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Rong S, Root E, Reilly SK. Massively parallel approaches for characterizing noncoding functional variation in human evolution. Curr Opin Genet Dev 2024; 88:102256. [PMID: 39217658 DOI: 10.1016/j.gde.2024.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
The genetic differences underlying unique phenotypes in humans compared to our closest primate relatives have long remained a mystery. Similarly, the genetic basis of adaptations between human groups during our expansion across the globe is poorly characterized. Uncovering the downstream phenotypic consequences of these genetic variants has been difficult, as a substantial portion lies in noncoding regions, such as cis-regulatory elements (CREs). Here, we review recent high-throughput approaches to measure the functions of CREs and the impact of variation within them. CRISPR screens can directly perturb CREs in the genome to understand downstream impacts on gene expression and phenotypes, while massively parallel reporter assays can decipher the regulatory impact of sequence variants. Machine learning has begun to be able to predict regulatory function from sequence alone, further scaling our ability to characterize genome function. Applying these tools across diverse phenotypes, model systems, and ancestries is beginning to revolutionize our understanding of noncoding variation underlying human evolution.
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Affiliation(s)
- Stephen Rong
- Department of Genetics, Yale University, New Haven, CT, USA.
| | - Elise Root
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Steven K Reilly
- Department of Genetics, Yale University, New Haven, CT, USA; Wu Tsai Institute, Yale University, New Haven, CT, USA.
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Tchoukalova YD, Phung TN, Kennedy MM, Miranda-Grandjean D, Becquer E, Chen L, Zhang N, Dinu V, Wilson MA, Lott DG. Idiopathic Subglottic Stenosis Is Associated With More Frequent and Abnormal Squamous Metaplasia. Ann Otol Rhinol Laryngol 2024; 133:214-223. [PMID: 37740367 DOI: 10.1177/00034894231201016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
OBJECTIVES Gain insights into the pathophysiology of idiopathic subglottic stenosis (iSGS) by investigating differences in transcriptome of subglottic mucosal tissue between patients with iSGS and controls, and between tracheal and subglottic tissue within patients. METHODS RNA sequencing was conducted on biopsied mucosal samples collected from subglottic and tracheal (in-patient control) regions in iSGS patients, and from subglottis in controls. The gene expression differences were validated on a protein level by (1) staining the tissue samples obtained from a second cohort of patients and controls; and (2) in vitro functional assays using primary subglottic epithelial cells from both iSGS patients and healthy donors. RESULTS We found 7 upregulated genes in the subglottic region of iSGS patients relative to both the tracheal mucosa and subglottic region of controls. A gene ontology enrichment analysis found that the epithelial cell differentiation and cornification pathways are significant, involving specifically 3 of the genes: involucrin (IVL), small proline rich protein 1B (SPRR1B), and keratin 16 (KRT16). Involvement of these pathways suggests squamous metaplasia of the epithelium. Histological analyses of epithelium in subglottic mucosal biopsies revealed squamous metaplasia in 41% of the samples from iSGS patients and in 25% from controls. Immunohistochemical evaluation of the samples presented with squamous epithelium revealed increased expression of the protein encoded by SPRR1B, hyperproliferative basal cells, shedding of apical layers, and accompanying lesions in iSGS compared to CTRL. Cultured primary subglottic epithelial cells from iSGS patients had higher proliferation rates compared to healthy donors and squamous metaplastic differentiation formed thinner epithelia with increased expression proteins encoded by INV, SPRR1B, and KRT16, suggesting intrinsic dysfunction of basal cells in iSGS. CONCLUSIONS Abnormal squamous differentiation of epithelial cells may contribute to the pathogenesis of iSGS. Patients having metaplastic epithelial phenotype may be sensitive to drugs that reverse it to a normal phenotype.
