scholarly journals Computational comparison of developmental cell lineage trees by alignments

2019 ◽  
Author(s):  
Meng Yuan ◽  
Xujiang Yang ◽  
Jinghua Lin ◽  
Xiaolong Cao ◽  
Feng Chen ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cell Lineage ◽  
Direct Determination ◽  
Cell Types ◽  
Developmental State ◽  
Alignment Algorithm ◽  
Lineage Tree ◽  
Tree Data ◽  
Multicellular Organisms ◽  
Lineage Trees

ABSTRACTThe developmental cell lineage tree, which records every cell division event and the terminal developmental state of each single cell, is one of the most important traits of multicellular organisms, as well as key to many significant unresolved questions in biology. Recent technological breakthroughs are paving the way for direct determination of cell lineage trees, yet a general framework for the computational analysis of lineage trees, in particular an algorithm to compare two lineage trees, is still lacking. Based on previous findings that the same developmental program can be invoked by different cells on the lineage tree to produce highly similar subtrees, we designedDevelopmental CellLineageTreeAlignment (DELTA), an algorithm that exhaustively searches for lineage trees with phenotypic resemblance in lineal organization of terminal cells, meanwhile resolving detailed correspondence between individual cells. Using simulated and nematode lineage trees, we demonstrated DELTA’s capability of revealing similarities of developmental programs by lineal resemblances. Moreover, DELTA successfully identifies gene deletion-triggered homeotic cell fate transformations, reveals functional relationship between mutants by quantifying their lineal similarities, and finds the evolutionary correspondence between cell types defined non-uniformly for different species. DELTA establishes novel foundation for comparative study of lineage trees, much like sequence alignment algorithm for biological sequences, and along with the increase of lineage tree data, will likely bring unique insights for the myriads of important questions surrounding cell lineage trees.

scholarly journals Maps of variability in cell lineage trees

2018 ◽  
Author(s):  
Damien G. Hicks ◽  
Terence P. Speed ◽  
Mohammed Yassin ◽  
Sarah M. Russell
Keyword(s):  
Cell Fate ◽  
Binary Tree ◽  
Cell Lineage ◽  
Population Level ◽  
Differentiation Potential ◽  
Cell Lineages ◽  
Lineage Tree ◽  
Founder Cells ◽  
Multicellular Organisms ◽  
Lineage Trees

AbstractNew approaches to lineage tracking allow the study of cell differentiation over many generations of cells during development in multicellular organisms. Understanding the variability observed in these lineage trees requires new statistical methods. Whereas invariant cell lineages, such as that for the nematode Caenorhabditis elegans, can be described using a lineage map, defined as the fixed pattern of phenotypes overlaid onto the binary tree structure, the variability of cell lineages from higher organisms makes it impossible to draw a single lineage map. Here, we introduce lineage variability maps which describe the pattern of second-order variation throughout the lineage tree. These maps can be undirected graphs of the partial correlations between every lineal position or directed graphs showing the dynamics of bifurcated patterns in each subtree. By using the symmetry invariance of a binary tree to develop a generalized spectral analysis for cell lineages, we show how to infer these graphical models for lineages of any depth from sample sizes of only a few pedigrees. When tested on pedigrees from C. elegans expressing a marker for pharyngeal differentiation potential, the maps recover essential features of the known lineage map. When applied to highly-variable pedigrees monitoring cell size in T lymphocytes, the maps show how most of the phenotype is set by the founder naive T cell. Lineage variability maps thus elevate the concept of the lineage map to the population level, addressing questions about the potency and dynamics of cell lineages and providing a way to quantify the progressive restriction of cell fate with increasing depth in the tree.Author summaryMulticellular organisms develop from a single fertilized egg by sequential cell divisions. The progeny from these divisions adopt different traits that are transmitted and modified through many generations. By tracking how cell traits change with each successive cell division throughout the family, or lineage, tree, it has been possible to understand where and how these modifications are controlled at the single-cell level, thereby addressing questions about, for example, the developmental origin of tissues, the sources of differentiation in immune cells, or the relationship between primary tumors and metastases. Such lineages often show large variability, with apparently identical founder cells giving rise to different patterns of descendants. Fundamental scientific questions, such as about the range of possible cell types a cell can give rise to, are often about this variability. To characterize this variation, and thus understand the lineage at the population level, we introduce lineage variability maps. Using data from worm and mammalian cell lineages we show how these maps provide quantifiable answers to questions about any developing lineage, such as the potency of founder cells and the progressive restriction of cell fate at each stage in the tree.

