' phenotype in RCM correlated with higher immune gene signatures and higher TLS/lymphocyte density. Increased plasma, CD8, activated CD4 memory and activated NK cells, M1 macrophages and monocytes, along with up-regulation of JAK-STAT, chemokine and cell adhesion signaling cascade were found in the ‘hot' RCM phenotype. Statistical modeling for correlating phenotypes with treatment outcomes was performed using principal component-linear discriminant analysis (PC-LDA). Two responders with tumor regression were predicted as ‘hot' phenotype while the non-responding patients (remaining 7) were classified as cold phenotype; suggesting that RCM 'hot' phenotype correlates with better treatment response. Thus, we demonstrate the potential utility of noninvasive RCM imaging in identifying ‘hot' and ‘cold' tumor phenotypes directly in patients.
Citation Format: Aditi Sahu, Melissa Gill, Miguel Cordova, Anthony Santella, Kivanc Kose, Teguru Tembo, Anabel Alfonso, Pratik Chandrani, Christi Fox, Salvador Gonzalez, Nicholas Kurtansky, Melissa Pulitzer, William Phillips, Madison Li, Kimeil King, Stephen Dusza, Shuaitong Liu, Ning Yang, Haaris Jilani, Paras Mehta, Ashfaq Marghoob, Allan Halpern, Anthony Rossi, Liang Deng, Chih-Shan Jason Chen, Milind Rajadhyaksha. Dynamic imaging of tumor-immune microenvironment (TiME) and microvasculature identifies ‘hot' and ‘cold' tumor phenotypes in vivo in patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2814.
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Affiliation(s)
- Aditi Sahu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Kivanc Kose
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Christi Fox
- 5Caliber Imaging and Diagnostics, Rochester, NY
| | | | | | | | | | | | - Kimeil King
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stephen Dusza
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shuaitong Liu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ning Yang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Paras Mehta
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Allan Halpern
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthony Rossi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liang Deng
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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8
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Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, Prince V, Waters JC, Annunziata CM, Hafner M, Mohler WA, Chitnis AB, Upadhyaya A, Usdin TB, Bao Z, Colón-Ramos D, La Riviere P, Liu H, Wu Y, Shroff H. Rapid image deconvolution and multiview fusion for optical microscopy. Nat Biotechnol 2020; 38:1337-1346. [PMID: 32601431 PMCID: PMC7642198 DOI: 10.1038/s41587-020-0560-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [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: 09/25/2019] [Accepted: 05/15/2020] [Indexed: 12/11/2022]
Abstract
The contrast and resolution of images obtained with optical microscopes can be improved by deconvolution and computational fusion of multiple views of the same sample, but these methods are computationally expensive for large datasets. Here we describe theoretical and practical advances in algorithm and software design that result in image processing times that are tenfold to several thousand fold faster than with previous methods. First, we show that an 'unmatched back projector' accelerates deconvolution relative to the classic Richardson-Lucy algorithm by at least tenfold. Second, three-dimensional image-based registration with a graphics processing unit enhances processing speed 10- to 100-fold over CPU processing. Third, deep learning can provide further acceleration, particularly for deconvolution with spatially varying point spread functions. We illustrate our methods from the subcellular to millimeter spatial scale on diverse samples, including single cells, embryos and cleared tissue. Finally, we show performance enhancement on recently developed microscopes that have improved spatial resolution, including dual-view cleared-tissue light-sheet microscopes and reflective lattice light-sheet microscopes.
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Affiliation(s)
- Min Guo
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Yue Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yijun Su
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Talley Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Damian Dalle Nogare
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mark W Moyle
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Leighton H Duncan
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Ikegami
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ivan Rey-Suarez
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Biophysics Program, University of Maryland, College Park, MD, USA
| | - Daniel Green
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Anastasia Beiriger
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Victoria Prince
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | | | - Christina M Annunziata
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - William A Mohler
- Department of Genetics and Genome Sciences and Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT, USA
| | - Ajay B Chitnis
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Ted B Usdin
- Section on Fundamental Neuroscience, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Daniel Colón-Ramos
- Departments of Neuroscience and Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Marine Biological Laboratory Fellows Program, Woods Hole, MA, USA
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Patrick La Riviere
- Marine Biological Laboratory Fellows Program, Woods Hole, MA, USA
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Huafeng Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.
| | - Yicong Wu
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Hari Shroff
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Marine Biological Laboratory Fellows Program, Woods Hole, MA, USA
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9
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Barnes KM, Fan L, Moyle MW, Brittin CA, Xu Y, Colón-Ramos DA, Santella A, Bao Z. Cadherin preserves cohesion across involuting tissues during C. elegans neurulation. eLife 2020; 9:e58626. [PMID: 33030428 PMCID: PMC7544503 DOI: 10.7554/elife.58626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
The internalization of the central nervous system, termed neurulation in vertebrates, is a critical step in embryogenesis. Open questions remain regarding how force propels coordinated tissue movement during the process, and little is known as to how internalization happens in invertebrates. We show that in C. elegans morphogenesis, apical constriction in the retracting pharynx drives involution of the adjacent neuroectoderm. HMR-1/cadherin mediates this process via inter-tissue attachment, as well as cohesion within the neuroectoderm. Our results demonstrate that HMR-1 is capable of mediating embryo-wide reorganization driven by a centrally located force generator, and indicate a non-canonical use of cadherin on the basal side of an epithelium that may apply to vertebrate neurulation. Additionally, we highlight shared morphology and gene expression in tissues driving involution, which suggests that neuroectoderm involution in C. elegans is potentially homologous with vertebrate neurulation and thus may help elucidate the evolutionary origin of the brain.
