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Li Z, Yang W, Wu P, Shan Y, Zhang X, Chen F, Yang J, Yang JR. Reconstructing cell lineage trees with genomic barcoding: approaches and applications. J Genet Genomics 2024; 51:35-47. [PMID: 37269980 DOI: 10.1016/j.jgg.2023.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 06/05/2023]
Abstract
In multicellular organisms, developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree (CLT). The reconstruction of the CLT has long been a major goal in developmental biology and other related fields. Recent technological advancements, especially those in editable genomic barcodes and single-cell high-throughput sequencing, have sparked a new wave of experimental methods for reconstructing CLTs. Here we review the existing experimental approaches to the reconstruction of CLT, which are broadly categorized as either image-based or DNA barcode-based methods. In addition, we present a summary of the related literature based on the biological insight provided by the obtained CLTs. Moreover, we discuss the challenges that will arise as more and better CLT data become available in the near future. Genomic barcoding-based CLT reconstructions and analyses, due to their wide applicability and high scalability, offer the potential for novel biological discoveries, especially those related to general and systemic properties of the developmental process.
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Affiliation(s)
- Zizhang Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wenjing Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Peng Wu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yuyan Shan
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaoyu Zhang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Feng Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Junnan Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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Passman AM, Haughey MJ, Carlotti E, Williams MJ, Cereser B, Lin ML, Devkumar S, Gabriel JP, Gringeri E, Cillo U, Russo FP, Hoare M, ChinAleong J, Jansen M, Wright NA, Kocher HM, Huang W, Alison MR, McDonald SAC. Hepatocytes undergo punctuated expansion dynamics from a periportal stem cell niche in normal human liver. J Hepatol 2023; 79:417-432. [PMID: 37088309 DOI: 10.1016/j.jhep.2023.03.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND & AIMS While normal human liver is thought to be generally quiescent, clonal hepatocyte expansions have been observed, though neither their cellular source nor their expansion dynamics have been determined. Knowing the hepatocyte cell of origin, and their subsequent dynamics and trajectory within the human liver will provide an important basis to understand disease-associated dysregulation. METHODS Herein, we use in vivo lineage tracing and methylation sequence analysis to demonstrate normal human hepatocyte ancestry. We exploit next-generation mitochondrial sequencing to determine hepatocyte clonal expansion dynamics across spatially distinct areas of laser-captured, microdissected, clones, in tandem with computational modelling in morphologically normal human liver. RESULTS Hepatocyte clones and rare SOX9+ hepatocyte progenitors commonly associate with portal tracts and we present evidence that clones can lineage-trace with cholangiocytes, indicating the presence of a bipotential common ancestor at this niche. Within clones, we demonstrate methylation CpG sequence diversity patterns indicative of periportal not pericentral ancestral origins, indicating a portal to central vein expansion trajectory. Using spatial analysis of mitochondrial DNA variants by next-generation sequencing coupled with mathematical modelling and Bayesian inference across the portal-central axis, we demonstrate that patterns of mitochondrial DNA variants reveal large numbers of spatially restricted mutations in conjunction with limited numbers of clonal mutations. CONCLUSIONS These datasets support the existence of a periportal progenitor niche and indicate that clonal patches exhibit punctuated but slow growth, then quiesce, likely due to acute environmental stimuli. These findings crucially contribute to our understanding of hepatocyte dynamics in the normal human liver. IMPACT AND IMPLICATIONS The liver is mainly composed of hepatocytes, but we know little regarding the source of these cells or how they multiply over time within the disease-free human liver. In this study, we determine a source of new hepatocytes by combining many different lab-based methods and computational predictions to show that hepatocytes share a common cell of origin with bile ducts. Both our experimental and computational data also demonstrate hepatocyte clones are likely to expand in slow waves across the liver in a specific trajectory, but often lie dormant for many years. These data show for the first time the expansion dynamics of hepatocytes in normal liver and their cell of origin enabling the accurate measurment of changes to their dynamics that may lead to liver disease. These findings are important for researchers determining cancer risk in human liver.