scholarly journals Decision tree models and cell fate choice

2020 ◽  
Author(s):  
Ivan Croydon Veleslavov ◽  
Michael P.H. Stumpf
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Fate ◽  
Cell Types ◽  
Lineage Tree ◽  
Tree Models ◽  
Fate Decision ◽  
Average Gene ◽  
Lineage Trees ◽  
Cell Data

AbstractSingle cell transcriptomics has laid bare the heterogeneity of apparently identical cells at the level of gene expression. For many cell-types we now know that there is variability in the abundance of many transcripts, and that average transcript abun-dance or average gene expression can be a unhelpful concept. A range of clustering and other classification methods have been proposed which use the signal in single cell data to classify, that is assign cell types, to cells based on their transcriptomic states. In many cases, however, we would like to have not just a classifier, but also a set of interpretable rules by which this classification occurs. Here we develop and demonstrate the interpretive power of one such approach, which sets out to establish a biologically interpretable classification scheme. In particular we are interested in capturing the chain of regulatory events that drive cell-fate decision making across a lineage tree or lineage sequence. We find that suitably defined decision trees can help to resolve gene regulatory programs involved in shaping lineage trees. Our approach combines predictive power with interpretabilty and can extract logical rules from single cell data.

scholarly journals Early developmental asymmetries in cell lineage trees in living individuals

2020 ◽  
Author(s):  
Liana Fasching ◽  
Yeongjun Jang ◽  
Simone Tomasi ◽  
Jeremy Schreiner ◽  
Livia Tomasini ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cell Lineage ◽  
Postmortem Brain ◽  
Cell Lineages ◽  
Human Specimen ◽  
Balanced Contributions ◽  
Health And Disease ◽  
Induced Pluripotent ◽  
Lineage Trees ◽  
Early Developmental

AbstractPost-zygotic mosaic mutations can be used to track cell lineages in humans. By using cell cloning and induced pluripotent cell lines, we analyzed early cell lineages in two living individuals (a patient and a control), and a postmortem human specimen. Of ten reconstructed post-zygotic divisions, none resulted in balanced contributions of daughter lineages to tissues. In both living individuals one of two lineages from the first cleavage was dominant across tissues, with 90% frequency in blood. We propose that the efficiency of DNA repair contributes to lineage imbalance. Allocation of lineages in postmortem brain correlated with anterior-posterior axis, associating lineage history with cell fate choices in embryos. Recurrence of germline variants as mosaic suggested that certain loci may be particularly susceptible to mutagenesis. We establish a minimally invasive framework for defining cell lineages in any living individual, which paves the way for studying their relevance in health and disease.

scholarly journals Universal principles of lineage architecture and stem cell identity in renewing tissues

2020 ◽  
Author(s):  
Philip Greulich ◽  
Ben D. MacArthur ◽  
Cristina Parigini ◽  
Rubén J. Sánchez-García
Keyword(s):  
Stem Cell ◽  
Cell Lineage ◽  
Adult Stem Cell ◽  
Feedback Regulation ◽  
Cell Types ◽  
Universal Principles ◽  
Formal Framework ◽  
Cell Niche ◽  
Multicellular Organisms ◽  
The Relationship

Adult tissues in multicellular organisms typically contain a variety of stem, progenitor and differentiated cell types arranged in a lineage hierarchy that regulates healthy tissue turnover and repair. Lineage hierarchies in disparate tissues often exhibit common features, yet the general principles regulating their architecture are not known. Here, we provide a formal framework for understanding the relationship between cell molecular ‘states’ (patterns of gene, protein expression etc. in the cell) and cell ‘types’ that uses notions from network science to decompose the structure of cell state trajectories into functional units. Using this framework we show that many widely experimentally observed features of cell lineage architectures – including the fact that a single adult stem cell type always resides at the apex of a lineage hierarchy – arise as a natural consequence of homeostasis, and indeed are the only possible way that lineage architectures can be constructed to support homeostasis in renewing tissues. Furthermore, under suitable feedback regulation, for example from the stem cell niche, we show that the property of ‘stemness’ is entirely determined by the cell environment. Thus, we argue that stem cell identities are contextual and not determined by hard-wired, cell-intrinsic, characteristics.