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Affiliation(s)
- Kristopher M Barnes
- Developmental Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Graduate Program in Neuroscience, Weill Cornell MedicineNew YorkUnited States
| | - Li Fan
- Developmental Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of MedicineNew HavenUnited States
| | - Christopher A Brittin
- Developmental Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Yichi Xu
- Developmental Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Daniel A Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of MedicineNew HavenUnited States
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto RicoSan JuanUnited States
| | - Anthony Santella
- Developmental Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Molecular Cytology Core, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Zhirong Bao
- Developmental Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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10
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Abstract
Cell shapes provide crucial biological information on complex tissues. Different cell types often have distinct cell shapes, and collective shape changes usually indicate morphogenetic events and mechanisms. The identification and detection of collective cell shape changes in an extensive collection of 3D time-lapse images of complex tissues is an important step in assaying such mechanisms but is a tedious and time-consuming task. Machine learning provides new opportunities to automatically detect cell shape changes. However, it is challenging to generate sufficient training samples for pattern identification through deep learning because of a limited amount of images and annotations. We present a deep learning approach with minimal well-annotated training samples and apply it to identify multicellular rosettes from 3D live images of the Caenorhabditis elegans embryo with fluorescently labeled cell membranes. Our strategy is to combine two approaches, namely, feature transfer and generative adversarial networks (GANs), to boost image classification with small training samples. Specifically, we use a GAN framework and conduct an unsupervised training to capture the general characteristics of cell membrane images with 11,250 unlabelled images. We then transfer the structure of the GAN discriminator into a new Alex-style neural network for further learning with several dozen labeled samples. Our experiments showed that with 10-15 well-labeled rosette images and 30-40 randomly selected nonrosette images our approach can identify rosettes with more than 80% accuracy and capture more than 90% of the model accuracy achieved with a training data et that is five times larger. We also established a public benchmark dataset for rosette detection. This GAN-based transfer approach can be applied to the study of other cellular structures with minimal training samples.
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Affiliation(s)
- Dali Wang
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37934, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zheng Lu
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37934, USA
| | - Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Z I Wang
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37934, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
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11
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Duncan LH, Moyle MW, Shao L, Sengupta T, Ikegami R, Kumar A, Guo M, Christensen R, Santella A, Bao Z, Shroff H, Mohler W, Colón-Ramos DA. Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution. J Vis Exp 2019. [PMID: 31233035 DOI: 10.3791/59533] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Caenorhabditis elegans (C. elegans) stands out as the only organism in which the challenge of understanding the cellular origins of an entire nervous system can be observed, with single cell resolution, in vivo. Here, we present an integrated protocol for the examination of neurodevelopment in C. elegans embryos. Our protocol combines imaging, lineaging and neuroanatomical tracing of single cells in developing embryos. We achieve long-term, four-dimensional (4D) imaging of living C. elegans embryos with nearly isotropic spatial resolution through the use of Dual-view Inverted Selective Plane Illumination Microscopy (diSPIM). Nuclei and neuronal structures in the nematode embryos are imaged and isotropically fused to yield images with resolution of ~330 nm in all three dimensions. These minute-by-minute high-resolution 4D data sets are then analyzed to correlate definitive cell-lineage identities with gene expression and morphological dynamics at single-cell and subcellular levels of detail. Our protocol is structured to enable modular implementation of each of the described steps and enhance studies on embryogenesis, gene expression, or neurodevelopment.
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Affiliation(s)
- Leighton H Duncan
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Lin Shao
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Titas Sengupta
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Richard Ikegami
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org
| | - Abhishek Kumar
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - Ryan Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - Anthony Santella
- Developmental Biology Program, Sloan Kettering Institute; WormGUIDES.org
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute; WormGUIDES.org
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health; WormGUIDES.org
| | - William Mohler
- Department of Genetics and Genome Sciences and Center for Cell Analysis and Modeling, University of Connecticut Health Center; WormGUIDES.org;
| | - Daniel A Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; WormGUIDES.org; Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico;
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12
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Christensen R, Bokinsky A, Santella A, Moyle M, Guo M, Lauziere A, Ardiel E, Vishwasrao HD, Harvey B, Levin M, Karaj N, Mohler W, Daniel Colón-Ramos D, Bao Z, Shroff H. Generating a 4D Atlas of Nuclear Positions in Embryonic Caenorhabditis elegans. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.3001] [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: 10/27/2022] Open
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13
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Katzman B, Tang D, Santella A, Bao Z. AceTree: a major update and case study in the long term maintenance of open-source scientific software. BMC Bioinformatics 2018; 19:121. [PMID: 29618316 PMCID: PMC5885296 DOI: 10.1186/s12859-018-2127-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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] [Received: 12/01/2017] [Accepted: 03/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. RESULTS Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration. CONCLUSION By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.