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Affiliation(s)
- Adam M Passman
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Magnus J Haughey
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Emanuela Carlotti
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Marc J Williams
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bianca Cereser
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Meng-Lay Lin
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Shruthi Devkumar
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jonathan P Gabriel
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Enrico Gringeri
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Umberto Cillo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Francesco Paolo Russo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Marnix Jansen
- Department of Cellular Pathology, University College London, London, UK; UCL Cancer Centre, University College London, London, UK
| | - Nicholas A Wright
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Hermant M Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK; Cancer Tissue Bank, Barts Cancer Institute, Queen Mary University of London, London, UK; Barts and the London HPB Centre, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, UK; Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Malcolm R Alison
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Stuart A C McDonald
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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Gabbutt C, Wright NA, Baker A, Shibata D, Graham TA. Lineage tracing in human tissues. J Pathol 2022; 257:501-512. [PMID: 35415852 PMCID: PMC9253082 DOI: 10.1002/path.5911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/21/2022] [Accepted: 04/09/2022] [Indexed: 11/11/2022]
Abstract
The dynamical process of cell division that underpins homeostasis in the human body cannot be directly observed in vivo, but instead is measurable from the pattern of somatic genetic or epigenetic mutations that accrue in tissues over an individual's lifetime. Because somatic mutations are heritable, they serve as natural lineage tracing markers that delineate clonal expansions. Mathematical analysis of the distribution of somatic clone sizes gives a quantitative readout of the rates of cell birth, death, and replacement. In this review we explore the broad range of somatic mutation types that have been used for lineage tracing in human tissues, introduce the mathematical concepts used to infer dynamical information from these clone size data, and discuss the insights of this lineage tracing approach for our understanding of homeostasis and cancer development. We use the human colon as a particularly instructive exemplar tissue. There is a rich history of human somatic cell dynamics surreptitiously written into the cell genomes that is being uncovered by advances in sequencing and careful mathematical analysis lineage of tracing data. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Calum Gabbutt
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Evolution and CancerInstitute of Cancer ResearchSuttonUK
- London Interdisciplinary Doctoral Training Programme (LIDo)LondonUK
| | - Nicholas A Wright
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Ann‐Marie Baker
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Evolution and CancerInstitute of Cancer ResearchSuttonUK
| | - Darryl Shibata
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Trevor A Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Evolution and CancerInstitute of Cancer ResearchSuttonUK
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4
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Refinetti P, Morgenthaler S, Thilly WG, Arstad C, Ekstrøm PO. Tracing of Human Tumor Cell Lineages by Mitochondrial Mutations. Front Oncol 2020; 10:523860. [PMID: 33344219 PMCID: PMC7745703 DOI: 10.3389/fonc.2020.523860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Previous studies have shown the value in studying lineage tracing in slices of human tumors. However, a tumor is not a two-dimensional structure and to better understand how a tumor, and its corresponding metastasis grow, a three-dimensional (3-D) view is necessary. Results Using somatic mitochondrial mutations as a marker for lineage tracing, it is possible to identify and follow tumor specific cell lineages. Using cycling temperature capillary electrophoresis (CTCE) a total of 8 tissues from 5 patients (4 primary tumors and 4 metastasis) containing clear mitochondrial markers of tumor lineages were selected. From these 8 tissues over 9,500 laser capture microdisection (LCM) samples were taken and analyzed, in a way that allows 3-D rendering of the observations. Conclusion Using CTCE combined with LCM makes it possible to study the 3-D patterns formed by tumors and metastasis as they grow. These results clearly show that the majority of the volume occupied by a tumor is not composed of tumor derived cells. These cells are most likely recruited from the neighboring tissue.
