1
|
Aalam SMM, Nguyen LV, Ritting ML, Kannan N. Clonal tracking in cancer and metastasis. Cancer Metastasis Rev 2024; 43:639-656. [PMID: 37910295 DOI: 10.1007/s10555-023-10149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
The eradication of many cancers has proven challenging due to the presence of functionally and genetically heterogeneous clones maintained by rare cancer stem cells (CSCs), which contribute to disease progression, treatment refractoriness, and late relapse. The characterization of functional CSC activity has necessitated the development of modern clonal tracking strategies. This review describes viral-based and CRISPR-Cas9-based cellular barcoding, lineage tracing, and imaging-based approaches. DNA-based cellular barcoding technology is emerging as a powerful and robust strategy that has been widely applied to in vitro and in vivo model systems, including patient-derived xenograft models. This review also highlights the potential of these methods for use in the clinical and drug discovery contexts and discusses the important insights gained from such approaches.
Collapse
Affiliation(s)
| | - Long Viet Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Megan L Ritting
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
- Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA.
- Center for Regenerative Biotherapeutics, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
2
|
Luo Y, Zheng W, Zhong Y, Liu H, Yu J, Qiu B, Liu J, Yang B. Generation of a human embryonic stem cell line (SMUDHe010-A-1A) carrying Brainbow cassette in the AAVS1 gene by CRISPR/Cas9-mediated homologous recombination. Stem Cell Res 2024; 77:103383. [PMID: 38507883 DOI: 10.1016/j.scr.2024.103383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/23/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024] Open
Abstract
Tracking single-cell lineages and their phenotypes longitudinally would help us better study skin development. Brainbow multicolor labeling approach is a genetic cell-labeling technique that tracks individual cells or analyzes cell lineages during development. Hence, we generated a stable Cre-inducible rainbow reporter human embryonic stem cell line (Named SMUDHe010-A-1A) by inserting the fluorescent protein gene (nGFP, YFP, RFP and CFP) at AAVS1 safe harbor locus using CRISPR/Cas9 technology. We verified that SMUDHe010-A-1A expressed the pluripotency markers and showed normal stem cell morphology. Furthermore, SMUDHe010-A-1A preserves normal karyotype and the ability to differentiate toward three germ layers. So the SMUDHe010-A-1A is effective for identifying and track cell populations.
Collapse
Affiliation(s)
- Yingying Luo
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Wen Zheng
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yadang Zhong
- Department of Dermatology, The First People's Hospital of Foshan, Foshan, China
| | - Huiting Liu
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jing Yu
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Biying Qiu
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jun Liu
- Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China.
| | - Bin Yang
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory of Dermatology Research, Guangzhou, China.
| |
Collapse
|
3
|
Manso BA, Rodriguez y Baena A, Forsberg EC. From Hematopoietic Stem Cells to Platelets: Unifying Differentiation Pathways Identified by Lineage Tracing Mouse Models. Cells 2024; 13:704. [PMID: 38667319 PMCID: PMC11048769 DOI: 10.3390/cells13080704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Platelets are the terminal progeny of megakaryocytes, primarily produced in the bone marrow, and play critical roles in blood homeostasis, clotting, and wound healing. Traditionally, megakaryocytes and platelets are thought to arise from multipotent hematopoietic stem cells (HSCs) via multiple discrete progenitor populations with successive, lineage-restricting differentiation steps. However, this view has recently been challenged by studies suggesting that (1) some HSC clones are biased and/or restricted to the platelet lineage, (2) not all platelet generation follows the "canonical" megakaryocytic differentiation path of hematopoiesis, and (3) platelet output is the default program of steady-state hematopoiesis. Here, we specifically investigate the evidence that in vivo lineage tracing studies provide for the route(s) of platelet generation and investigate the involvement of various intermediate progenitor cell populations. We further identify the challenges that need to be overcome that are required to determine the presence, role, and kinetics of these possible alternate pathways.
Collapse
Affiliation(s)
- Bryce A. Manso
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alessandra Rodriguez y Baena
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Program in Biomedical Sciences and Engineering, Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - E. Camilla Forsberg
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| |
Collapse
|
4
|
Hu J, Yang F, Liu C, Wang N, Xiao Y, Zhai Y, Wang X, Zhang R, Gao L, Xu M, Wang J, Liu Z, Huang S, Liu W, Hu Y, Liu F, Guo Y, Wang L, Yuan J, Zhang Z, Chu J. UFObow: A single-wavelength excitable Brainbow for simultaneous multicolor ex-vivo and in-vivo imaging of mammalian cells. Commun Biol 2024; 7:394. [PMID: 38561421 PMCID: PMC10984974 DOI: 10.1038/s42003-024-06062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Brainbow is a genetic cell-labeling technique that allows random colorization of multiple cells and real-time visualization of cell fate within a tissue, providing valuable insights into understanding complex biological processes. However, fluorescent proteins (FPs) in Brainbow have distinct excitation spectra with peak difference greater than 35 nm, which requires sequential imaging under multiple excitations and thus leads to long acquisition times. In addition, they are not easily used together with other fluorophores due to severe spectral bleed-through. Here, we report the development of a single-wavelength excitable Brainbow, UFObow, incorporating three newly developed blue-excitable FPs. We have demonstrated that UFObow enables not only tracking the growth dynamics of tumor cells in vivo but also mapping spatial distribution of immune cells within a sub-cubic centimeter tissue, revealing cell heterogeneity. This provides a powerful means to explore complex biology in a simultaneous imaging manner at a single-cell resolution in organs or in vivo.
Collapse
Affiliation(s)
- Jiahong Hu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fangfang Yang
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chong Liu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Nengzhi Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yinghan Xiao
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yujie Zhai
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xinru Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ren Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Lulu Gao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Mengli Xu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Jialu Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zheng Liu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Songlin Huang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Wenfeng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yajing Hu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Feng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yuqi Guo
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Liang Wang
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jing Yuan
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Zhihong Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China.
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen, 518055, China.
| |
Collapse
|
5
|
Davis D, Dovey J, Sagoshi S, Thaweepanyaporn K, Ogawa S, Vasudevan N. Steroid hormone-mediated regulation of sexual and aggressive behaviour by non-genomic signalling. Steroids 2023; 200:109324. [PMID: 37820890 DOI: 10.1016/j.steroids.2023.109324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Sex and aggression are well studied examples of social behaviours that are common to most animals and are mediated by an evolutionary conserved group of interconnected nuclei in the brain called the social behaviour network. Though glucocorticoids and in particular estrogen regulate these social behaviours, their effects in the brain are generally thought to be mediated by genomic signalling, a slow transcriptional regulation mediated by nuclear hormone receptors. In the last decade or so, there has been renewed interest in understanding the physiological significance of rapid, non-genomic signalling mediated by steroids. Though the identity of the membrane hormone receptors that mediate this signalling is not clearly understood and appears to be different in different cell types, such signalling contributes to physiologically relevant behaviours such as sex and aggression. In this short review, we summarise the evidence for this phenomenon in the rodent, by focusing on estrogen and to some extent, glucocorticoid signalling. The use of these signals, in relation to genomic signalling is manifold and ranges from potentiation of transcription to the possible transduction of environmental signals.
Collapse
Affiliation(s)
- DeAsia Davis
- School of Biological Sciences, University of Reading, United Kingdom
| | - Janine Dovey
- School of Biological Sciences, University of Reading, United Kingdom
| | - Shoko Sagoshi
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, United States; Laboratory of Behavioural Neuroendocrinology, University of Tsukuba, Tsukuba, Japan
| | | | - Sonoko Ogawa
- Laboratory of Behavioural Neuroendocrinology, University of Tsukuba, Tsukuba, Japan
| | - Nandini Vasudevan
- School of Biological Sciences, University of Reading, United Kingdom.
| |
Collapse
|
6
|
Thawani A, Maunsell HR, Zhang H, Ankamreddy H, Groves AK. The Foxi3 transcription factor is necessary for the fate restriction of placodal lineages at the neural plate border. Development 2023; 150:dev202047. [PMID: 37756587 PMCID: PMC10617604 DOI: 10.1242/dev.202047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
The Foxi3 transcription factor, expressed in the neural plate border at the end of gastrulation, is necessary for the formation of posterior placodes and is thus important for ectodermal patterning. We have created two knock-in mouse lines expressing GFP or a tamoxifen-inducible Cre recombinase to show that Foxi3 is one of the earliest genes to label the border between the neural tube and epidermis, and that Foxi3-expressing neural plate border progenitors contribute primarily to cranial placodes and epidermis from the onset of expression, but not to the neural crest or neural tube lineages. By simultaneously knocking out Foxi3 in neural plate border cells and following their fates, we show that neural plate border cells lacking Foxi3 contribute to all four lineages of the ectoderm - placodes, epidermis, crest and neural tube. We contrast Foxi3 with another neural plate border transcription factor, Zic5, the progenitors of which initially contribute broadly to all germ layers until gastrulation and gradually become restricted to the neural crest lineage and dorsal neural tube cells. Our study demonstrates that Foxi3 uniquely acts early at the neural plate border to restrict progenitors to a placodal and epidermal fate.