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Affiliation(s)
- Braden Katzman
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA
| | - Doris Tang
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA.
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14
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Shah PK, Santella A, Jacobo A, Siletti K, Hudspeth AJ, Bao Z. An In Toto Approach to Dissecting Cellular Interactions in Complex Tissues. Dev Cell 2017; 43:530-540.e4. [PMID: 29161596 DOI: 10.1016/j.devcel.2017.10.021] [Citation(s) in RCA: 14] [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: 05/08/2017] [Revised: 09/01/2017] [Accepted: 10/20/2017] [Indexed: 11/27/2022]
Abstract
Single-cell measurements have broadened our understanding of heterogeneity in biology, yet have been limited to mostly observational studies of normal or globally perturbed systems. Typically, perturbations are utilized in an open-ended approach wherein an endpoint is assayed during or after the biological event of interest. Here we describe ShootingStar, a platform for perturbation analysis in vivo, which combines live imaging, real-time image analysis, and automated optical perturbations. ShootingStar builds a quantitative record of the state of the sample being analyzed, which is used to automate the identification of target cells for perturbation, as well as to validate the impacts of the perturbation. We used ShootingStar to dissect the cellular basis of development, morphogenesis, and polarity in the lateral line of Danio rerio and the embryo of Caenorhabditis elegans. ShootingStar can be extended to diverse optical manipulations and enables more robust and informative single-cell perturbations in complex tissues.
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Affiliation(s)
- Pavak Kirit Shah
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065 USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065 USA
| | - Adrian Jacobo
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - Kimberly Siletti
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - A J Hudspeth
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065 USA.
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15
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Kumar A, Christensen R, Guo M, Chandris P, Duncan W, Wu Y, Santella A, Moyle M, Winter PW, Colón-Ramos D, Bao Z, Shroff H. Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM). Biol Bull 2016; 231:26-39. [PMID: 27638693 PMCID: PMC5481201 DOI: 10.1086/689589] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Dual-view inverted selective plane illumination microscopy (diSPIM) enables high-speed, long-term, four-dimensional (4D) imaging with isotropic spatial resolution. It is also compatible with conventional sample mounting on glass coverslips. However, broadening of the light sheet at distances far from the beam waist and sample-induced scattering degrades diSPIM contrast and optical sectioning. We describe two simple improvements that address both issues and entail no additional hardware modifications to the base diSPIM. First, we demonstrate improved diSPIM sectioning by keeping the light sheet and detection optics stationary, and scanning the sample through the stationary light sheet (rather than scanning the broadening light sheet and detection plane through the stationary sample, as in conventional diSPIM). This stage-scanning approach allows a thinner sheet to be used when imaging laterally extended samples, such as fixed microtubules or motile mitochondria in cell monolayers, and produces finer contrast than does conventional diSPIM. We also used stage-scanning diSPIM to obtain high-quality, 4D nuclear datasets derived from an uncompressed nematode embryo, and performed lineaging analysis to track 97% of cells until twitching. Second, we describe the improvement of contrast in thick, scattering specimens by synchronizing light-sheet synthesis with the rolling, electronic shutter of our scientific complementary metal-oxide-semiconductor (sCMOS) detector. This maneuver forms a virtual confocal slit in the detection path, partially removing out-of-focus light. We demonstrate the applicability of our combined stage- and slit-scanning- methods by imaging pollen grains and nuclear and neuronal structures in live nematode embryos. All acquisition and analysis code is freely available online.
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Affiliation(s)
- Abhishek Kumar
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710;
| | - Ryan Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
| | - Panos Chandris
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
| | - William Duncan
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
| | - Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York 10065; and
| | - Mark Moyle
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Department of Cell Biology, Yale University, New Haven, Connecticut 06511
| | - Peter W Winter
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
| | - Daniel Colón-Ramos
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Department of Cell Biology, Yale University, New Haven, Connecticut 06511
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York 10065; and
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892-7710
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16
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Santella A, Kovacevic I, Herndon LA, Hall DH, Du Z, Bao Z. Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. Nucleic Acids Res 2016; 44:D781-5. [PMID: 26503254 PMCID: PMC4702815 DOI: 10.1093/nar/gkv1119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 08/14/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022] Open
Abstract
Developmental systems biology is poised to exploit large-scale data from two approaches: genomics and live imaging. The combination of the two offers the opportunity to map gene functions and gene networks in vivo at single-cell resolution using cell tracking and quantification of cellular phenotypes. Here we present Digital Development (http://www.digital-development.org), a database of cell lineage differentiation with curated phenotypes, cell-specific gene functions and a multiscale model. The database stores data from recent systematic studies of cell lineage differentiation in the C. elegans embryo containing ∼ 200 conserved genes, 1400 perturbed cell lineages and 600,000 digitized single cells. Users can conveniently browse, search and download four categories of phenotypic and functional information from an intuitive web interface. This information includes lineage differentiation phenotypes, cell-specific gene functions, differentiation landscapes and fate choices, and a multiscale model of lineage differentiation. Digital Development provides a comprehensive, curated, multidimensional database for developmental biology. The scale, resolution and richness of biological information presented here facilitate exploration of gene-specific and systems-level mechanisms of lineage differentiation in Metazoans.
