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Harkin EE, Browne JA, Murphy BA. Evaluation of short-term hair follicle storage conditions for maintenance of RNA integrity. PLoS One 2024; 19:e0294089. [PMID: 38820307 PMCID: PMC11142484 DOI: 10.1371/journal.pone.0294089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
Hair follicles provide an easily accessible tissue for interrogating gene expression for multiple purposes in mammals. RNAlater® is a liquid storage solution that stabilises and preserves cellular RNA, eliminating the need to immediately process or freeze tissue specimens. The manufacturer advises storage of samples at 2-8°C overnight before transfer to -20°C. This study aimed to evaluate RNA integrity in hair follicle samples collected from horses, stabilized in RNAlater®, and stored under three short-term storage conditions. Mane hair samples complete with follicles were collected from four horses at a single time point. Approximately 15 hairs were placed in each of three 2 mL tubes containing 0.75ml RNAlater® solution. Test group A was stored at 4°C for 24-h, then decanted and stored at -20°C. Test groups B and C were stored at 4°C and 19°C (room temperature) respectively for 7 days, then decanted and stored at -20°C. RNA was isolated from all samples and RNA quantity and quality were measured. One-way ANOVA revealed no difference in RNA concentration (A:516 +/-125 ng/ml, B:273+/-93 ng/ml, C:476+/-176 ng/ml;P = 0.2) or quality (A:9.5 +/-0.19, B:9.8+/-0.09, C:9.2+/-0.35 RIN; P = 0.46) between the test groups. There were no group differences in mean Cycle Threshold values from qPCR validation assays confirming high-quality template cDNA. The results suggest that storage of hair follicles for one week in RNAlater® at cool or room temperature conditions will not compromise RNA integrity and will permit extended transport times from remote sampling locations without the need for freezing.
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Affiliation(s)
- Eilís E. Harkin
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - John A. Browne
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Barbara A. Murphy
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
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Naboulsi R, Cieślak J, Headon D, Jouni A, Negro JJ, Andersson G, Lindgren G. The Enrichment of Specific Hair Follicle-Associated Cell Populations in Plucked Hairs Offers an Opportunity to Study Gene Expression Underlying Hair Traits. Int J Mol Sci 2022; 24:ijms24010561. [PMID: 36614000 PMCID: PMC9820680 DOI: 10.3390/ijms24010561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
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.
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Affiliation(s)
- Rakan Naboulsi
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Correspondence:
| | - Jakub Cieślak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznań, Poland
| | - Denis Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Ahmad Jouni
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Juan J. Negro
- Department of Evolutionary Ecology, Doñana Biological Station, CSIC, 41092 Seville, Spain
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
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Kowalczyk A, Chikina M, Clark N. Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness. eLife 2022; 11:76911. [PMID: 36342464 PMCID: PMC9803358 DOI: 10.7554/elife.76911] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Body hair is a defining mammalian characteristic, but several mammals, such as whales, naked mole-rats, and humans, have notably less hair. To find the genetic basis of reduced hair quantity, we used our evolutionary-rates-based method, RERconverge, to identify coding and noncoding sequences that evolve at significantly different rates in so-called hairless mammals compared to hairy mammals. Using RERconverge, we performed a genome-wide scan over 62 mammal species using 19,149 genes and 343,598 conserved noncoding regions. In addition to detecting known and potential novel hair-related genes, we also discovered hundreds of putative hair-related regulatory elements. Computational investigation revealed that genes and their associated noncoding regions show different evolutionary patterns and influence different aspects of hair growth and development. Many genes under accelerated evolution are associated with the structure of the hair shaft itself, while evolutionary rate shifts in noncoding regions also included the dermal papilla and matrix regions of the hair follicle that contribute to hair growth and cycling. Genes that were top ranked for coding sequence acceleration included known hair and skin genes KRT2, KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary rate shifts in nearby noncoding regions. Conversely, accelerated noncoding regions are most strongly enriched near regulatory hair-related genes and microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show rate shifts in their protein-coding sequences. Such dichotomy highlights the interplay between the evolution of protein sequence and regulatory sequence to contribute to the emergence of a convergent phenotype.