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Affiliation(s)
- Paulo Refinetti
- Chair of Applied Statistics, Mathematics Section, School of Basic Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Stephan Morgenthaler
- Chair of Applied Statistics, Mathematics Section, School of Basic Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - William G Thilly
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Christian Arstad
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo, Norway
| | - Per O Ekstrøm
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo, Norway
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5
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Alison MR. The cellular origins of cancer with particular reference to the gastrointestinal tract. Int J Exp Pathol 2020; 101:132-151. [PMID: 32794627 PMCID: PMC7495846 DOI: 10.1111/iep.12364] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 12/18/2022] Open
Abstract
Stem cells or their closely related committed progenitor cells are the likely founder cells of most neoplasms. In the continually renewing and hierarchically organized epithelia of the oesophagus, stomach and intestine, homeostatic stem cells are located at the beginning of the cell flux, in the basal layer of the oesophagus, the isthmic region of gastric oxyntic glands and at the bottom of gastric pyloric-antral glands and colonic crypts. The introduction of mutant oncogenes such as KrasG12D or loss of Tp53 or Apc to specific cell types expressing the likes of Lgr5 and Mist1 can be readily accomplished in genetically engineered mouse models to initiate tumorigenesis. Other origins of cancer are discussed including 'reserve' stem cells that may be activated by damage or through disruption of morphogen gradients along the crypt axis. In the liver and pancreas, with little cell turnover and no obvious stem cell markers, the importance of regenerative hyperplasia associated with chronic inflammation to tumour initiation is vividly apparent, though inflammatory conditions in the renewing populations are also permissive for tumour induction. In the liver, hepatocytes, biliary epithelial cells and hepatic progenitor cells are embryologically related, and all can give rise to hepatocellular carcinoma and cholangiocarcinoma. In the exocrine pancreas, both acinar and ductal cells can give rise to pancreatic ductal adenocarcinoma (PDAC), although the preceding preneoplastic states are quite different: acinar-ductal metaplasia gives rise to pancreatic intraepithelial neoplasia culminating in PDAC, while ducts give rise to PDAC via. mucinous cell metaplasia that may have a polyclonal origin.
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Affiliation(s)
- Malcolm R. Alison
- Centre for Tumour BiologyBarts Cancer Institute, Charterhouse SquareBarts and The London School of Medicine and DentistryLondonUK
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Abstract
Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial DNA as well as variations in DNA methylation status. It is also apparent that the scientific community is on the verge of being able to make a comprehensive and detailed cell lineage map of human embryonic and fetal development. In this review, we discuss the advantages and disadvantages of different approaches and markers for lineage tracing. We also describe the general conceptual design for how to derive a lineage map for humans.
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Affiliation(s)
- Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA;
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, Connecticut 06520, USA;
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7
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Buczacki S. Fate plasticity in the intestine: The devil is in the detail. World J Gastroenterol 2019; 25:3116-3122. [PMID: 31333305 PMCID: PMC6626720 DOI: 10.3748/wjg.v25.i25.3116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023] Open
Abstract
The intestinal epithelium possesses a remarkable ability for both proliferation and regeneration. The last two decades have generated major advances in our understanding of the stem cell populations responsible for its maintenance during homeostasis and more recently the events that occur during injury induced regeneration. These fundamental discoveries have capitalised on the use of transgenic mouse models and in vivo lineage tracing to make their conclusions. It is evident that maintenance is driven by rapidly proliferating crypt base stem cells, but complexities associated with the technicality of mouse modelling have led to several overlapping populations being held responsible for the same behaviour. Similarly, it has been shown that essentially any population in the intestinal crypt can revert to a stem cell state given the correct stimulus during epithelial regeneration. Whilst these observations are profound it is uncertain how relevant they are to human intestinal homeostasis and pathology. Here, these recent studies are presented, in context with technical considerations of the models used, to argue that their conclusions may indeed not be applicable in understanding "homeostatic regeneration" and experimental suggestions presented for validating their results in human tissue.
