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Research article - Peer-reviewed, 2023

The Enrichment of Specific Hair Follicle-Associated Cell Populations in Plucked Hairs Offers an Opportunity to Study Gene Expression Underlying Hair Traits

Naboulsi, Rakan; Cieslak, Jakub; Headon, Denis; Jouni, Ahmad; Negro, Juan J.; Andersson, Goran; Lindgren, Gabriella


Gene expression differences can assist in characterizing important underlying genetic mechanisms between different phenotypic traits. However, when population-dense tissues are studied, the signals from scarce populations are diluted. Therefore, appropriately choosing a sample collection method that enriches a particular type of effector cells might yield more specific results. To address this issue, we performed a polyA-selected RNA-seq experiment of domestic horse (Equus ferus caballus) plucked-hair samples and skin biopsies. Then, we layered the horse gene abundance results against cell type-specific marker genes generated from a scRNA-seq supported with spatial mapping of laboratory mouse (Mus musculus) skin to identify the captured populations. The hair-plucking and skin-biopsy sample-collection methods yielded comparable quality and quantity of RNA-seq results. Keratin-related genes, such as KRT84 and KRT75, were among the genes that showed higher abundance in plucked hairs, while genes involved in cellular processes and enzymatic activities, such as MGST1, had higher abundance in skin biopsies. We found an enrichment of hair-follicle keratinocytes in plucked hairs, but detected an enrichment of other populations, including epidermis keratinocytes, in skin biopsies. In mammalian models, biopsies are often the method of choice for a plethora of gene expression studies and to our knowledge, this is a novel study that compares the cell-type enrichment between the non-invasive hair-plucking and the invasive skin-biopsy sample-collection methods. Here, we show that the non-invasive and ethically uncontroversial plucked-hair method is recommended depending on the research question. In conclusion, our study will allow downstream -omics approaches to better understand integumentary conditions in both health and disease in horses as well as other mammals.


equine; skin; hair; follicle; RNA-seq

Published in

International Journal of Molecular Sciences
2023, volume: 24, number: 1, article number: 561
Publisher: MDPI

Authors' information

Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Cieslak, Jakub
Poznan University of Life Sciences
Headon, Denis
University of Edinburgh
Headon, Denis
Biotechnology and Biological Sciences Research Council (BBSRC)
Jouni, Ahmad
SLU Dummy
Negro, Juan J.
CSIC - Estacion Biologica de Donana (EBD)
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
University of Leuven (KU Leuven)

UKÄ Subject classification

Animal and Dairy Science

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