scholarly journals Massively parallel single cell lineage tracing using CRISPR/Cas9 induced genetic scars

2017 ◽  
Author(s):  
Bastiaan Spanjaard ◽  
Bo Hu ◽  
Nina Mitic ◽  
Jan Philipp Junker
Keyword(s):  
Single Cell ◽  
Computational Analysis ◽  
Systematic Approach ◽  
Single Cells ◽  
Cell Lineage ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Lineage Tracing ◽  
Lineage Trees ◽  
Different Cell Types

A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many different cell types. Single-cell RNA-sequencing (scRNA-seq) has become a widely-used method due to its ability to identify all cell types in a tissue or organ in a systematic manner 1–3. However, a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here, we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses, LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences) can be used as a systematic approach for identifying the lineage origin of novel cell types, or of known cell types under different conditions.

scholarly journals Oncogenes, Proto-Oncogenes, and Lineage Restriction of Cancer Stem Cells

2021 ◽  
Vol 22 (18) ◽  
pp. 9667
Author(s):  
Geoffrey Brown
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Cell Fate ◽  
Cell Lineage ◽  
Cell Types ◽  
Mature Cell ◽  
Cellular Gene ◽  
Hematopoietic Stem ◽  
Homeostatic Process ◽  
Epigenetic Events

In principle, an oncogene is a cellular gene (proto-oncogene) that is dysfunctional, due to mutation and fusion with another gene or overexpression. Generally, oncogenes are viewed as deregulating cell proliferation or suppressing apoptosis in driving cancer. The cancer stem cell theory states that most, if not all, cancers are a hierarchy of cells that arises from a transformed tissue-specific stem cell. These normal counterparts generate various cell types of a tissue, which adds a new dimension to how oncogenes might lead to the anarchic behavior of cancer cells. It is that stem cells, such as hematopoietic stem cells, replenish mature cell types to meet the demands of an organism. Some oncogenes appear to deregulate this homeostatic process by restricting leukemia stem cells to a single cell lineage. This review examines whether cancer is a legacy of stem cells that lose their inherent versatility, the extent that proto-oncogenes play a role in cell lineage determination, and the role that epigenetic events play in regulating cell fate and tumorigenesis.

Modifications of cell fate specification in equal-cleaving nemertean embryos: alternate patterns of spiralian development

Development ◽  
1995 ◽  
Vol 121 (10) ◽  
pp. 3175-3185 ◽  
Author(s):  
M.Q. Martindale ◽  
J.Q. Henry
Keyword(s):  
Cell Fate ◽  
Cell Lineage ◽  
Cell Types ◽  
Embryonic Cell ◽  
Specific Cell ◽  
Cell Fate Specification ◽  
Cell Fates ◽  
Developmental Potential ◽  
Fate Specification ◽  
Symmetry Properties

The nemerteans belong to a phylum of coelomate worms that display a highly conserved pattern of cell divisions referred to as spiral cleavage. It has recently been shown that the fates of the four embryonic cell quadrants in two species of nemerteans are not homologous to those in other spiralian embryos, such as the annelids and molluscs (Henry, J. Q. and Martindale, M. Q. (1994a) Develop. Genetics 15, 64–78). Equal-cleaving molluscs utilize inductive interactions to establish quadrant-specific cell fates and embryonic symmetry properties following fifth cleavage. In order to elucidate the manner in which cell fates are established in nemertean embryos, we have conducted cell isolation and deletion experiments to examine the developmental potential of the early cleavage blastomeres of two equal-cleaving nemerteans, Nemertopsis bivittata and Cerebratulus lacteus. These two species display different modes of development: N. bivittata develops directly via a non-feeding larvae, while C. lacteus develops to form a feeding pilidium larva which undergoes a radical metamorphosis to give rise to the juvenile worm. By examining the development of certain structures and cell types characteristic of quadrant-specific fates for each of these species, we have shown that isolated blastomeres of the indirect-developing nemertean, C. lacteus, are capable of generating cell fates that are not a consequence of that cell's normal developmental program. For instance, dorsal blastomeres can form muscle fibers when cultured in isolation. In contrast, isolated blastomeres of the direct-developing species, N. bivittata do not regulate their development to the same extent. Some cell fates are specified in a precocious manner in this species, such as those that give rise to the eyes. Thus, these findings indicate that equal-cleaving spiralian embryos can utilize different mechanisms of cell fate and axis specification. The implications of these patterns of nemertean development are discussed in relation to experimental work in other spiralian embryos, and a model is presented that accounts for possible evolutionary changes in cell lineage and the process of cell fate specification amongst these protostome phyla.