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Affiliation(s)
- Amanda Kowalczyk
- Carnegie Mellon-University of Pittsburgh PhD Program in Computational BiologyPittsburghUnited States,Department of Computational Biology, University of PittsburghPittsburghUnited States
| | - Maria Chikina
- Department of Computational Biology, University of PittsburghPittsburghUnited States
| | - Nathan Clark
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
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Zhang J, Hadj-Moussa H, Storey KB. Marine periwinkle stress-responsive microRNAs: A potential factor to reflect anoxia and freezing survival adaptations. Genomics 2020; 112:4385-4398. [DOI: 10.1016/j.ygeno.2020.07.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
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Transcriptional responses in newly-hatched Japanese medaka (Oryzias latipes) associated with developmental malformations following diluted bitumen exposure. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100685. [DOI: 10.1016/j.cbd.2020.100685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/21/2022]
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Discovery and molecular analysis of conserved circRNAs from cashmere goat reveal their integrated regulatory network and potential roles in secondary hair follicle. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Zhang J, Knight R, Wang Y, Sawyer TW, Martyniuk CJ, Langlois VS. Hair follicle miRNAs: a novel biomarker for primary blast Induced-Mild traumatic brain injury. Biomarkers 2018; 24:166-179. [DOI: 10.1080/1354750x.2018.1531929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jing Zhang
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, Canada
| | - Rosalinda Knight
- Canadian River Institute, University of New Brunswick, Fredericton, NB, Canada
| | - Yushan Wang
- Suffield Research Centre, Defence Research and Development Canada, Medicine Hat, AB, Canada
| | - Thomas W. Sawyer
- Suffield Research Centre, Defence Research and Development Canada, Medicine Hat, AB, Canada
| | | | - Valérie S. Langlois
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, Canada
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Zhang J, Wallace SJ, Shiu MY, Smith I, Rhind SG, Langlois VS. Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low-volume, high-intensity interval training. Physiol Rep 2017; 5. [PMID: 29212859 PMCID: PMC5727284 DOI: 10.14814/phy2.13534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/08/2017] [Accepted: 11/11/2017] [Indexed: 12/22/2022] Open
Abstract
High‐intensity interval training (HIIT) has become a popular fitness training approach under both civilian and military settings. Consisting of brief and intense exercise intervals, HIIT requires less time commitment yet is able to produce the consistent targeted physical adaptations as conventional endurance training. To effectively characterize and monitor HIIT‐induced cellular and molecular responses, a highly accessible yet comprehensive biomarker discovery source is desirable. Both gene differential expression (DE) and gene set (GS) analyses were conducted using hair follicle transcriptome established from pre and postexercise subjects upon a 10‐day HIIT program by RNA‐Seq, Comparing between pre and posttraining groups, differentially expressed protein coding genes were identified. To interpret the functional significance of the DE results, a comprehensive GS analysis approach featuring multiple algorithms was used to enrich gene ontology (GO) terms and KEGG pathways. The GS analysis revealed enriched themes such as energy metabolism, cell proliferation/growth/survival, muscle adaptations, and cytokine–cytokine interaction, all of which have been previously proposed as HIIT responses. Moreover, related cell signaling pathways were also measured. Specifically, G‐protein‐mediated signal transduction, phosphatidylinositide 3‐kinases (PI3K) – protein kinase B (PKB) and Janus kinase (JAK) – Signal Transducer and Activator of Transcription (STAT) signaling cascades were over‐represented. Additionally, the RNA‐Seq analysis also identified several HIIT‐responsive microRNAs (miRNAs) that were involved in regulating hair follicle‐specific processes, such as miR‐99a. For the first time, this study demonstrated that both existing and new biomarkers like miRNA can be explored for HIIT using the transcriptomic responses exhibited by the hair follicle.
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Affiliation(s)
- Jing Zhang
- Chemistry and Chemical Engineering Department, Royal Military College of Canada, Kingston, ON, Canada
| | - Sarah J Wallace
- Chemistry and Chemical Engineering Department, Royal Military College of Canada, Kingston, ON, Canada
| | - Maria Y Shiu
- Defense Research and Development Canada, Toronto Research Centre, Toronto, ON, Canada
| | - Ingrid Smith
- Defense Research and Development Canada, Toronto Research Centre, Toronto, ON, Canada
| | - Shawn G Rhind
- Defense Research and Development Canada, Toronto Research Centre, Toronto, ON, Canada
| | - Valerie S Langlois
- Chemistry and Chemical Engineering Department, Royal Military College of Canada, Kingston, ON, Canada
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