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Affiliation(s)
- Simon Buczacki
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Addenbrooke’s Biomedical Campus, Cambridge CB2 0AF, United Kingdom
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8
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Abstract
Every animal grows from a single fertilized egg into an intricate network of cell types and organ systems. This process is captured in a lineage tree: a diagram of every cell's ancestry back to the founding zygote. Biologists have long sought to trace this cell lineage tree in individual organisms and have developed a variety of technologies to map the progeny of specific cells. However, there are billions to trillions of cells in complex organisms, and conventional approaches can only map a limited number of clonal populations per experiment. A new generation of tools that use molecular recording methods integrated with single cell profiling technologies may provide a solution. Here, we summarize recent breakthroughs in these technologies, outline experimental and computational challenges, and discuss biological questions that can be addressed using single cell dynamic lineage tracing.
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Affiliation(s)
- Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - James A Gagnon
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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9
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Alison MR. The many ways to mend your liver: A critical appraisal. Int J Exp Pathol 2018; 99:106-112. [PMID: 29882223 DOI: 10.1111/iep.12272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022] Open
Abstract
In the latter half of the 20th century, our understanding of mammalian liver regeneration was shaped by the manner of compensatory hyperplasia occurring after a partial rat liver resection. This response involves almost all hepatocytes and thus is unlikely to be the outcome of the multiple cycling of a small stem cell population. It was most intense in the outer third of lobule, the location closest to the afferent arterial blood supply. With the advent of heritable genetic labelling techniques, usually applied to mice, hitherto unrecognized hepatocytes with clonogenic potential have been discovered, contributing to homoeostatic renewal and/or regenerative responses after tissue loss. This review combines observations from cell lineage tracing studies with other data to summarize the Four proposed anatomical locations for hepatocyte stem cells: the periportal zone, the pericentral zone, a randomized distribution and finally within the intrahepatic biliary tree. As in other endodermal-derived tissues, it appears that there are both homoeostatic stem cells and regenerative stem cells, while some normally homoeostatic stem cells can become more active to boost regeneration.
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Affiliation(s)
- Malcolm R Alison
- Centre for Tumour Biology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, London, UK
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10
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Comparative biochemistry of cytochrome c oxidase in animals. Comp Biochem Physiol B Biochem Mol Biol 2017; 224:170-184. [PMID: 29180239 DOI: 10.1016/j.cbpb.2017.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of the electron transport system, is central to aerobic metabolism of animals. Many aspects of its structure and function are highly conserved, yet, paradoxically, it is also an important model for studying the evolution of the metabolic phenotype. In this review, part of a special issue honouring Peter Hochachka, we consider the biology of COX from the perspective of comparative and evolutionary biochemistry. The approach is to consider what is known about the enzyme in the context of conventional biochemistry, but focus on how evolutionary researchers have used this background to explore the role of the enzyme in biochemical adaptation of animals. In synthesizing the conventional and evolutionary biochemistry, we hope to identify synergies and future research opportunities. COX represents a rare opportunity for researchers to design studies that span the breadth of biology: molecular genetics, protein biochemistry, enzymology, metabolic physiology, organismal performance, evolutionary biology, and phylogeography.
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Tidwell TR, Søreide K, Hagland HR. Aging, Metabolism, and Cancer Development: from Peto's Paradox to the Warburg Effect. Aging Dis 2017; 8:662-676. [PMID: 28966808 PMCID: PMC5614328 DOI: 10.14336/ad.2017.0713] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Medical advances made over the last century have increased our lifespan, but age-related diseases are a fundamental health burden worldwide. Aging is therefore a major risk factor for cardiovascular disease, cancer, diabetes, obesity, and neurodegenerative diseases, all increasing in prevalence. However, huge inter-individual variations in aging and disease risk exist, which cannot be explained by chronological age, but rather physiological age decline initiated even at young age due to lifestyle. At the heart of this lies the metabolic system and how this is regulated in each individual. Metabolic turnover of food to energy leads to accumulation of co-factors, byproducts, and certain proteins, which all influence gene expression through epigenetic regulation. How these epigenetic markers accumulate over time is now being investigated as the possible link between aging and many diseases, such as cancer. The relationship between metabolism and cancer was described as early as the late 1950s by Dr. Otto Warburg, before the identification of DNA and much earlier than our knowledge of epigenetics. However, when the stepwise gene mutation theory of cancer was presented, Warburg's theories garnered little attention. Only in the last decade, with epigenetic discoveries, have Warburg's data on the metabolic shift in cancers been brought back to life. The stepwise gene mutation theory fails to explain why large animals with more cells, do not have a greater cancer incidence than humans, known as Peto's paradox. The resurgence of research into the Warburg effect has given us insight to what may explain Peto's paradox. In this review, we discuss these connections and how age-related changes in metabolism are tightly linked to cancer development, which is further affected by lifestyle choices modulating the risk of aging and cancer through epigenetic control.