scholarly journals Lineage Decision-Making within Normal Haematopoietic and Leukemic Stem Cells

2020 ◽  
Vol 21 (6) ◽  
pp. 2247
Author(s):  
Geoffrey Brown ◽  
Lucía Sánchez ◽  
Isidro Sánchez-García
Keyword(s):  
Stem Cells ◽  
Cell Fate ◽  
Immune Cell ◽  
Alternative Pathway ◽  
Cell Lineage ◽  
Cell Types ◽  
Haematopoietic Stem Cell ◽  
Haematopoietic Stem Cells ◽  
Wide Range ◽  
Lineage Decision

To produce the wide range of blood and immune cell types, haematopoietic stem cells can “choose” directly from the entire spectrum of blood cell fate-options. Affiliation to a single cell lineage can occur at the level of the haematopoietic stem cell and these cells are therefore a mixture of some pluripotent cells and many cells with lineage signatures. Even so, haematopoietic stem cells and their progeny that have chosen a particular fate can still “change their mind” and adopt a different developmental pathway. Many of the leukaemias arise in haematopoietic stem cells with the bulk of the often partially differentiated leukaemia cells belonging to just one cell type. We argue that the reason for this is that an oncogenic insult to the genome “hard wires” leukaemia stem cells, either through development or at some stage, to one cell lineage. Unlike normal haematopoietic stem cells, oncogene-transformed leukaemia stem cells and their progeny are unable to adopt an alternative pathway.

scholarly journals Early developmental asymmetries in cell lineage trees in living individuals

Science ◽  
2021 ◽  
Vol 371 (6535) ◽  
pp. 1245-1248
Author(s):  
Liana Fasching ◽  
Yeongjun Jang ◽  
Simone Tomasi ◽  
Jeremy Schreiner ◽  
Livia Tomasini ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cell Lineage ◽  
Embryonic Cell ◽  
Postmortem Brain ◽  
Cell Lineages ◽  
Human Specimen ◽  
Balanced Contributions ◽  
Health And Disease ◽  
Lineage Trees ◽  
Early Developmental

Mosaic mutations can be used to track cell lineages in humans. We used cell cloning to analyze embryonic cell lineages in two living individuals and a postmortem human specimen. Of 10 reconstructed postzygotic divisions, none resulted in balanced contributions of daughter lineages to tissues. In both living individuals, one of two lineages from the first cleavage was dominant across tissues, with 90% frequency in blood. We propose that the efficiency of DNA repair contributes to lineage imbalance. Allocation of lineages in postmortem brain correlated with anterior-posterior axis, associating lineage history with cell fate choices in embryos. We establish a minimally invasive framework for defining cell lineages in any living individual, which paves the way for studying their relevance in health and disease.

scholarly journals Estimation of cell lineage trees by maximum-likelihood phylogenetics

2019 ◽  
Author(s):  
Jean Feng ◽  
William S DeWitt ◽  
Aaron McKenna ◽  
Noah Simon ◽  
Amy Willis ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Large Scale ◽  
Ad Hoc ◽  
Cell Lineage ◽  
Likelihood Estimation ◽  
Lineage Tracing ◽  
Tissue Type ◽  
Lineage Tree ◽  
Organismal Development ◽  
Multicellular Organisms

AbstractCRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and outmoded computational methods to reconstruct the cell lineage tree from the mutated barcodes. Because these methods are agnostic to the biological mechanism, they are unable to take full advantage of the data’s structure. We propose a statistical model for the mutation process and develop a procedure to estimate the tree topology, branch lengths, and mutation parameters by iteratively applying penalized maximum likelihood estimation. In contrast to existing techniques, our method estimates time along each branch, rather than number of mutation events, thus providing a detailed account of tissue-type differentiation. Via simulations, we demonstrate that our method is substantially more accurate than existing approaches. Our reconstructed trees also better recapitulate known aspects of zebrafish development and reproduce similar results across fish replicates.

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