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Affiliation(s)
| | | | | | - David H Hall
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zhuo Du
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhirong Bao
- Sloan Kettering Institute, New York, NY 10065, USA
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17
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Roy D, Michaelson D, Hochman T, Santella A, Bao Z, Goldberg JD, Hubbard EJA. Cell cycle features of C. elegans germline stem/progenitor cells vary temporally and spatially. Dev Biol 2016; 409:261-271. [PMID: 26577869 PMCID: PMC4827254 DOI: 10.1016/j.ydbio.2015.10.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 08/19/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 11/24/2022]
Abstract
Many organisms accumulate a pool of germline stem cells during development that is maintained in later life. The dynamics of establishment, expansion and homeostatic maintenance of this pool are subject to both developmental and physiological influences including the availability of a suitable niche microenvironment, nutritional status, and age. Here, we investigated the dynamics of germline proliferation during stages of expansion and homeostasis, using the C. elegans germ line as a model. The vast majority of germ cells in the proliferative zone are in interphase stages of mitosis (G1, S, G2) rather than in the active mitotic (M) phase. We examined mitotic index and DNA content, comparing different life stages, mutants, and physiological conditions. We found that germ cells in larval stages cycle faster than in adult stages, but that this difference could not be attributed to sexual fate of the germ cells. We also found that larval germ cells exhibit a lower average DNA content compared to adult germ cells. We extended our analysis to consider the effects of distance from the niche and further found that the spatial pattern of DNA content differs between larval and adult stages in the wild type and among mutants in pathways that interfere with cell cycle progression, cell fate, or both. Finally, we characterized expansion of the proliferative pool of germ cells during adulthood, using a regeneration paradigm (ARD recovery) in which animals are starved and re-fed. We compared adult stage regeneration and larval stage expansion, and found that the adult germ line is capable of rapid accumulation but does not sustain a larval-level mitotic index nor does it recapitulate the larval pattern of DNA content. The regenerated germ line does not reach the number of proliferative zone nuclei seen in the continuously fed adult. Taken together, our results suggest that cell cycle dynamics are under multiple influences including distance from the niche, age and/or maturation of the germ line, nutrition and, possibly, latitude for physical expansion.
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Affiliation(s)
- Debasmita Roy
- Skirball Institute of Biomolecular Medicine, Helen L. and Martin S. Kimmel Center for Stem Cell Biology, Departments of Cell Biology and Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - David Michaelson
- Skirball Institute of Biomolecular Medicine, Helen L. and Martin S. Kimmel Center for Stem Cell Biology, Departments of Cell Biology and Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Tsivia Hochman
- Departments of Population Health and Environmental Medicine, Division of Biostatistics, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Judith D Goldberg
- Departments of Population Health and Environmental Medicine, Division of Biostatistics, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Helen L. and Martin S. Kimmel Center for Stem Cell Biology, Departments of Cell Biology and Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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18
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Graziano P, Dell'Aversana Orabona G, Astarita F, Ponzo LM, Nunziata R, Salzano G, Maglitto F, Solari D, Santella A, Cappabianca M, Iaconetta G, Califano L. Bilateral hypertrophy of masseteric and temporalis muscles, our fifteen patients and review of literature. Eur Rev Med Pharmacol Sci 2016; 20:7-11. [PMID: 26813447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
OBJECTIVE The association of bilateral hypertrophy of temporalis and masseteric muscles is a rare clinical entity. The origin of the condition is unclear, causing cosmetic problems, pain, and functional impairment. PATIENTS AND METHODS In this paper we analyzed 15 patients treated at the Department of Maxillo-Facial Surgery of the University of Naples Federico II, from 2000 to 2013, for temporalis and/or masseteric muscle hypertrophy, and in particular, a rare case of a patient with a marked bilateral swelling of the temporalis and masseteric region, in conjunction with a review of the literature. RESULTS Fourteen patients have not any kind of postoperatively problems. The last patient had been aware of the swelling for many years and complained of recurrent headaches. We adopted a new protocol fort this patients and the patient was very pleased with the treatment results, and reported a reduction in headaches and a continuation of his well-being, in addition to greater self-confidence. The last follow-up was performed three years after the first treatment, and the patient showed a complete resolution of his symptoms, and just a small increase of the swelling. CONCLUSIONS The treatment of temporalis and masseteric hypertrophy with Botulin toxin could be an effective option compared to conservative treatment or surgical intervention, although the review of the literature shows that this is only a temporary treatment. In fact, surgery still remains the best option. The treatment must be repeated every 4/6 months for 2-3 consecutive years before having stable benefits. To overcome this problem, an association with a bite treatment allowed us to achieve more lasting and more stable results over time without a recurrence of symptoms between the treatments. Furthermore, this association has enabled us to obtain a more rapid reduction of the hypertrophy.
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Affiliation(s)
- P Graziano
- Maxillo-Facial Surgery Department, University Federico II, Naples, Italy.
