Developmental Cell Lineages

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R-HSA-9734767
Type
CellLineagePath
Species
Homo sapiens
ReviewStatus
5/5
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Developmental Cell Lineages
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Our bodies are built of >30 trillion cells specialized to fulfill diverse roles within our tissues, organs, and organ systems. All these cells originate from a single cell, a zygote formed at conception. From zygote to fetus, and throughout childhood, adolescence, and adulthood, cells divide and commit to different fates in order for the organism to develop, sustain and regenerate. The series of steps that lead from an undifferentiated progenitor cell, such as a stem cell, to one of its several possible specialized descendants constitutes a cell lineage path (Burgess et al. 2018). Cell lineage paths are organized by organ systems. Each cell lineage path cross-references a Gene Ontology (GO) biological process (The Gene Ontology Consortium 2019), and consists of a series of causally connected cell development steps. Cell development steps describe the transition between cell states during development or differentiation and are characterized by regulators (molecules promoting or inhibiting the step) and, when established, “required input components” (cell state biomarkers required for the action of regulators). Each cell state is characterized by a cell type defined in Cell Ontology (Sarntivijai et al. 2014; Osumi-Sutherland 2017), anatomical location from UBERON (Haendel et al. 2014), and a unique combination of protein and/or RNA markers with references, when available, to CellMarker (Hu et al. 2023) and PanglaoDB (Franzen et al. 2019). For a more detailed data model description, please refer to Milacic et al. 2024. Recent technological advances have allowed researchers to harvest high-throughput omics data from single cells of multicellular organisms and use it to track and manipulate cell fates (Burgess 2018; Saelens et al. 2019). This opens the door to the possibility of deciphering cell lineage paths at single-cell resolution, a critical requirement for the advancement of regenerative medicine and cancer medicine.

The cell lineage path “Differentiation of keratinocytes in interfollicular epidermis in mammalian skin” describes the differentiation of keratinocytes from stem cells to corneocytes in the interfollicular epidermis, the skin surface layer in between the adnexa (hair follicles, sweat glands, and sebaceous glands).
Literature References
PubMed ID Title Journal Year
37941124 The Reactome Pathway Knowledgebase 2024

Orlic-Milacic, M, Beavers, D, Conley, P, Gong, C, Gillespie, ME, Griss, J, Haw, R, Jassal, B, Matthews, L, May, B, Petryszak, R, Ragueneau, E, Rothfels, K, Sevilla, C, Shamovsky, V, Tiwari, K, Varusai, T, Weiser, J, Wright, A, Wu, G, Stein, L, Hermjakob, H, D'Eustachio, P

Nucleic Acids Res 2024
25009735 Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Haendel, MA, Balhoff, JP, Bastian, FB, Blackburn, DC, Blake, JA, Bradford, Y, Comte, A, Dahdul, WM, Dececchi, TA, Druzinsky, RE, Hayamizu, TF, Ibrahim, N, Lewis, SE, Mabee, PM, Niknejad, A, Robinson-Rechavi, M, Sereno, PC, Mungall, CJ

J Biomed Semantics 2014
29322914 Cell ontology in an age of data-driven cell classification

Osumi-Sutherland, D

BMC Bioinformatics 2017
30951143 PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data

Franzén, O, Gan, LM, Björkegren, JLM

Database (Oxford) 2019
30936559 A comparison of single-cell trajectory inference methods

Saelens, W, Cannoodt, R, Todorov, H, Saeys, Y

Nat Biotechnol 2019
36300619 CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data

Hu, C, Li, T, Xu, Y, Zhang, X, Li, F, Bai, J, Chen, J, Jiang, W, Yang, K, Ou, Q, Li, X, Wang, P, Zhang, Y

Nucleic Acids Res 2022
25852852 CLO: The cell line ontology

Sarntivijai, S, Lin, Y, Xiang, Z, Meehan, TF, Diehl, AD, Vempati, UD, Schürer, SC, Pang, C, Malone, J, Parkinson, H, Liu, Y, Takatsuki, T, Saijo, K, Masuya, H, Nakamura, Y, Brush, MH, Haendel, MA, Zheng, J, Stoeckert, CJ, Peters, B, Mungall, CJ, Carey, TE, States, DJ, Athey, BD, He, Y

J Biomed Semantics 2014
29713013 Tracing cell-lineage histories

Burgess, DJ

Nat Rev Genet 2018
30395331 The Gene Ontology Resource: 20 years and still GOing strong

Consortium, GO

Nucleic Acids Res 2019
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Authored
Orlic-Milacic, M  (2021-06-18)
Reviewed
Matthews, L  (2024-02-28)
Matthews, L  (2024-11-05)
Matthews, L  (2025-02-26)
Matthews, L  (2025-05-26)
Created
Orlic-Milacic, M  (2021-06-18)
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