Collapse
Affiliation(s)
- Ankita Thawani
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Helen R. Maunsell
- Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongyuan Zhang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Andrew K. Groves
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
7
|
Daigle N, Duan S, Song H, Lima N, Sontz R, Merchant JL, Sawyer TW. Wide field-of-view fluorescence imaging for organ-level lineage tracing of rare intestinal stem cell populations. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:096004. [PMID: 37711357 PMCID: PMC10499363 DOI: 10.1117/1.jbo.28.9.096004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Significance Lineage tracing using fluorescent reporters is a common tool for monitoring the expression of genes and transcription factors in stem cell populations and their progeny. The zinc-binding protein 89 (ZBP-89/Zfp148 mouse gene) is a transcription factor that plays a role in gastrointestinal (GI) stem cell maintenance and cellular differentiation and has been linked to the progression of colon cancer. While lineage tracing is a useful tool, it is commonly performed with high-magnification microscopy on a small field of view within tissue sections, thereby limiting the ability to resolve reporter expression at the organ level. Furthermore, this technique requires extensive tissue processing, which is time consuming and requires euthanizing the animal. Further knowledge could be elucidated by measuring the expression of fluorescent reporters across entire organs with minimal tissue processing. Aim We present the application of wide-field fluorescence imaging for whole-organ lineage tracing of an inducible Zfp148-tdTomato-expressing transgenic mouse line to assess the expression of ZBP-89/Zfp148 in the GI tract. Approach We measured tdTomato fluorescence in ex vivo organs at time points between 24 h and 6 months post-induction. Fluctuations in tdTomato expression were validated by fluorescence microscopy of tissue sections. Results Quantification of the wide field-of-view images showed a statistically significant increase in fluorescent signal across the GI tract between transgenic mice and littermate controls. The results also showed a gradient of decreasing reporter expression from proximal to distal intestine, suggesting a higher abundance of ZBP-89 expressing stem cells, or higher expression of ZBP-89 within the stem cells, in the proximal intestine. Conclusions We demonstrate that wide-field fluorescence imaging is a valuable tool for monitoring whole-organ expression of fluorescent reporters. This technique could potentially be applied in vivo for longitudinal assessment of a single animal, further enhancing our ability to resolve rare stem cell lineages spatially and temporally.
Collapse
Affiliation(s)
- Noelle Daigle
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Suzann Duan
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Heyu Song
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Natzem Lima
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Ricky Sontz
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | | | - Travis W. Sawyer
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| |
Collapse
|
8
|
McCarthy M, Dodd WB, Lu X, Pritko DJ, Patel ND, Haskell CV, Sanabria H, Blenner MA, Birtwistle MR. Theory for High-Throughput Genetic Interaction Screening. ACS Synth Biol 2023; 12:2290-2300. [PMID: 37463472 PMCID: PMC10443530 DOI: 10.1021/acssynbio.2c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 07/20/2023]
Abstract
Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼105 spectrally unique, genetically encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
Collapse
Affiliation(s)
- Madeline
E. McCarthy
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Xiaoming Lu
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Daniel J. Pritko
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Nishi D. Patel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Charlotte V. Haskell
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Hugo Sanabria
- Department
of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, United States
| | - Mark A. Blenner
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29631, United States
| |
Collapse
|
9
|
Loder S, Patel N, Morgani S, Sambon M, Leucht P, Levi B. Genetic models for lineage tracing in musculoskeletal development, injury, and healing. Bone 2023; 173:116777. [PMID: 37156345 PMCID: PMC10860167 DOI: 10.1016/j.bone.2023.116777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
Musculoskeletal development and later post-natal homeostasis are highly dynamic processes, marked by rapid structural and functional changes across very short periods of time. Adult anatomy and physiology are derived from pre-existing cellular and biochemical states. Consequently, these early developmental states guide and predict the future of the system as a whole. Tools have been developed to mark, trace, and follow specific cells and their progeny either from one developmental state to the next or between circumstances of health and disease. There are now many such technologies alongside a library of molecular markers which may be utilized in conjunction to allow for precise development of unique cell 'lineages'. In this review, we first describe the development of the musculoskeletal system beginning as an embryonic germ layer and at each of the key developmental stages that follow. We then discuss these structures in the context of adult tissues during homeostasis, injury, and repair. Special focus is given in each of these sections to the key genes involved which may serve as markers of lineage or later in post-natal tissues. We then finish with a technical assessment of lineage tracing and the techniques and technologies currently used to mark cells, tissues, and structures within the musculoskeletal system.
Collapse
Affiliation(s)
- Shawn Loder
- Department of Plastic Surgery, University of Pittsburgh, Scaife Hall, Suite 6B, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Nicole Patel
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | - Benjamin Levi
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
10
|
Stevenson ZC, Moerdyk-Schauwecker MJ, Banse SA, Patel DS, Lu H, Phillips PC. High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS). eLife 2023; 12:RP84831. [PMID: 37401921 PMCID: PMC10328503 DOI: 10.7554/elife.84831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.
Collapse
Affiliation(s)
| | | | - Stephen A Banse
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of OregonEugeneUnited States
| |
Collapse
|
11
|
Hutchison V, Lynch A, Gamez AMG, Chen J. An inducible tricolor reporter mouse for simultaneous imaging of lysosomes, mitochondria and microtubules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541817. [PMID: 37293075 PMCID: PMC10245888 DOI: 10.1101/2023.05.22.541817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cell-type-specific use of the same DNA blueprint generates diverse cell types. Such diversity must also be executed via differential deployment of the same subcellular machinery. However, our understanding of the size, distribution, and dynamics of subcellular machinery in native tissues, and their connection to cellular diversity, remain limited. We generate and characterize an inducible tricolor reporter mouse, dubbed "kaleidoscope", for simultaneous imaging of lysosomes, mitochondria and microtubules in any cell type and at a single cell resolution. The expected subcellular compartments are labeled in culture and in tissues with no impact on cellular and organismal viability. Quantitative and live imaging of the tricolor reporter captures cell-type-specific organelle features and kinetics in the lung, as well as their changes after Sendai virus infection. Yap/Taz mutant lung epithelial cells undergo accelerated lamellar body maturation, a subcellular manifestation of their molecular defects. A comprehensive toolbox of reporters for all subcellular structures is expected to transform our understanding of cell biology in tissues.
Collapse
Affiliation(s)
- Vera Hutchison
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Anne Lynch
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Jichao Chen
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
12
|
Anwar A, Mur M, Humar M. Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications. ACS PHOTONICS 2023; 10:1202-1224. [PMID: 37215324 PMCID: PMC10197175 DOI: 10.1021/acsphotonics.2c01611] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Indexed: 05/24/2023]
Abstract
Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.
Collapse
Affiliation(s)
- Abdur
Rehman Anwar
- Department
of Condensed Matter Physics, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Maruša Mur
- Department
of Condensed Matter Physics, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Matjaž Humar
- Department
of Condensed Matter Physics, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
- CENN
Nanocenter, Jamova 39, SI-1000 Ljubljana, Slovenia
- Faculty
of Mathematics and Physics, University of
Ljubljana, Jadranska
19, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
13
|
Salavaty A, Azadian E, Naik SH, Currie PD. Clonal selection parallels between normal and cancer tissues. Trends Genet 2023; 39:358-380. [PMID: 36842901 DOI: 10.1016/j.tig.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/28/2023]
Abstract
Clonal selection and drift drive both normal tissue and cancer development. However, the biological mechanisms and environmental conditions underpinning these processes remain to be elucidated. Clonal selection models are centered in Darwinian evolutionary theory, where some clones with the fittest features are selected and populate the tissue or tumor. We suggest that different subclasses of stem cells, each of which is responsible for a distinct feature of the selection process, share common features between normal and cancer conditions. While active stem cells populate the tissue, dormant cells account for tissue replenishment/regeneration in both normal and cancerous tissues. We also discuss potential mechanisms that drive clonal drift, their interactions with clonal selection, and their similarities during normal and cancer tissue development.
Collapse
Affiliation(s)
- Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia.
| | - Esmaeel Azadian
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Shalin H Naik
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; EMBL Australia, Monash University, Clayton, VIC 3800, Australia.
| |
Collapse
|
14
|
Single-Cell Labeling Strategies to Dissect Neuronal Structures and Local Functions. BIOLOGY 2023; 12:biology12020321. [PMID: 36829594 PMCID: PMC9953318 DOI: 10.3390/biology12020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
The brain network consists of ten billion neurons and is the most complex structure in the universe. Understanding the structure of complex brain networks and neuronal functions is one of the main goals of modern neuroscience. Since the seminal invention of Golgi staining, single-cell labeling methods have been among the most potent approaches for dissecting neuronal structures and neural circuits. Furthermore, the development of sparse single-cell transgenic methods has enabled single-cell gene knockout studies to examine the local functions of various genes in neural circuits and synapses. Here, we review non-transgenic single-cell labeling methods and recent advances in transgenic strategies for sparse single neuronal labeling. These methods and strategies will fundamentally contribute to the understanding of brain structure and function.