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Affiliation(s)
- Tia R. Tidwell
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hanne R. Hagland
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
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Schmidt ST, Zimmerman SM, Wang J, Kim SK, Quake SR. Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding. ACS Synth Biol 2017; 6:936-942. [PMID: 28264564 DOI: 10.1021/acssynbio.6b00309] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lineage tracing by the determination and mapping of progeny arising from single cells is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a dynamic sequence-based barcode system for synthetic lineage tracing and have demonstrated its performance in C. elegans, a model organism whose lineage tree is well established. The strategy we use creates lineage trees based upon the introduction of synthetically controlled mutations into cells and the propagation of these mutations to daughter cells at each cell division. We analyzed this experimental proof of concept along with a corresponding simulation and analytical model to gain a deeper understanding of the coding capacity of the system. Our results provide specific bounds on the fidelity of lineage tracing using such approaches.
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Affiliation(s)
| | | | - Jianbin Wang
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Stuart K. Kim
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- Department
of Developmental Biology, Stanford University, Stanford, California 94305, United States
| | - Stephen R. Quake
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, San Francisco, California 94518, United States
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13
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Refinetti P, Arstad C, Thilly WG, Morgenthaler S, Ekstrøm PO. Mapping mitochondrial heteroplasmy in a Leydig tumor by laser capture micro-dissection and cycling temperature capillary electrophoresis. BMC Clin Pathol 2017; 17:6. [PMID: 28405177 PMCID: PMC5385042 DOI: 10.1186/s12907-017-0042-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/27/2017] [Indexed: 12/13/2022] Open
Abstract
Background The growth of tumor cells is accompanied by mutations in nuclear and mitochondrial genomes creating marked genetic heterogeneity. Tumors also contain non-tumor cells of various origins. An observed somatic mitochondrial mutation would have occurred in a founding cell and spread through cell division. Micro-anatomical dissection of a tumor coupled with assays for mitochondrial point mutations permits new insights into this growth process. More generally, the ability to detect and trace, at a histological level, somatic mitochondrial mutations in human tissues and tumors, makes these mutations into markers for lineage tracing. Method A tumor was first sampled by a large punch biopsy and scanned for any significant degree of heteroplasmy in a set of sequences containing known mutational hotspots of the mitochondrial genome. A heteroplasmic tumor was sliced at a 12 μm thickness and placed on membranes. Laser capture micro-dissection was used to take 25000 μm2 subsamples or spots. After DNA amplification, cycling temperature capillary electrophoresis (CTCE) was used on the laser captured samples to quantify mitochondrial mutant fractions. Results Of six testicular tumors studied, one, a Leydig tumor, was discovered to carry a detectable degree of heteroplasmy for two separate point mutations: a C → T mutation at bp 64 and a T → C mutation found at bp 152. From this tumor, 381 spots were sampled with laser capture micro-dissection. The ordered distribution of spots exhibited a wide range of fractions of the mutant sequences from 0 to 100% mutant copies. The two mutations co-distributed in the growing tumor indicating they were present on the same genome copies in the founding cell. Conclusion Laser capture microdissection of sliced tumor samples coupled with CTCE-based point mutation assays provides an effective and practical means to obtain maps of mitochondrial mutational heteroplasmy within human tumors.