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19
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Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H. Untwisting the Caenorhabditis elegans embryo. eLife 2015; 4. [PMID: 26633880 PMCID: PMC4764590 DOI: 10.7554/elife.10070] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/25/2015] [Indexed: 01/08/2023] Open
Abstract
The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis. DOI:http://dx.doi.org/10.7554/eLife.10070.001 Understanding how the brain and nervous system develops from a few cells into complex, interconnected networks is a key goal for neuroscientists. Although researchers have identified many of the genes involved in this process, how these work together to form an entire brain remains unknown. A simple worm called Caenorhabiditis elegans is commonly used to study brain development because it has only about 300 neurons, simplifying the study of its nervous system. The worms are easy to grow in the laboratory and are transparent, allowing scientists to observe how living worms develop using a microscope. Researchers have learned a great deal about the initial growth of the nervous system in C. elegans embryos. However, it has been difficult to study the embryos once their muscles have formed because they constantly twist, fold, and move, making it hard to track the cells. Now, Christensen, Bokinsky, Santella, Wu et al. have developed a computer program that allows scientists to virtually untwist the embryos and follow the development of the nervous system from its beginning to when the embryo hatches. First, images are taken of worm embryos that produce fluorescent proteins marking certain body parts. The program, with user input, labels the fluorescent cells in the images, which indicates how the embryo is bending and allows the program to straighten the worm. The program can also track how cells move around the embryo during development and show the positional relationships between different cells at different stages of development. Christensen et al. have made the program freely available for other researchers to use. The next step is to increase automation, making the software faster and more straightforward for users. Ultimately, the software could help in the challenge to comprehensively examine the development of each neuron in the worm. DOI:http://dx.doi.org/10.7554/eLife.10070.002
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Affiliation(s)
- Ryan Patrick Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Alexandra Bokinsky
- Biomedical Imaging Research Services Section, Center for Information Technology, National Institutes of Health, Bethesda, United States
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Javier Marquina-Solis
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Cell Biology, Yale University School of Medicine, New Haven, United States
| | - Min Guo
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.,State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Ismar Kovacevic
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - Abhishek Kumar
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Cell Biology, Yale University School of Medicine, New Haven, United States
| | - Peter W Winter
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Nicole Tashakkori
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Evan McCreedy
- Biomedical Imaging Research Services Section, Center for Information Technology, National Institutes of Health, Bethesda, United States
| | - Huafeng Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Matthew McAuliffe
- Biomedical Imaging Research Services Section, Center for Information Technology, National Institutes of Health, Bethesda, United States
| | - William Mohler
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Daniel A Colón-Ramos
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Cell Biology, Yale University School of Medicine, New Haven, United States
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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Du Z, Santella A, He F, Shah PK, Kamikawa Y, Bao Z. The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo. Dev Cell 2015; 34:592-607. [PMID: 26321128 DOI: 10.1016/j.devcel.2015.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 01/25/2015] [Revised: 05/21/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022]
Abstract
Elucidating the mechanism of cell lineage differentiation is critical for our understanding of development and fate manipulation. Here we combined systematic perturbation and direct lineaging to map the regulatory landscape of lineage differentiation in early C. elegans embryogenesis. High-dimensional phenotypic analysis of 204 essential genes in 1,368 embryos revealed that cell lineage differentiation follows a canalized landscape with barriers shaped by lineage distance and genetic robustness. We assigned function to 201 genes in regulating lineage differentiation, including 175 switches of binary fate choices. We generated a multiscale model that connects gene networks and cells to the experimentally mapped landscape. Simulations showed that the landscape topology determines the propensity of differentiation and regulatory complexity. Furthermore, the model allowed us to identify the chromatin assembly complex CAF-1 as a context-specific repressor of Notch signaling. Our study presents a systematic survey of the regulatory landscape of lineage differentiation of a metazoan embryo.
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Affiliation(s)
- Zhuo Du
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
| | - Anthony Santella
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Fei He
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Pavak K Shah
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Yuko Kamikawa
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Zhirong Bao
- Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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Vidal B, Santella A, Serrano-Saiz E, Bao Z, Chuang CF, Hobert O. C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types. Development 2015; 142:2464-77. [PMID: 26153233 DOI: 10.1242/dev.125740] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 04/26/2015] [Accepted: 05/28/2015] [Indexed: 12/31/2022]
Abstract
Neurogenesis involves deeply conserved patterning molecules, such as the proneural basic helix-loop-helix transcription factors. Sox proteins and specifically members of the SoxB and SoxC groups are another class of conserved transcription factors with an important role in neuronal fate commitment and differentiation in various species. In this study, we examine the expression of all five Sox genes of the nematode C. elegans and analyze the effect of null mutant alleles of all members of the SoxB and SoxC groups on nervous system development. Surprisingly, we find that, unlike in other systems, neither of the two C. elegans SoxB genes sox-2 (SoxB1) and sox-3 (SoxB2), nor the sole C. elegans SoxC gene sem-2, is broadly expressed throughout the embryonic or adult nervous system and that all three genes are mostly dispensable for embryonic neurogenesis. Instead, sox-2 is required to maintain the developmental potential of blast cells that are generated in the embryo but divide only postembryonically to give rise to differentiated neuronal cell types. Moreover, sox-2 and sox-3 have selective roles in the terminal differentiation of specific neuronal cell types. Our findings suggest that the common themes of SoxB gene function across phylogeny lie in specifying developmental potential and, later on, in selectively controlling terminal differentiation programs of specific neuron types, but not in broadly controlling neurogenesis.