Collapse
|
15
|
Espinosa-Medina I, Feliciano D, Belmonte-Mateos C, Linda Miyares R, Garcia-Marques J, Foster B, Lindo S, Pujades C, Koyama M, Lee T. TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages. Neuron 2023; 111:345-361.e10. [PMID: 36417906 DOI: 10.1016/j.neuron.2022.10.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/15/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022]
Abstract
During development, regulatory factors appear in a precise order to determine cell fates over time. Consequently, to investigate complex tissue development, it is necessary to visualize and manipulate cell lineages with temporal control. Current strategies for tracing vertebrate cell lineages lack genetic access to sequentially produced cells. Here, we present TEMPO (Temporal Encoding and Manipulation in a Predefined Order), an imaging-readable genetic tool allowing differential labeling and manipulation of consecutive cell generations in vertebrates. TEMPO is based on CRISPR and powered by a cascade of gRNAs that drive orderly activation and inactivation of reporters and/or effectors. Using TEMPO to visualize zebrafish and mouse neurogenesis, we recapitulated birth-order-dependent neuronal fates. Temporally manipulating cell-cycle regulators in mouse cortex progenitors altered the proportion and distribution of neurons and glia, revealing the effects of temporal gene perturbation on serial cell fates. Thus, TEMPO enables sequential manipulation of molecular factors, crucial to study cell-type specification.
Collapse
Affiliation(s)
| | - Daniel Feliciano
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Carla Belmonte-Mateos
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, PRBB, Barcelona 08003, Spain
| | - Rosa Linda Miyares
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jorge Garcia-Marques
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid 28049, Spain
| | - Benjamin Foster
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sarah Lindo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Cristina Pujades
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, PRBB, Barcelona 08003, Spain
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Tzumin Lee
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| |
Collapse
|
16
|
Abstract
In this series of papers on light microscopy imaging, we have covered the fundamentals of microscopy, super-resolution microscopy, and lightsheet microscopy. This last review covers multi-photon microscopy with a brief reference to intravital imaging and Brainbow labeling. Multi-photon microscopy is often referred to as two-photon microscopy. Indeed, using two-photon microscopy is by far the most common way of imaging thick tissues; however, it is theoretically possible to use a higher number of photons, and three-photon microscopy is possible. Therefore, this review is titled "multi-photon microscopy." Another term for describing multi-photon microscopy is "non-linear" microscopy because fluorescence intensity at the focal spot depends upon the average squared intensity rather than the squared average intensity; hence, non-linear optics (NLO) is an alternative name for multi-photon microscopy. It is this non-linear relationship (or third exponential power in the case of three-photon excitation) that determines the axial optical sectioning capability of multi-photon imaging. In this paper, the necessity for two-photon or multi-photon imaging is explained, and the method of optical sectioning by multi-photon microscopy is described. Advice is also given on what fluorescent markers to use and other practical aspects of imaging thick tissues. The technique of Brainbow imaging is discussed. The review concludes with a description of intravital imaging of the mouse. © 2023 Wiley Periodicals LLC.
Collapse
|
17
|
Niu H, Li H, Guan Y, Zhou X, Li Z, Zhao SL, Chen P, Tan T, Zhu H, Bergdall V, Xu X, Ma J, Guan J. Sustained delivery of rhMG53 promotes diabetic wound healing and hair follicle development. Bioact Mater 2022; 18:104-115. [PMID: 35387169 PMCID: PMC8961467 DOI: 10.1016/j.bioactmat.2022.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 12/26/2022] Open
Abstract
MG53 is an essential component of the cell membrane repair machinery, participating in the healing of dermal wounds. Here we develop a novel delivery system using recombinant human MG53 (rhMG53) protein and a reactive oxygen species (ROS)-scavenging gel to treat diabetic wounds. Mice with ablation of MG53 display defective hair follicle structure, and topical application of rhMG53 can promote hair growth in the mg53 -/- mice. Cell lineage tracing studies reveal a physiological function of MG53 in modulating the proliferation of hair follicle stem cells (HFSCs). We find that rhMG53 protects HFSCs from oxidative stress-induced apoptosis and stimulates differentiation of HSFCs into keratinocytes. The cytoprotective function of MG53 is mediated by STATs and MAPK signaling in HFSCs. The thermosensitive ROS-scavenging gel encapsulated with rhMG53 allows for sustained release of rhMG53 and promotes healing of chronic cutaneous wounds and hair follicle development in the db/db mice. These findings support the potential therapeutic value of using rhMG53 in combination with ROS-scavenging gel to treat diabetic wounds.
Collapse
Affiliation(s)
- Hong Niu
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Haichang Li
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Ya Guan
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Xin Zhou
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.,Laboratory of Cell Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Zhongguang Li
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Serana Li Zhao
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peng Chen
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Tao Tan
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Hua Zhu
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Valerie Bergdall
- Department of Veterinary Preventive Medicine, University Laboratory Animals Resources, The Ohio State University, Columbus, OH, 43210, USA
| | - Xuehong Xu
- Laboratory of Cell Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, 710062, China
| | - Jianjie Ma
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Jianjun Guan
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| |
Collapse
|
18
|
Chen C, Liao Y, Peng G. Connecting past and present: single-cell lineage tracing. Protein Cell 2022; 13:790-807. [PMID: 35441356 PMCID: PMC9237189 DOI: 10.1007/s13238-022-00913-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/06/2022] [Indexed: 01/16/2023] Open
Abstract
Central to the core principle of cell theory, depicting cells’ history, state and fate is a fundamental goal in modern biology. By leveraging clonal analysis and single-cell RNA-seq technologies, single-cell lineage tracing provides new opportunities to interrogate both cell states and lineage histories. During the past few years, many strategies to achieve lineage tracing at single-cell resolution have been developed, and three of them (integration barcodes, polylox barcodes, and CRISPR barcodes) are noteworthy as they are amenable in experimentally tractable systems. Although the above strategies have been demonstrated in animal development and stem cell research, much care and effort are still required to implement these methods. Here we review the development of single-cell lineage tracing, major characteristics of the cell barcoding strategies, applications, as well as technical considerations and limitations, providing a guide to choose or improve the single-cell barcoding lineage tracing.
Collapse
Affiliation(s)
- Cheng Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yuanxin Liao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangdun Peng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
19
|
Procyk CA, Rodgers J, Zindy E, Lucas RJ, Milosavljevic N. Quantitative characterisation of ipRGCs in retinal degeneration using a computation platform for extracting and reconstructing single neurons in 3D from a multi-colour labeled population. Front Cell Neurosci 2022; 16:1009321. [PMID: 36385954 PMCID: PMC9664085 DOI: 10.3389/fncel.2022.1009321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Light has a profound impact on mammalian physiology and behavior. Intrinsically photosensitive retinal ganglion cells (ipRGCs) express the photopigment melanopsin, rendering them sensitive to light, and are involved in both image-forming vision and non-image forming responses to light such as circadian photo-entrainment and the pupillary light reflex. Following outer photoreceptor degeneration, the death of rod and cone photoreceptors results in global re-modeling of the remnant neural retina. Although ipRGCs can continue signaling light information to the brain even in advanced stages of degeneration, it is unknown if all six morphologically distinct subtypes survive, or how their dendritic architecture may be affected. To answer these questions, we generated a computational platform-BRIAN (Brainbow Analysis of individual Neurons) to analyze Brainbow labeled tissues by allowing objective identification of voxels clusters in Principal Component Space, and their subsequent extraction to produce 3D images of single neurons suitable for analysis with existing tracing technology. We show that BRIAN can efficiently recreate single neurons or individual axonal projections from densely labeled tissue with sufficient anatomical resolution for subtype quantitative classification. We apply this tool to generate quantitative morphological information about ipRGCs in the degenerate retina including soma size, dendritic field size, dendritic complexity, and stratification. Using this information, we were able to identify cells whose characteristics match those reported for all six defined subtypes of ipRGC in the wildtype mouse retina (M1-M6), including the rare and complex M3 and M6 subtypes. This indicates that ipRGCs survive outer retinal degeneration with broadly normal morphology. We additionally describe one cell in the degenerate retina which matches the description of the Gigantic M1 cell in Humans which has not been previously identified in rodent.
Collapse
Affiliation(s)
- Christopher A. Procyk
- Ocular Cell and Gene Therapy Group, Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Jessica Rodgers
- Faculty of Biology Medicine and Health, Centre for Biological Timing and Division of Neuroscience, University of Manchester, Manchester, United Kingdom
| | - Egor Zindy
- Centre for Microscopy and Molecular Imaging, Université Libre de Bruxelles, Brussels, Belgium
| | - Robert J. Lucas
- Faculty of Biology Medicine and Health, Centre for Biological Timing and Division of Neuroscience, University of Manchester, Manchester, United Kingdom
| | - Nina Milosavljevic
- Faculty of Biology Medicine and Health, Centre for Biological Timing and Division of Neuroscience, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
20
|
Caviglia S, Unterweger IA, Gasiūnaitė A, Vanoosthuyse AE, Cutrale F, Trinh LA, Fraser SE, Neuhauss SCF, Ober EA. FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish. Development 2022; 149:276363. [DOI: 10.1242/dev.199615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Visualizing cell shapes and interactions of differentiating cells is instrumental for understanding organ development and repair. Across species, strategies for stochastic multicolour labelling have greatly facilitated in vivo cell tracking and mapping neuronal connectivity. Yet integrating multi-fluorophore information into the context of developing zebrafish tissues is challenging given their cytoplasmic localization and spectral incompatibility with common fluorescent markers. Inspired by Drosophila Raeppli, we developed FRaeppli (Fish-Raeppli) by expressing bright membrane- or nuclear-targeted fluorescent proteins for efficient cell shape analysis and tracking. High spatiotemporal activation flexibility is provided by the Gal4/UAS system together with Cre/lox and/or PhiC31 integrase. The distinct spectra of the FRaeppli fluorescent proteins allow simultaneous imaging with GFP and infrared subcellular reporters or tissue landmarks. We demonstrate the suitability of FRaeppli for live imaging of complex internal organs, such as the liver, and have tailored hyperspectral protocols for time-efficient acquisition. Combining FRaeppli with polarity markers revealed previously unknown canalicular topologies between differentiating hepatocytes, reminiscent of the mammalian liver, suggesting common developmental mechanisms. The multispectral FRaeppli toolbox thus enables the comprehensive analysis of intricate cellular morphologies, topologies and lineages at single-cell resolution in zebrafish.