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Affiliation(s)
- Paulo Refinetti
- Chair of Applied Statistics, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Christian Arstad
- Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - William G Thilly
- Laboratory in Metakaryotic Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Stephan Morgenthaler
- Chair of Applied Statistics, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Per Olaf Ekstrøm
- Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
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Rulands S, Simons BD. Tracing cellular dynamics in tissue development, maintenance and disease. Curr Opin Cell Biol 2016; 43:38-45. [PMID: 27474807 DOI: 10.1016/j.ceb.2016.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022]
Abstract
The coordination of cell proliferation and differentiation is central to the development and maintenance of tissues, while its dysregulation underlies the transition to diseased states. By combining lineage tracing with transcriptional profiling and marker-based assays, statistical methods are delivering insights into the dynamics of stem cells and their developmental precursors. These studies have provided evidence for molecular heterogeneity and fate priming, and have revealed a role for stochasticity in stem cell fate, refocusing the search for regulatory mechanisms. At the same time, they present a quantitative platform to study the initiation and progression of disease. Here, we review how quantitative lineage tracing strategies are shaping our understanding of the cellular mechanisms of tissue development, maintenance and disease.
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Affiliation(s)
- Steffen Rulands
- Cavendish Laboratory, Department of Physics, J. J. Thomson Avenue, Cambridge CB3 0HE, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, UK
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, J. J. Thomson Avenue, Cambridge CB3 0HE, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, UK.
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Abstract
Under normal homeostatic conditions, hepatocyte renewal is a slow process and complete turnover likely takes at least a year. Studies of hepatocyte regeneration after a two-thirds partial hepatectomy (2/3 PH) have strongly suggested that periportal hepatocytes are the driving force behind regenerative re-population, but recent murine studies have brought greater complexity to the issue. Although periportal hepatocytes are still considered pre-eminent in the response to 2/3 PH, new studies suggest that normal homeostatic renewal is driven by pericentral hepatocytes under the control of Wnts, while pericentral injury provokes the clonal expansion of a subpopulation of periportal hepatocytes expressing low levels of biliary duct genes such as Sox9 and osteopontin. Furthermore, some clarity has been given to the debate on the ability of biliary-derived hepatic progenitor cells to generate physiologically meaningful numbers of hepatocytes in injury models, demonstrating that under appropriate circumstances these cells can re-populate the whole liver.
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Affiliation(s)
- Malcolm R. Alison
- Centre for Tumour Biology, Barts and The London School of Medicine and Dentistry, London, UK
| | - Wey-Ran Lin
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan
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Fate Mapping Mammalian Corneal Epithelia. Ocul Surf 2016; 14:82-99. [PMID: 26774909 DOI: 10.1016/j.jtos.2015.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 02/07/2023]
Abstract
The anterior aspect of the cornea consists of a stratified squamous epithelium, thought to be maintained by a rare population of stem cells (SCs) that reside in the limbal transition zone. Although migration of cells that replenish the corneal epithelium has been studied for over a century, the process is still poorly understood and not well characterized. Numerous techniques have been employed to examine corneal epithelial dynamics, including visualization by light microscopy, the incorporation of vital dyes and DNA labels, and transplantation of genetically marked cells that have acted as cell and lineage beacons. Modern-day lineage tracing utilizes molecular methods to determine the fate of a specific cell and its progeny over time. Classically employed in developmental biology, lineage tracing has been used more recently to track the progeny of adult SCs in a number of organs to pin-point their location and understand their movement and influence on tissue regeneration. This review highlights key discoveries that have led researchers to develop cutting-edge genetic tools to effectively and more accurately monitor turnover and displacement of cells within the mammalian corneal epithelium. Collating information on the basic biology of SCs will have clinical ramifications in furthering our knowledge of the processes that govern their role in homeostasis, wound-healing, transplantation, and how we can improve current unsatisfactory SC-based therapies for patients suffering blinding corneal disease.
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