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Affiliation(s)
- Berta Vidal
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Esther Serrano-Saiz
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Chiou-Fen Chuang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Oliver Hobert
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
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22
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Dell'Aversana Orabona G, Salzano G, Iaconetta G, Piombino P, Ponzo L, Santella A, Astarita F, Solari D, Salzano FA, Califano L. Facial osteomas: fourteen cases and a review of literature. Eur Rev Med Pharmacol Sci 2015; 19:1796-1802. [PMID: 26044223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE Osteomas are benign tumors that frequently affect the cranio-facial region, especially the temporal bones, jaw and sinus. This lesion very rarely involves the maxillary bones. The aim of our study is to describe our surgical case series and to evaluate the diagnosis and management of peripheral craniofacial osteomas with a review of the literature. PATIENTS AND METHODS We retrospectively analyzed a series of 14 patients that underwent surgery for the removal of a cranio-facial osteoma, 10 cases were peripheral osteoma of the lower jaw and 4 were peripheral osteomas of the upper jaw. The 14 patients included 8 females and 6 males, with a mean age of 42 years. The median follow up period was 48 months. RESULTS All patients received a total surgical removal and we did not have any intraoperative complications with optimal cosmetic and functional results. Pain resolved in all cases and a single case postoperative dysesthesia occurred. NO recurrence has been detected at last follow-up visit. CONCLUSIONS Osteomas must be well identified and differentiated from other solid diseases of the bone and should be treated if symptomatic. The elective treatment is surgical removal, resulting in a complete resolution of the pathology.
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Affiliation(s)
- G Dell'Aversana Orabona
- Division of Maxillo-Facial surgery, Department of Neurosciences, Reproductive and Odontostomatological Sciences, Università degli Studi di Napoli Federico II, Naples, Italy.
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Eckert BS, Santella A, Beric B, Westervelt S. Tools of the Trade. Health Promot Pract 2014; 15:617-8. [DOI: 10.1177/1524839914540267] [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: 11/17/2022]
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Abstract
BACKGROUND Advances in fluorescence labeling and imaging have made it possible to acquire in vivo records of complex biological processes. Analysis has lagged behind acquisition in part because of the difficulty and computational expense of accurate cell tracking. In vivo analysis requires, at minimum, tracking hundreds of cells over hundreds of time points in complex three dimensional environments. We address this challenge with a computational framework capable of efficiently and accurately tracing entire cell lineages. RESULTS The bulk of the tracking problem-tracking cells during interphase-is straightforward and can be executed with simple and fast methods. Difficult cases originate from detection errors and relatively rare large motions. Therefore, our method focuses computational effort on difficult cases identified by local increases in cell number. We force these cases into tentative cell track bifurcations, which define natural semi-local neighborhoods that permit Bayesian judgment about the underlying cell behavior. The bifurcation judgment process not only correctly tracks through cell divisions and large movements, but also offers corrections to detection errors. We demonstrate that this method enables large scale analysis of Caenorhabditis elegans development, an ideal validation platform because of an invariant cell lineage. CONCLUSION The high accuracy achieved by our method suggests that a bifurcation-based semi-local neighborhood provides sufficient information to recognize dependencies between nearby tracking choices, and to interpret difficult tracking cases without reverting to global optimization. Our method makes large amounts of lineage data accessible and opens the door to new types of statistical analysis of complex in vivo processes.
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Affiliation(s)
- Anthony Santella
- Developmental Biology, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
| | - Zhuo Du
- Developmental Biology, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
| | - Zhirong Bao
- Developmental Biology, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
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25
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Vogel JLM, Michaelson D, Santella A, Hubbard EJA, Bao Z. Irises: A practical tool for image-based analysis of cellular DNA content. Worm 2014; 3:e29041. [PMID: 25254149 DOI: 10.4161/worm.29041] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/16/2014] [Accepted: 04/28/2014] [Indexed: 01/02/2023]
Abstract
The DNA content of nuclei is a valuable measure of cell cycle status. Irises is a software tool to facilitate systematic in situ determination of DNA content for cell cycle analysis at single-nucleus resolution within complex tissues. We demonstrate the utility of the tool with analysis of DNA content in germline nuclei of C. elegans. Compared with results obtained by manual analysis, we find the tool greatly facilitates analysis by improving speed at least 5-fold while maintaining accuracy. The source code and instruction manual (including installation for both Mac and PC) are provided.