Collapse
Affiliation(s)
- Sara Caviglia
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Iris A. Unterweger
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Akvilė Gasiūnaitė
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Alexandre E. Vanoosthuyse
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Stephan C. F. Neuhauss
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Elke A. Ober
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| |
Collapse
|
21
|
Liu B, Jing Z, Zhang X, Chen Y, Mao S, Kaundal R, Zou Y, Wei G, Zang Y, Wang X, Lin W, Di M, Sun Y, Chen Q, Li Y, Xia J, Sun J, Lin CP, Huang X, Chi T. Large-scale multiplexed mosaic CRISPR perturbation in the whole organism. Cell 2022; 185:3008-3024.e16. [PMID: 35870449 DOI: 10.1016/j.cell.2022.06.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/23/2022] [Accepted: 06/20/2022] [Indexed: 12/13/2022]
Abstract
Here, we report inducible mosaic animal for perturbation (iMAP), a transgenic platform enabling in situ CRISPR targeting of at least 100 genes in parallel throughout the mouse body. iMAP combines Cre-loxP and CRISPR-Cas9 technologies and utilizes a germline-transmitted transgene carrying a large array of individually floxed, tandemly linked gRNA-coding units. Cre-mediated recombination triggers expression of all the gRNAs in the array but only one of them per cell, converting the mice to mosaic organisms suitable for phenotypic characterization and also for high-throughput derivation of conventional single-gene perturbation lines via breeding. Using gRNA representation as a readout, we mapped a miniature Perturb-Atlas cataloging the perturbations of 90 genes across 39 tissues, which yields rich insights into context-dependent gene functions and provides a glimpse of the potential of iMAP in genome decoding.
Collapse
Affiliation(s)
- Bo Liu
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhengyu Jing
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaoming Zhang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuxin Chen
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shaoshuai Mao
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ravinder Kaundal
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
| | - Yan Zou
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ge Wei
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ying Zang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xinxin Wang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenyang Lin
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Minghui Di
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiwen Sun
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qin Chen
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yongqin Li
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Xia
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jianlong Sun
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chao-Po Lin
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xingxu Huang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tian Chi
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA.
| |
Collapse
|
22
|
Hilzenrat G, Gill ET, McArthur SL. Imaging approaches for monitoring three-dimensional cell and tissue culture systems. JOURNAL OF BIOPHOTONICS 2022; 15:e202100380. [PMID: 35357086 DOI: 10.1002/jbio.202100380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The past decade has seen an increasing demand for more complex, reproducible and physiologically relevant tissue cultures that can mimic the structural and biological features of living tissues. Monitoring the viability, development and responses of such tissues in real-time are challenging due to the complexities of cell culture physical characteristics and the environments in which these cultures need to be maintained in. Significant developments in optics, such as optical manipulation, improved detection and data analysis, have made optical imaging a preferred choice for many three-dimensional (3D) cell culture monitoring applications. The aim of this review is to discuss the challenges associated with imaging and monitoring 3D tissues and cell culture, and highlight topical label-free imaging tools that enable bioengineers and biophysicists to non-invasively characterise engineered living tissues.
Collapse
Affiliation(s)
- Geva Hilzenrat
- Bioengineering Engineering Group, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria, Australia
| | - Emma T Gill
- Bioengineering Engineering Group, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria, Australia
| | - Sally L McArthur
- Bioengineering Engineering Group, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton, Victoria, Australia
| |
Collapse
|
23
|
Skuhersky M, Wu T, Yemini E, Nejatbakhsh A, Boyden E, Tegmark M. Toward a more accurate 3D atlas of C. elegans neurons. BMC Bioinformatics 2022; 23:195. [PMID: 35643434 PMCID: PMC9145532 DOI: 10.1186/s12859-022-04738-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas” of labeled neuronal positions and other identifying characteristics. Previous analyses of such C. elegans datasets have been hampered by the limited accuracy of such atlases, especially for neurons present in the ventral nerve cord, and also by time-consuming manual elements of the alignment process.
Results
We present a novel automated alignment method for sparse and incomplete point clouds of the sort resulting from typical C. elegans fluorescence microscopy datasets. This method involves a tunable learning parameter and a kernel that enforces biologically realistic deformation. We also present a pipeline for creating alignment atlases from datasets of the recently developed NeuroPAL transgene. In combination, these advances allow us to label neurons in volumetric images with confidence much higher than previous methods.
Conclusions
We release, to the best of our knowledge, the most complete full-body C. elegans 3D positional neuron atlas, incorporating positional variability derived from at least 7 animals per neuron, for the purposes of cell-type identity prediction for myriad applications (e.g., imaging neuronal activity, gene expression, and cell-fate).
Collapse
|
24
|
Phillips S, Ramos PV, Veeraraghavan P, Young SM. VikAD, a Vika site-specific recombinase-based system for efficient and scalable helper-dependent adenovirus production. Mol Ther Methods Clin Dev 2022; 24:117-126. [PMID: 35024378 PMCID: PMC8718833 DOI: 10.1016/j.omtm.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/04/2021] [Indexed: 11/09/2022]
Abstract
Recombinant viral vectors have become integral tools for basic in vivo research applications. Helper-dependent adenoviral (HdAd) vectors have a large packaging capacity of ∼36 kb of DNA that mediate long-term transgene expression in vitro and in vivo. The large carrying capacity of HdAd enables basic research or clinical applications requiring the delivery of large genes or multiple transgenes, which cannot be packaged into other widely used viral vectors. Currently, common HdAd production systems use an Ad helper virus (HV) with a packaging signal (Ψ) that is flanked by either loxP or FRT sites, which is excised in producer cells expressing Cre or Flp recombinases to prevent HV packaging. However, these production systems prevent the use of HdAd vectors for genetic strategies that rely on Cre or Flp recombination for cell-type-specific expression. To overcome these limitations, we developed the VikAD production system, which is based on producer cells expressing the Vika recombinase and an HV that contains a Ψ flanked by vox sites. The availability of this production system will greatly expand the utility and flexibility of HdAd vectors for use in research applications to monitor and manipulate cellular activity with increased specificity.
Collapse
Affiliation(s)
- Stacia Phillips
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Paula Valino Ramos
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Priyadharishini Veeraraghavan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Samuel M. Young
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
- Department of Otolaryngology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| |
Collapse
|
25
|
Bonilla-Pons SÀ, Nakagawa S, Bahima EG, Fernández-Blanco Á, Pesaresi M, D'Antin JC, Sebastian-Perez R, Greco D, Domínguez-Sala E, Gómez-Riera R, Compte RIB, Dierssen M, Pulido NM, Cosma MP. Müller glia fused with adult stem cells undergo neural differentiation in human retinal models. EBioMedicine 2022; 77:103914. [PMID: 35278743 PMCID: PMC8917309 DOI: 10.1016/j.ebiom.2022.103914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 12/15/2022] Open
Abstract
Background Visual impairments are a critical medical hurdle to be addressed in modern society. Müller glia (MG) have regenerative potential in the retina in lower vertebrates, but not in mammals. However, in mice, in vivo cell fusion between MG and adult stem cells forms hybrids that can partially regenerate ablated neurons. Methods We used organotypic cultures of human retina and preparations of dissociated cells to test the hypothesis that cell fusion between human MG and adult stem cells can induce neuronal regeneration in human systems. Moreover, we established a microinjection system for transplanting human retinal organoids to demonstrate hybrid differentiation. Findings We first found that cell fusion occurs between MG and adult stem cells, in organotypic cultures of human retina as well as in cell cultures. Next, we showed that the resulting hybrids can differentiate and acquire a proto-neural electrophysiology profile when the Wnt/beta-catenin pathway is activated in the adult stem cells prior fusion. Finally, we demonstrated the engraftment and differentiation of these hybrids into human retinal organoids. Interpretation We show fusion between human MG and adult stem cells, and demonstrate that the resulting hybrid cells can differentiate towards neural fate in human model systems. Our results suggest that cell fusion-mediated therapy is a potential regenerative approach for treating human retinal dystrophies. Funding This work was supported by La Caixa Health (HR17-00231), Velux Stiftung (976a) and the Ministerio de Ciencia e Innovación, (BFU2017-86760-P) (AEI/FEDER, UE), AGAUR (2017 SGR 689, 2017 SGR 926).
Collapse
Affiliation(s)
- Sergi Àngel Bonilla-Pons
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain; Universitat de Barcelona (UB), Barcelona, Spain
| | - Shoma Nakagawa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Elena Garreta Bahima
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Álvaro Fernández-Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martina Pesaresi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Justin Christopher D'Antin
- Centro de Oftalmología Barraquer, Barcelona, Spain; Institut Universitari Barraquer, Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Ruben Sebastian-Perez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Daniela Greco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eduardo Domínguez-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Raúl Gómez-Riera
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Rafael Ignacio Barraquer Compte
- Centro de Oftalmología Barraquer, Barcelona, Spain; Institut Universitari Barraquer, Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Biomedical Research Networking Centre On Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
| | - Nuria Montserrat Pulido
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell an Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, Guangzhou 510530, China.
| |
Collapse
|
26
|
Sneve MA, Piatkevich KD. Towards a Comprehensive Optical Connectome at Single Synapse Resolution via Expansion Microscopy. Front Synaptic Neurosci 2022; 13:754814. [PMID: 35115916 PMCID: PMC8803729 DOI: 10.3389/fnsyn.2021.754814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/17/2021] [Indexed: 12/04/2022] Open
Abstract
Mapping and determining the molecular identity of individual synapses is a crucial step towards the comprehensive reconstruction of neuronal circuits. Throughout the history of neuroscience, microscopy has been a key technology for mapping brain circuits. However, subdiffraction size and high density of synapses in brain tissue make this process extremely challenging. Electron microscopy (EM), with its nanoscale resolution, offers one approach to this challenge yet comes with many practical limitations, and to date has only been used in very small samples such as C. elegans, tadpole larvae, fruit fly brain, or very small pieces of mammalian brain tissue. Moreover, EM datasets require tedious data tracing. Light microscopy in combination with tissue expansion via physical magnification-known as expansion microscopy (ExM)-offers an alternative approach to this problem. ExM enables nanoscale imaging of large biological samples, which in combination with multicolor neuronal and synaptic labeling offers the unprecedented capability to trace and map entire neuronal circuits in fully automated mode. Recent advances in new methods for synaptic staining as well as new types of optical molecular probes with superior stability, specificity, and brightness provide new modalities for studying brain circuits. Here we review advanced methods and molecular probes for fluorescence staining of the synapses in the brain that are compatible with currently available expansion microscopy techniques. In particular, we will describe genetically encoded probes for synaptic labeling in mice, zebrafish, Drosophila fruit flies, and C. elegans, which enable the visualization of post-synaptic scaffolds and receptors, presynaptic terminals and vesicles, and even a snapshot of the synaptic activity itself. We will address current methods for applying these probes in ExM experiments, as well as appropriate vectors for the delivery of these molecular constructs. In addition, we offer experimental considerations and limitations for using each of these tools as well as our perspective on emerging tools.
Collapse
Affiliation(s)
- Madison A Sneve
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| |
Collapse
|
27
|
Hickey SM, Ung B, Bader C, Brooks R, Lazniewska J, Johnson IRD, Sorvina A, Logan J, Martini C, Moore CR, Karageorgos L, Sweetman MJ, Brooks DA. Fluorescence Microscopy-An Outline of Hardware, Biological Handling, and Fluorophore Considerations. Cells 2021; 11:35. [PMID: 35011596 PMCID: PMC8750338 DOI: 10.3390/cells11010035] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
Fluorescence microscopy has become a critical tool for researchers to understand biological processes at the cellular level. Micrographs from fixed and live-cell imaging procedures feature in a plethora of scientific articles for the field of cell biology, but the complexities of fluorescence microscopy as an imaging tool can sometimes be overlooked or misunderstood. This review seeks to cover the three fundamental considerations when designing fluorescence microscopy experiments: (1) hardware availability; (2) amenability of biological models to fluorescence microscopy; and (3) suitability of imaging agents for intended applications. This review will help equip the reader to make judicious decisions when designing fluorescence microscopy experiments that deliver high-resolution and informative images for cell biology.
Collapse
Affiliation(s)
- Shane M. Hickey
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
| | - Ben Ung
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Li Y, Walker LA, Zhao Y, Edwards EM, Michki NS, Cheng HPJ, Ghazzi M, Chen TY, Chen M, Roossien DH, Cai D. Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains. Front Neural Circuits 2021; 15:732183. [PMID: 34744636 PMCID: PMC8564373 DOI: 10.3389/fncir.2021.732183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying the cellular origins and mapping the dendritic and axonal arbors of neurons have been century old quests to understand the heterogeneity among these brain cells. Current Brainbow based transgenic animals take the advantage of multispectral labeling to differentiate neighboring cells or lineages, however, their applications are limited by the color capacity. To improve the analysis throughput, we designed Bitbow, a digital format of Brainbow which exponentially expands the color palette to provide tens of thousands of spectrally resolved unique labels. We generated transgenic Bitbow Drosophila lines, established statistical tools, and streamlined sample preparation, image processing, and data analysis pipelines to conveniently mapping neural lineages, studying neuronal morphology and revealing neural network patterns with unprecedented speed, scale, and resolution.
Collapse
Affiliation(s)
- Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Logan A Walker
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States
| | - Yimeng Zhao
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Erica M Edwards
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nigel S Michki
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States
| | - Hon Pong Jimmy Cheng
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Marya Ghazzi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Tiffany Y Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Maggie Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Douglas H Roossien
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States.,Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
29
|
Mantesso A, Zhang Z, Warner KA, Herzog AE, Pulianmackal AJ, Nör JE. Pulpbow: A Method to Study the Vasculogenic Potential of Mesenchymal Stem Cells from the Dental Pulp. Cells 2021; 10:2804. [PMID: 34831027 PMCID: PMC8616523 DOI: 10.3390/cells10112804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/06/2023] Open
Abstract
Understanding how Mesenchymal Stem Cells (MSCs) form blood vessels is critical for creating mechanism-based approaches for the therapeutic use of these cells. In addition, understanding the determinants and factors involved in lineage hierarchy is fundamental to creating accurate and reliable techniques for the study of stem cells in tissue engineering and repair. Dental Pulp Stem Cells (DPSC) from permanent teeth and Stem cells from Human Exfoliated Deciduous teeth (SHED) are particularly interesting sources for tissue engineering as they are easily accessible and expandable. Previously, we have shown that DPSCs and SHEDs can differentiate into endothelial cells and form functional blood vessels through vasculogenesis. Here, we described how we created the "pulpbow" (pulp + rainbow), a multicolor tag experimental model that is stable, permanent, unique to each cell and passed through generations. We used the pulpbow to understand how dental pulp stem cells contributed to blood vessel formation in 3D models in in vitro and ex vivo live cell tracking, and in vivo transplantation assays. Simultaneous tracking of cells during sprout formation revealed that no single multicolor-tagged cell was more prone to vasculogenesis. During this process, there was intense cell motility with minimal proliferation in early time points. In later stages, when the availability of undifferentiated cells around the forming sprout decreased, there was local clonal proliferation mediated by proximity. These results unveiled that the vasculogenesis process mediated by dental pulp stem cells is dynamic and proximity to the sprouting area is critical for cell fate decisions.
Collapse
Affiliation(s)
- Andrea Mantesso
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA; (A.M.); (Z.Z.); (K.A.W.); (A.E.H.)
| | - Zhaocheng Zhang
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA; (A.M.); (Z.Z.); (K.A.W.); (A.E.H.)
| | - Kristy A. Warner
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA; (A.M.); (Z.Z.); (K.A.W.); (A.E.H.)
| | - Alexandra E. Herzog
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA; (A.M.); (Z.Z.); (K.A.W.); (A.E.H.)
| | - Ajai J. Pulianmackal
- Department of Molecular, Cellular and Developmental Biology, University of Michigan College of Literature, Science and the Arts, Ann Arbor, MI 48109, USA;
| | - Jacques E. Nör
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA; (A.M.); (Z.Z.); (K.A.W.); (A.E.H.)
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
- Department of Otolaryngology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| |
Collapse
|
30
|
Tanaka K, Tanaka J, Aizawa R, Kato-Tanaka M, Ueno H, Mishima K, Yamamoto M. Structure of junctional epithelium is maintained by cell populations supplied from multiple stem cells. Sci Rep 2021; 11:18860. [PMID: 34552180 PMCID: PMC8458500 DOI: 10.1038/s41598-021-98398-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/31/2021] [Indexed: 11/09/2022] Open
Abstract
The junctional epithelium (JE) is an epithelial component that attaches directly to the tooth surface and performs the unique function of protecting against bacterial infections; its destruction causes inflammation of the periodontal tissue and loss of alveolar bone. A recent study that used the single-color lineage tracing method reported that JE is maintained by its stem cells. However, the process by which individual stem cells form the entire JE around a whole tooth remains unclear. Using a 4-color lineage tracing method, we performed a detailed examination of the dynamics of individual stem cells that constitute the entire JE. The multicolor lineage tracing method showed that single-color areas, which were derived from each cell color, replaced all the constituent JE cells 168 d after the administration of tamoxifen. The horizontal section of the first molar showed that the single-color areas in the JE expanded widely. We detected putative stem cells at the external basal layer farthest from the enamel. In this study, JE cells that were supplied from different stem cells were visualized as individual monochromatic regions, and the JE around the first molar was maintained by several JE-specific stem cells. These findings indicated that the JE consisted of several cell populations that were supplied from their multiple stem cells and could help to explore the mechanisms involved in periodontal tissue homeostasis.