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Affiliation(s)
| | - David Michaelson
- New York University School of Medicine; Skirball Institute of Biomolecular Medicine; New York, NY USA
| | - Anthony Santella
- Developmental Biology Program; Sloan-Kettering Institute; New York, NY USA
| | - E Jane Albert Hubbard
- New York University School of Medicine; Skirball Institute of Biomolecular Medicine; New York, NY USA ; Department of Pathology and Helen L. and Martin S. Kimmel Center for Stem Cell Biology; New York, NY USA
| | - Zhirong Bao
- Developmental Biology Program; Sloan-Kettering Institute; New York, NY USA
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26
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Du Z, Santella A, He F, Tiongson M, Bao Z. De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. Cell 2014; 156:359-72. [PMID: 24439388 DOI: 10.1016/j.cell.2013.11.046] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/25/2013] [Accepted: 11/11/2013] [Indexed: 12/21/2022]
Abstract
Elucidation of complex phenotypes for mechanistic insights presents a significant challenge in systems biology. We report a strategy to automatically infer mechanistic models of cell fate differentiation based on live-imaging data. We use cell lineage tracing and combinations of tissue-specific marker expression to assay progenitor cell fate and detect fate changes upon genetic perturbation. Based on the cellular phenotypes, we further construct a model for how fate differentiation progresses in progenitor cells and predict cell-specific gene modules and cell-to-cell signaling events that regulate the series of fate choices. We validate our approach in C. elegans embryogenesis by perturbing 20 genes in over 300 embryos. The result not only recapitulates current knowledge but also provides insights into gene function and regulated fate choice, including an unexpected self-renewal. Our study provides a powerful approach for automated and quantitative interpretation of complex in vivo information.
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Affiliation(s)
- Zhuo Du
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Fei He
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Michael Tiongson
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.
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27
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Wu Y, Wawrzusin P, Senseney J, Fischer RS, Christensen R, Santella A, York AG, Winter PW, Waterman CM, Bao Z, Colón-Ramos DA, McAuliffe M, Shroff H. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat Biotechnol 2013; 31:1032-8. [PMID: 24108093 DOI: 10.1038/nbt.2713] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 09/10/2013] [Indexed: 01/23/2023]
Abstract
Optimal four-dimensional imaging requires high spatial resolution in all dimensions, high speed and minimal photobleaching and damage. We developed a dual-view, plane illumination microscope with improved spatiotemporal resolution by switching illumination and detection between two perpendicular objectives in an alternating duty cycle. Computationally fusing the resulting volumetric views provides an isotropic resolution of 330 nm. As the sample is stationary and only two views are required, we achieve an imaging speed of 200 images/s (i.e., 0.5 s for a 50-plane volume). Unlike spinning-disk confocal or Bessel beam methods, which illuminate the sample outside the focal plane, we maintain high spatiotemporal resolution over hundreds of volumes with negligible photobleaching. To illustrate the ability of our method to study biological systems that require high-speed volumetric visualization and/or low photobleaching, we describe microtubule tracking in live cells, nuclear imaging over 14 h during nematode embryogenesis and imaging of neural wiring during Caenorhabditis elegans brain development over 5 h.
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Affiliation(s)
- Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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28
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Santella A, Pollack A, Harrison C, Sawleshwarkar S, Britt H, Hillman R. P2.168 Management of Sexually Transmitted Infections by Australian General Practitioners. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0432] [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: 11/04/2022]
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29
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Pohl C, Tiongson M, Moore JL, Santella A, Bao Z. Actomyosin-based self-organization of cell internalization during C. elegans gastrulation. BMC Biol 2012; 10:94. [PMID: 23198792 PMCID: PMC3583717 DOI: 10.1186/1741-7007-10-94] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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: 09/29/2012] [Accepted: 11/30/2012] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Gastrulation is a key transition in embryogenesis; it requires self-organized cellular coordination, which has to be both robust to allow efficient development and plastic to provide adaptability. Despite the conservation of gastrulation as a key event in Metazoan embryogenesis, the morphogenetic mechanisms of self-organization (how global order or coordination can arise from local interactions) are poorly understood. RESULTS We report a modular structure of cell internalization in Caenorhabditis elegans gastrulation that reveals mechanisms of self-organization. Cells that internalize during gastrulation show apical contractile flows, which are correlated with centripetal extensions from surrounding cells. These extensions converge to seal over the internalizing cells in the form of rosettes. This process represents a distinct mode of monolayer remodeling, with gradual extrusion of the internalizing cells and simultaneous tissue closure without an actin purse-string. We further report that this self-organizing module can adapt to severe topological alterations, providing evidence of scalability and plasticity of actomyosin-based patterning. Finally, we show that globally, the surface cell layer undergoes coplanar division to thin out and spread over the internalizing mass, which resembles epiboly. CONCLUSIONS The combination of coplanar division-based spreading and recurrent local modules for piecemeal internalization constitutes a system-level solution of gradual volume rearrangement under spatial constraint. Our results suggest that the mode of C. elegans gastrulation can be unified with the general notions of monolayer remodeling and with distinct cellular mechanisms of actomyosin-based morphogenesis.