Collapse
Affiliation(s)
- Keisuke Tanaka
- Department of Periodontology, Showa University School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Junichi Tanaka
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Ryo Aizawa
- Department of Periodontology, Showa University School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
| | - Mayu Kato-Tanaka
- Department of Periodontology, Showa University School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
| | - Hiroo Ueno
- Department of Stem Cell Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Matsuo Yamamoto
- Department of Periodontology, Showa University School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan.
| |
Collapse
|
31
|
Zhu J, Liu X, Deng Y, Li D, Yu T, Zhu D. Tissue optical clearing for 3D visualization of vascular networks: A review. Vascul Pharmacol 2021; 141:106905. [PMID: 34506969 DOI: 10.1016/j.vph.2021.106905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022]
Abstract
Reconstruction of the vasculature of intact tissues/organs down to the capillary level is essential for understanding the development and remodeling of vascular networks under physiological and pathological conditions. Optical imaging techniques can provide sufficient resolution to distinguish small vessels with several microns, but the imaging depth is somewhat limited due to the high light scattering of opaque tissue. Recently, various tissue optical clearing methods have been developed to overcome light attenuation and improve the imaging depth both for ex-vivo and in-vivo visualizations. Tissue clearing combined with vessel labeling techniques and advanced optical tomography enables successful mapping of the vasculature of different tissues/organs, as well as dynamically monitoring vessel function under normal and pathological conditions. Here, we briefly introduce the commonly-used labeling strategies for entire vascular networks, the current tissue optical clearing techniques available for various tissues, as well as the advanced optical imaging techniques for fast, high-resolution structural and functional imaging for blood vessels. We also discuss the applications of these techniques in the 3D visualization of vascular networks in normal tissues, and the vascular remodeling in several typical pathological models in clinical research. This review is expected to provide valuable insights for researchers to study the potential mechanisms of various vessel-associated diseases using tissue optical clearing pipeline.
Collapse
Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| |
Collapse
|
32
|
Wolf S, Wan Y, McDole K. Current approaches to fate mapping and lineage tracing using image data. Development 2021; 148:dev198994. [PMID: 34498046 DOI: 10.1242/dev.198994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visualizing, tracking and reconstructing cell lineages in developing embryos has been an ongoing effort for well over a century. Recent advances in light microscopy, labelling strategies and computational methods to analyse complex image datasets have enabled detailed investigations into the fates of cells. Combined with powerful new advances in genomics and single-cell transcriptomics, the field of developmental biology is able to describe the formation of the embryo like never before. In this Review, we discuss some of the different strategies and applications to lineage tracing in live-imaging data and outline software methodologies that can be applied to various cell-tracking challenges.
Collapse
Affiliation(s)
- Steffen Wolf
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yinan Wan
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Katie McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| |
Collapse
|
33
|
Dujardin P, Baginska AK, Urban S, Grüner BM. Unraveling Tumor Heterogeneity by Using DNA Barcoding Technologies to Develop Personalized Treatment Strategies in Advanced-Stage PDAC. Cancers (Basel) 2021; 13:4187. [PMID: 34439341 PMCID: PMC8394487 DOI: 10.3390/cancers13164187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 12/14/2022] Open
Abstract
Tumor heterogeneity is a hallmark of many solid tumors, including pancreatic ductal adenocarcinoma (PDAC), and an inherent consequence of the clonal evolution of cancers. As such, it is considered the underlying concept of many characteristics of the disease, including the ability to metastasize, adapt to different microenvironments, and to develop therapy resistance. Undoubtedly, the high mortality of PDAC can be attributed to a high extent to these properties. Despite its apparent importance, studying tumor heterogeneity has been a challenging task, mainly due to its complexity and lack of appropriate methods. However, in recent years molecular DNA barcoding has emerged as a sophisticated tool that allows mapping of individual cells or subpopulations in a cell pool to study heterogeneity and thus devise new personalized treatment strategies. In this review, we provide an overview of genetic and non-genetic inter- and intra-tumor heterogeneity and its impact on (personalized) treatment strategies in PDAC and address how DNA barcoding technologies work and can be applied to study this clinically highly relevant question.
Collapse
Affiliation(s)
- Philip Dujardin
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
| | - Anna K. Baginska
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
| | - Sebastian Urban
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
| | - Barbara M. Grüner
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen at the University Duisburg-Essen, 45147 Essen, Germany; (A.K.B.); (S.U.)
- German Cancer Consortium (DKTK) Partner Site Essen/Düsseldorf, 45147 Essen, Germany
| |
Collapse
|
34
|
Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martínez I, Zhang H, Chow KHK, Kwak IY, Retkute R, Prusokiene A, Prusokas A, Khodaverdian A, Zhang R, Rao S, Wang R, Rennert P, Saipradeep VG, Sivadasan N, Rao A, Joseph T, Srinivasan R, Peng J, Han L, Shang X, Garry DJ, Yu T, Chung V, Mason M, Liu Z, Guan Y, Yosef N, Shendure J, Telford MJ, Shapiro E, Elowitz MB, Meyer P. Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees. Cell Syst 2021; 12:810-826.e4. [PMID: 34146472 DOI: 10.1016/j.cels.2021.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 12/20/2022]
Abstract
The recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve the ones of more complex organisms. To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells. To benchmark such methods, we decided to organize a DREAM challenge using in vitro experimental intMEMOIR recordings and in silico data for a C. elegans lineage tree of about 1,000 cells and a Mus musculus tree of 10,000 cells. Some of the 22 approaches submitted had excellent performance, but structural features of the trees prevented optimal reconstructions. Using smaller sub-trees as training sets proved to be a good approach for tuning algorithms to reconstruct larger trees. The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.
Collapse
Affiliation(s)
- Wuming Gong
- Lillehei Heart Institute, University of Minnesota, 2231 6th St S.E, 4-165 CCRB, Minneapolis, MN 55114, USA
| | | | - Jingyuan Hu
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew G Jones
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA; Integrative Program of Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Irepan Salvador-Martínez
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Hanrui Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ke-Huan K Chow
- California Institute of Technology, Pasadena, CA 91125, USA
| | - Il-Youp Kwak
- Department of Applied Statistics, College of Business & Economics, Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea
| | - Renata Retkute
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alisa Prusokiene
- School of Natural and Environmental Sciences, Newcastle University, Newcastle NE1 7RU, UK
| | | | - Alex Khodaverdian
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Richard Zhang
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Suhas Rao
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Wang
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Phil Rennert
- EC Wise Inc., 1299 4th St #505, San Rafael, CA 94901, USA
| | | | - Naveen Sivadasan
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Aditya Rao
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Thomas Joseph
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Rajgopal Srinivasan
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Lu Han
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, 2231 6th St S.E, 4-165 CCRB, Minneapolis, MN 55114, USA
| | - Thomas Yu
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA
| | - Verena Chung
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA
| | - Michael Mason
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA
| | - Zhandong Liu
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nir Yosef
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | | | - Pablo Meyer
- T.J. Watson Research Center, IBM, Healthcare & Life Sciences, 1101 Kitchawan Rd 10598, Yorktown Heights, NY 10598, USA.
| |
Collapse
|
35
|
Li CC, Shen Z, Bavarian R, Yang F, Bhattacharya A. Oral Cancer: Genetics and the Role of Precision Medicine. Surg Oncol Clin N Am 2021; 29:127-144. [PMID: 31757309 DOI: 10.1016/j.soc.2019.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is one of the leading cancers in the world. OSCC patients are managed with surgery and/or chemoradiation. Prognoses and survival rates are dismal, however, and have not improved for more than 20 years. Recently, the concept of precision medicine was introduced, and the introduction of targeted therapeutics demonstrated promising outcomes. This article reviews the current understanding of initiation, progression, and metastasis of OSCC from both genetic and epigenetic perspectives. In addition, the applications and integration of omics technologies in biomarker discovery and drug development for treating OSCC are reviewed.
Collapse
Affiliation(s)
- Chia-Cheng Li
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115, USA.
| | - Zhen Shen
- Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115, USA
| | - Roxanne Bavarian
- Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115, USA; Division of Oral Medicine and Dentistry, Brigham and Women's Hospital, Francis Street, Boston, MA 02115, USA
| | - Fan Yang
- Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115, USA
| | - Aditi Bhattacharya
- Department of Oral and Maxillofacial Surgery, NYU College of Dentistry, East 24th Street, New York, NY 10010, USA
| |
Collapse
|
36
|
Lewis SM, Asselin-Labat ML, Nguyen Q, Berthelet J, Tan X, Wimmer VC, Merino D, Rogers KL, Naik SH. Spatial omics and multiplexed imaging to explore cancer biology. Nat Methods 2021; 18:997-1012. [PMID: 34341583 DOI: 10.1038/s41592-021-01203-6] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/04/2021] [Indexed: 01/19/2023]
Abstract
Understanding intratumoral heterogeneity-the molecular variation among cells within a tumor-promises to address outstanding questions in cancer biology and improve the diagnosis and treatment of specific cancer subtypes. Single-cell analyses, especially RNA sequencing and other genomics modalities, have been transformative in revealing novel biomarkers and molecular regulators associated with tumor growth, metastasis and drug resistance. However, these approaches fail to provide a complete picture of tumor biology, as information on cellular location within the tumor microenvironment is lost. New technologies leveraging multiplexed fluorescence, DNA, RNA and isotope labeling enable the detection of tens to thousands of cancer subclones or molecular biomarkers within their native spatial context. The expeditious growth in these techniques, along with methods for multiomics data integration, promises to yield a more comprehensive understanding of cell-to-cell variation within and between individual tumors. Here we provide the current state and future perspectives on the spatial technologies expected to drive the next generation of research and diagnostic and therapeutic strategies for cancer.
Collapse
Affiliation(s)
- Sabrina M Lewis
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marie-Liesse Asselin-Labat
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.,Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Quan Nguyen
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jean Berthelet
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Xiao Tan
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Verena C Wimmer
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Delphine Merino
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Kelly L Rogers
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Shalin H Naik
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.
| |
Collapse
|
37
|
Weaver CJ, Poulain FE. From whole organism to ultrastructure: progress in axonal imaging for decoding circuit development. Development 2021; 148:271122. [PMID: 34328171 DOI: 10.1242/dev.199717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Since the pioneering work of Ramón y Cajal, scientists have sought to unravel the complexities of axon development underlying neural circuit formation. Micrometer-scale axonal growth cones navigate to targets that are often centimeters away. To reach their targets, growth cones react to dynamic environmental cues that change in the order of seconds to days. Proper axon growth and guidance are essential to circuit formation, and progress in imaging has been integral to studying these processes. In particular, advances in high- and super-resolution microscopy provide the spatial and temporal resolution required for studying developing axons. In this Review, we describe how improved microscopy has revolutionized our understanding of axonal development. We discuss how novel technologies, specifically light-sheet and super-resolution microscopy, led to new discoveries at the cellular scale by imaging axon outgrowth and circuit wiring with extreme precision. We next examine how advanced microscopy broadened our understanding of the subcellular dynamics driving axon growth and guidance. We finally assess the current challenges that the field of axonal biology still faces for imaging axons, and examine how future technology could meet these needs.
Collapse
Affiliation(s)
- Cory J Weaver
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Fabienne E Poulain
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| |
Collapse
|
38
|
Brown SDM. Advances in mouse genetics for the study of human disease. Hum Mol Genet 2021; 30:R274-R284. [PMID: 34089057 PMCID: PMC8490014 DOI: 10.1093/hmg/ddab153] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 01/11/2023] Open
Abstract
The mouse is the pre-eminent model organism for studies of mammalian gene function and has provided an extraordinarily rich range of insights into basic genetic mechanisms and biological systems. Over several decades, the characterization of mouse mutants has illuminated the relationship between gene and phenotype, providing transformational insights into the genetic bases of disease. However, if we are to deliver the promise of genomic and precision medicine, we must develop a comprehensive catalogue of mammalian gene function that uncovers the dark genome and elucidates pleiotropy. Advances in large-scale mouse mutagenesis programmes allied to high-throughput mouse phenomics are now addressing this challenge and systematically revealing novel gene function and multi-morbidities. Alongside the development of these pan-genomic mutational resources, mouse genetics is employing a range of diversity resources to delineate gene–gene and gene–environment interactions and to explore genetic context. Critically, mouse genetics is a powerful tool for assessing the functional impact of human genetic variation and determining the causal relationship between variant and disease. Together these approaches provide unique opportunities to dissect in vivo mechanisms and systems to understand pathophysiology and disease. Moreover, the provision and utility of mouse models of disease has flourished and engages cumulatively at numerous points across the translational spectrum from basic mechanistic studies to pre-clinical studies, target discovery and therapeutic development.
Collapse
|
39
|
van Gestel J, Wagner A. Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation. PLoS Biol 2021; 19:e3001250. [PMID: 33983920 PMCID: PMC8148357 DOI: 10.1371/journal.pbio.3001250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 05/25/2021] [Accepted: 04/28/2021] [Indexed: 12/20/2022] Open
Abstract
The repeated evolution of multicellularity led to a wide diversity of organisms, many of which are sessile, including land plants, many fungi, and colonial animals. Sessile organisms adhere to a surface for most of their lives, where they grow and compete for space. Despite the prevalence of surface-associated multicellularity, little is known about its evolutionary origin. Here, we introduce a novel theoretical approach, based on spatial lineage tracking of cells, to study this origin. We show that multicellularity can rapidly evolve from two widespread cellular properties: cell adhesion and the regulatory control of adhesion. By evolving adhesion, cells attach to a surface, where they spontaneously give rise to primitive cell collectives that differ in size, life span, and mode of propagation. Selection in favor of large collectives increases the fraction of adhesive cells until a surface becomes fully occupied. Through kin recognition, collectives then evolve a central-peripheral polarity in cell adhesion that supports a division of labor between cells and profoundly impacts growth. Despite this spatial organization, nascent collectives remain cryptic, lack well-defined boundaries, and would require experimental lineage tracking technologies for their identification. Our results suggest that cryptic multicellularity could readily evolve and originate well before multicellular individuals become morphologically evident.
Collapse
Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| |
Collapse
|
40
|
Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O. NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell 2021; 184:272-288.e11. [PMID: 33378642 PMCID: PMC10494711 DOI: 10.1016/j.cell.2020.12.012] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering a multicolor transgene called NeuroPAL (a neuronal polychromatic atlas of landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that resolves all neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. We showcase three applications that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding for these stimuli.
Collapse
Affiliation(s)
- Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Amin Nejatbakhsh
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Erdem Varol
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Ruoxi Sun
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Gonzalo E Mena
- Department of Statistics and Data Science Initiative, Harvard University, Cambridge, MA 02138, USA
| | - Aravinthan D T Samuel
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Liam Paninski
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | | | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| |
Collapse
|
41
|
Zhao J, Lai HM, Qi Y, He D, Sun H. Current Status of Tissue Clearing and the Path Forward in Neuroscience. ACS Chem Neurosci 2021; 12:5-29. [PMID: 33326739 DOI: 10.1021/acschemneuro.0c00563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.
Collapse
Affiliation(s)
- Jiajia Zhao
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuwei Qi
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Dian He
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Haitao Sun
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| |
Collapse
|
42
|
Browne TJ, Hughes DI, Dayas CV, Callister RJ, Graham BA. Projection Neuron Axon Collaterals in the Dorsal Horn: Placing a New Player in Spinal Cord Pain Processing. Front Physiol 2020; 11:560802. [PMID: 33408637 PMCID: PMC7779806 DOI: 10.3389/fphys.2020.560802] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 11/26/2020] [Indexed: 11/13/2022] Open
Abstract
The pain experience depends on the relay of nociceptive signals from the spinal cord dorsal horn to higher brain centers. This function is ultimately achieved by the output of a small population of highly specialized neurons called projection neurons (PNs). Like output neurons in other central nervous system (CNS) regions, PNs are invested with a substantial axon collateral system that ramifies extensively within local circuits. These axon collaterals are widely distributed within and between spinal cord segments. Anatomical data on PN axon collaterals have existed since the time of Cajal, however, their function in spinal pain signaling remains unclear and is absent from current models of spinal pain processing. Despite these omissions, some insight on the potential role of PN axon collaterals can be drawn from axon collateral systems of principal or output neurons in other CNS regions, such as the hippocampus, amygdala, olfactory cortex, and ventral horn of the spinal cord. The connectivity and actions of axon collaterals in these systems have been well-defined and used to confirm crucial roles in memory, fear, olfaction, and movement control, respectively. We review this information here and propose a framework for characterizing PN axon collateral function in the dorsal horn. We highlight that experimental approaches traditionally used to delineate axon collateral function in other CNS regions are not easily applied to PNs because of their scarcity relative to spinal interneurons (INs), and the lack of cellular organization in the dorsal horn. Finally, we emphasize how the rapid development of techniques such as viral expression of optogenetic or chemogenetic probes can overcome these challenges and allow characterization of PN axon collateral function. Obtaining detailed information of this type is a necessary first step for incorporation of PN collateral system function into models of spinal sensory processing.