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Affiliation(s)
- Christian Pohl
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
- Buchmann Institute for Molecular Life Sciences, Institute of Biochemistry II, Goethe University, Max-von-Laue-Strasse 15, 60438 Frankfurt, Germany
| | - Michael Tiongson
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Julia L Moore
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
- Program in Computational Biology and Medicine, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
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Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z. A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. BMC Bioinformatics 2010; 11:580. [PMID: 21114815 PMCID: PMC3008706 DOI: 10.1186/1471-2105-11-580] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 11/29/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND To exploit the flood of data from advances in high throughput imaging of optically sectioned nuclei, image analysis methods need to correctly detect thousands of nuclei, ideally in real time. Variability in nuclear appearance and undersampled volumetric data make this a challenge. RESULTS We present a novel 3D nuclear identification method, which subdivides the problem, first segmenting nuclear slices within each 2D image plane, then using a shape model to assemble these slices into 3D nuclei. This hybrid 2D/3D approach allows accurate accounting for nuclear shape but exploits the clear 2D nuclear boundaries that are present in sectional slices to avoid the computational burden of fitting a complex shape model to volume data. When tested over C. elegans, Drosophila, zebrafish and mouse data, our method yielded 0 to 3.7% error, up to six times more accurate as well as being 30 times faster than published performances. We demonstrate our method's potential by reconstructing the morphogenesis of the C. elegans pharynx. This is an important and much studied developmental process that could not previously be followed at this single cell level of detail. CONCLUSIONS Because our approach is specialized for the characteristics of optically sectioned nuclear images, it can achieve superior accuracy in significantly less time than other approaches. Both of these characteristics are necessary for practical analysis of overwhelmingly large data sets where processing must be scalable to hundreds of thousands of cells and where the time cost of manual error correction makes it impossible to use data with high error rates. Our approach is fast, accurate, available as open source software and its learned shape model is easy to retrain. As our pharynx development example shows, these characteristics make single cell analysis relatively easy and will enable novel experimental methods utilizing complex data sets.
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Affiliation(s)
- Anthony Santella
- Developmental Biology, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA
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Santella A, Shi L, Campbell C. Factors associated with hospital length of stay among HIV-infected adults in Louisiana. J La State Med Soc 2010; 162:325-6, 328-30, 332 passim. [PMID: 21294489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This retrospective study aimed to evaluate the effect of predisposing (demographic), enabling (organizational), and illness (health status) factors on human immunodeficiency virus (HIV)/acquired immunodeficiency virus (AIDS)-related hospital length of stay (LOS). Inpatient hospital visit record data from 1998 through 2003 was abstracted from the Louisiana Hospital Inpatient Discharge Database. We hypothesized that enabling, not predisposing or illness factors, influenced hospital LOS among HIV-infected persons in Louisiana. Analyses were performed for the six-year period and then repeated for each year of admission. Aggregate multivariable analysis revealed that the LOS for rural residents was more than one-third longer than for urban residents (p = 0.025). This effect was consistent for each year of analysis, although it failed to reach statistical significance after adjusting for other covariates. Subjects' gender and age categories were found to be insignificant predictors for the LOS, controlling for other covariates in model. Other significant independent predictors of LOS in the aggregate time series model were number of comorbid conditions, number of inpatient medical procedures, presence of an AIDS defining illness, and source and type of admission; although effects of only the first two predictors were significant at each year of analysis (all p-values < .05). This study shows that neither gender nor age of HIV patients is a significant predictor of HIV-related LOS. However, the number of comorbid conditions and inpatient medical procedures are significant.
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32
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Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EHK. Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat Methods 2010; 7:637-42. [PMID: 20601950 DOI: 10.1038/nmeth.1476] [Citation(s) in RCA: 430] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 05/26/2010] [Indexed: 02/03/2023]
Abstract
Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-quality data of late development or of less transparent organisms. We combined digital scanned laser light-sheet fluorescence microscopy with incoherent structured-illumination microscopy (DSLM-SI) and created structured-illumination patterns with continuously adjustable frequencies. Our method discriminates the specimen-related scattered background from signal fluorescence, thereby removing out-of-focus light and optimizing the contrast of in-focus structures. DSLM-SI provides rapid control of the illumination pattern, exceptional imaging quality and high imaging speeds. We performed long-term imaging of zebrafish development for 58 h and fast multiple-view imaging of early Drosophila melanogaster development. We reconstructed cell positions over time from the Drosophila DSLM-SI data and created a fly digital embryo.
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Affiliation(s)
- Philipp J Keller
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Santella A, Laraque F, Hilger J, Camhi E. The development and implementation of a user-friendly priority setting tool for HIV care and treatment services in New York City. J Community Health 2010; 36:158-65. [PMID: 20593229 DOI: 10.1007/s10900-010-9293-y] [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: 11/25/2022]
Abstract
The Ryan White Human Immunodeficiency Virus (HIV) Program is the largest federal program designed to provide medical and social support services for HIV infected persons who are uninsured or underinsured. In 2008, the Ryan White budget was $2.2 billion, of which over $100 million went to the New York City (NYC) eligible metropolitan area (EMA), which receives the largest Ryan White allocation targeted to any EMA. The NYC Department of Health and Mental Hygiene (DOHMH) is the grantee for the EMA. To implement HIV care and treatment programs funded by this grant, the DOHMH works closely with the NYC Ryan White Planning Council, a local community planning body that assesses needs, plans for service delivery and sets priorities for funds. This article describes priority setting principles, practices, findings and lessons learned. It also outlines how the legislatively mandated community planning body has developed and implemented a user-friendly priority setting process and tool.
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Affiliation(s)
- Anthony Santella
- Master of Public Health Program, Long Island University School of Health Professions, 1 University Plaza, Brooklyn, NY 11201, USA.
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