Collapse
Affiliation(s)
- Tyler J Browne
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW, Australia
| | - David I Hughes
- Institute of Neuroscience Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christopher V Dayas
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW, Australia
| | - Robert J Callister
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW, Australia
| | - Brett A Graham
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW, Australia
| |
Collapse
|
43
|
Kazerouni AS, Gadde M, Gardner A, Hormuth DA, Jarrett AM, Johnson KE, Lima EAF, Lorenzo G, Phillips C, Brock A, Yankeelov TE. Integrating Quantitative Assays with Biologically Based Mathematical Modeling for Predictive Oncology. iScience 2020; 23:101807. [PMID: 33299976 PMCID: PMC7704401 DOI: 10.1016/j.isci.2020.101807] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We provide an overview on the use of biological assays to calibrate and initialize mechanism-based models of cancer phenomena. Although artificial intelligence methods currently dominate the landscape in computational oncology, mathematical models that seek to explicitly incorporate biological mechanisms into their formalism are of increasing interest. These models can guide experimental design and provide insights into the underlying mechanisms of cancer progression. Historically, these models have included a myriad of parameters that have been difficult to quantify in biologically relevant systems, limiting their practical insights. Recently, however, there has been much interest calibrating biologically based models with the quantitative measurements available from (for example) RNA sequencing, time-resolved microscopy, and in vivo imaging. In this contribution, we summarize how a variety of experimental methods quantify tumor characteristics from the molecular to tissue scales and describe how such data can be directly integrated with mechanism-based models to improve predictions of tumor growth and treatment response.
Collapse
Affiliation(s)
- Anum S. Kazerouni
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Manasa Gadde
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrea Gardner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - David A. Hormuth
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
| | - Angela M. Jarrett
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kaitlyn E. Johnson
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ernesto A.B. F. Lima
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Guillermo Lorenzo
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Caleb Phillips
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas E. Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Oncology, The University of Texas at Austin, Austin, TX 78712, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
44
|
Liang Y, Walczak P. Long term intravital single cell tracking under multiphoton microscopy. J Neurosci Methods 2020; 349:109042. [PMID: 33340557 DOI: 10.1016/j.jneumeth.2020.109042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Visualizing and tracking cells over time in a living organism has been a much-coveted dream before the invention of intravital microscopy. The opaque nature of tissue was a major hurdle that was remedied by the multiphoton microscopy. With the advancement of optical imaging and fluorescent labeling tools, intravital high resolution imaging has become increasingly accessible over the past few years. Long-term intravital tracking of single cells (LIST) under multiphoton microscopy provides a unique opportunity to gain insight into the longitudinal changes in the morphology, migration, or function of cells or subcellular structures. It is particularly suitable for studying slow-evolving cellular and molecular events during normal development or disease progression, without losing the opportunity of catching fast events such as calcium signals. Here, we review the application of LIST under 2-photon microscopy in various fields of neurobiology and discuss challenges and new directions in labeling and imaging methods for LIST. Overall, this review provides an overview of current applications of LIST in mammals, which is an emerging field that will contribute to a better understanding of essential molecular and cellular events in health and disease.
Collapse
Affiliation(s)
- Yajie Liang
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Piotr Walczak
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
45
|
Zhang X, Powell K, Li L. Breast Cancer Stem Cells: Biomarkers, Identification and Isolation Methods, Regulating Mechanisms, Cellular Origin, and Beyond. Cancers (Basel) 2020; 12:E3765. [PMID: 33327542 PMCID: PMC7765014 DOI: 10.3390/cancers12123765] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Despite recent advances in diagnosis and treatment, breast cancer (BC) is still a major cause of cancer-related mortality in women. Breast cancer stem cells (BCSCs) are a small but significant subpopulation of heterogeneous breast cancer cells demonstrating strong self-renewal and proliferation properties. Accumulating evidence has proved that BCSCs are the driving force behind BC tumor initiation, progression, metastasis, drug resistance, and recurrence. As a heterogeneous disease, BC contains a full spectrum of different BC subtypes, and different subtypes of BC further exhibit distinct subtypes and proportions of BCSCs, which correspond to different treatment responses and disease-specific outcomes. This review summarized the current knowledge of BCSC biomarkers and their clinical relevance, the methods for the identification and isolation of BCSCs, and the mechanisms regulating BCSCs. We also discussed the cellular origin of BCSCs and the current advances in single-cell lineage tracing and transcriptomics and their potential in identifying the origin and lineage development of BCSCs.
Collapse
Affiliation(s)
- Xiaoli Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210, USA;
| | | | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 320B Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210, USA;
| |
Collapse
|
46
|
The art of lineage tracing: From worm to human. Prog Neurobiol 2020; 199:101966. [PMID: 33249090 DOI: 10.1016/j.pneurobio.2020.101966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022]
Abstract
Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.
Collapse
|
47
|
Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development. Dev Cell 2020; 56:7-21. [PMID: 33217333 DOI: 10.1016/j.devcel.2020.10.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/15/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022]
Abstract
Lineage tracing and fate mapping, overlapping yet distinct disciplines to follow cells and their progeny, have evolved rapidly over the last century. Lineage tracing aims to identify all progeny arising from an individual cell, placing them within a lineage hierarchy. The recent emergence of genomic technologies, such as single-cell and spatial transcriptomics, has fostered sophisticated new methods to reconstruct lineage relationships at high resolution. In contrast, fate maps, schematics showing which parts of the embryo will develop into which tissue, have remained relatively static since the 1970s. However, fate maps provide spatial information, often lost in lineage reconstruction, that can offer fundamental mechanistic insight into development. Here, we broadly review the origins of fate mapping and lineage tracing approaches. We focus on the most recent developments in lineage tracing, permitted by advances in single-cell genomics. Finally, we explore the current potential to leverage these new technologies to synthesize high-resolution fate maps and discuss their potential for interrogating development at new depths.
Collapse
|
48
|
Das RN, Yaniv K. Discovering New Progenitor Cell Populations through Lineage Tracing and In Vivo Imaging. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035618. [PMID: 32041709 DOI: 10.1101/cshperspect.a035618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identification of progenitor cells that generate differentiated cell types during development, regeneration, and disease states is central to understanding the mechanisms governing such transitions. For more than a century, different lineage-tracing strategies have been developed, which helped disentangle the complex relationship between progenitor cells and their progenies. In this review, we discuss how lineage-tracing analyses have evolved alongside technological advances, and how this approach has contributed to the identification of progenitor cells in different contexts of cell differentiation. We also highlight a few examples in which lineage-tracing experiments have been instrumental for resolving long-standing debates and for identifying unexpected cellular origins. This discussion emphasizes how this century-old quest to delineate cellular lineage relationships is still active, and new discoveries are being made with the development of newer methodologies.
Collapse
Affiliation(s)
- Rudra Nayan Das
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
49
|
Wolny A, Cerrone L, Vijayan A, Tofanelli R, Barro AV, Louveaux M, Wenzl C, Strauss S, Wilson-Sánchez D, Lymbouridou R, Steigleder SS, Pape C, Bailoni A, Duran-Nebreda S, Bassel GW, Lohmann JU, Tsiantis M, Hamprecht FA, Schneitz K, Maizel A, Kreshuk A. Accurate and versatile 3D segmentation of plant tissues at cellular resolution. eLife 2020; 9:e57613. [PMID: 32723478 PMCID: PMC7447435 DOI: 10.7554/elife.57613] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on fixed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, acquisition settings even on non plant samples. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface.
Collapse
Affiliation(s)
- Adrian Wolny
- Heidelberg Collaboratory for Image Processing, Heidelberg UniversityHeidelbergGermany
- EMBLHeidelbergGermany
| | - Lorenzo Cerrone
- Heidelberg Collaboratory for Image Processing, Heidelberg UniversityHeidelbergGermany
| | - Athul Vijayan
- School of Life Sciences Weihenstephan, Technical University of MunichFreisingGermany
| | - Rachele Tofanelli
- School of Life Sciences Weihenstephan, Technical University of MunichFreisingGermany
| | | | - Marion Louveaux
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Christian Wenzl
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - David Wilson-Sánchez
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Rena Lymbouridou
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | | | - Constantin Pape
- Heidelberg Collaboratory for Image Processing, Heidelberg UniversityHeidelbergGermany
- EMBLHeidelbergGermany
| | - Alberto Bailoni
- Heidelberg Collaboratory for Image Processing, Heidelberg UniversityHeidelbergGermany
| | | | - George W Bassel
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Jan U Lohmann
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Fred A Hamprecht
- Heidelberg Collaboratory for Image Processing, Heidelberg UniversityHeidelbergGermany
| | - Kay Schneitz
- School of Life Sciences Weihenstephan, Technical University of MunichFreisingGermany
| | - Alexis Maizel
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | | |
Collapse
|
50
|
Site-Specific Recombination with Inverted Target Sites: A Cautionary Tale of Dicentric and Acentric Chromosomes. Genetics 2020; 215:923-930. [PMID: 32586890 DOI: 10.1534/genetics.120.303394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
Site-specific recombinases are widely used tools for analysis of genetics, development, and cell biology, and many schemes have been devised to alter gene expression by recombinase-mediated DNA rearrangements. Because the FRT and lox target sites for the commonly used FLP and Cre recombinases are asymmetrical, and must pair in the same direction to recombine, construct design must take into account orientation of the target sites. Both direct and inverted configurations have been used. However, the outcome of recombination between target sites on sister chromatids is frequently overlooked. This is especially consequential with inverted target sites, where exchange between oppositely oriented target sites on sisters will produce dicentric and acentric chromosomes. By using constructs that have inverted target sites in Drosophila melanogaster and in mice, we show here that dicentric chromosomes are produced in the presence of recombinase, and that the frequency of this event is quite high. The negative effects on cell viability and behavior can be significant, and should be considered when using such constructs.
Collapse
|