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Affiliation(s)
- Yourka D Tchoukalova
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Tanya N Phung
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Faculty of Science, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maeve M Kennedy
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Baylor College of Medicine, Houston, TX, USA
| | | | - Emanuel Becquer
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Contexture, Phoenix, AZ, USA
| | - Longwen Chen
- Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Nan Zhang
- Department of Quantitative Health Sciences, Mayo, AZ Clinic, Scottsdale, AZ, USA
| | - Valentin Dinu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Basic Medical Sciences, Arizona State University, Phoenix, AZ, USA
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - David G Lott
- Head and Neck Regenerative Medicine Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, USA
- Department of Otolaryngology-Head and Neck Surgery, Division of Laryngology, Mayo Clinic Arizona, Phoenix, AZ, USA
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Schmidt AD, Miciano C, Zheng Q, Mathyer ME, Grice EA, de Guzman Strong C. Involucrin Modulates Vitamin D Receptor Activity in the Epidermis. J Invest Dermatol 2023; 143:1052-1061.e3. [PMID: 36642403 PMCID: PMC10240284 DOI: 10.1016/j.jid.2022.12.009] [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: 04/04/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 01/14/2023]
Abstract
Terminally differentiated keratinocytes are critical for epidermal function and are surrounded by involucrin (IVL). Increased IVL expression is associated with a near-selective sweep in European populations compared with those in Africa. This positive selection for increased IVL in the epidermis identifies human adaptation outside of Africa. The functional significance is unclear. We hypothesize that IVL modulates the environmentally sensitive vitamin D receptor (VDR) in the epidermis. We investigated VDR activity in Ivl‒/‒ and wild-type mice using vitamin D agonist (MC903) treatment and comprehensively determined the inflammatory response using single-cell RNA sequencing and associated skin microbiome changes using 16S bacterial phylotyping. VDR activity and target gene expression were reduced in Ivl‒/‒ mouse skin, with decreased MC903-mediated skin inflammation and significant reductions in CD4+ T cells, basophils, macrophages, monocytes, and type II basal keratinocytes and an increase in suprabasal keratinocytes. Coinciding with the dampened MC903-mediated inflammation, the skin microbiota of Ivl‒/‒ mice was more stable than that of the wild-type mice, which exhibited an MC903-responsive increase in Bacteroidetes and a decrease in Firmicutes. Together, our studies in Ivl‒/‒ mice identify a functional role for IVL to positively impact VDR activity and suggest an emerging IVL/VDR paradigm for adaptation in the human epidermis.
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Affiliation(s)
- Alina D Schmidt
- Division of Dermatology, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for Pharmacogenomics, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Charlene Miciano
- Division of Dermatology, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for Pharmacogenomics, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Qi Zheng
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mary Elizabeth Mathyer
- Division of Dermatology, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for Pharmacogenomics, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cristina de Guzman Strong
- Division of Dermatology, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for Pharmacogenomics, John T. Milliken Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Center for Cutaneous Biology and Immunology Research, Department of Dermatology, Henry Ford Health, Detroit, Michigan, USA; Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, Michigan, USA; Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, Michigan, USA.
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McDonald JMC, Reed RD. Patterns of selection across gene regulatory networks. Semin Cell Dev Biol 2022; 145:60-67. [PMID: 35474149 DOI: 10.1016/j.semcdb.2022.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.
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Affiliation(s)
- Jeanne M C McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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Starr I, Seiffert-Sinha K, Sinha AA, Gokcumen O. Evolutionary context of psoriatic immune skin response. Evol Med Public Health 2022; 9:474-486. [PMID: 35154781 PMCID: PMC8830311 DOI: 10.1093/emph/eoab042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/22/2021] [Indexed: 12/18/2022] Open
Abstract
The skin is vital for protecting the body and perceiving external stimuli in the environment. Ability to adapt between environments is in part based on skin phenotypic plasticity, indicating evolved homeostasis between skin and environment. This homeostasis reflects the greater relationship between the body and the environment, and disruptions in this balance may lead to accumulation of susceptibility factors for autoimmune conditions like psoriasis. In this study, we examined the relationship between rapid, lineage-specific evolution of human skin and formation of psoriatic skin responses at the transcriptome level. We collected skin tissue biopsies from individuals with psoriasis and compared gene expression in psoriatic plaques to non-plaque psoriatic skin. We then compared these data with non-psoriatic skin transcriptome data from multiple primate species. We found 67 genes showing human-specific skin expression that are also differentially regulated in psoriatic skin; these genes are significantly enriched for skin barrier function, immunity and neuronal development. We identified six gene clusters with differential expression in the context of human evolution and psoriasis, suggesting underlying regulatory mechanisms in these loci. Human and psoriasis-specific enrichment of neuroimmune genes shows the importance of the ongoing evolved homeostatic relationship between skin and external environment. These results have implications for both evolutionary medicine and public health, using transcriptomic data to acknowledge the importance of an individual’s surroundings on their overall health. The skin is important for protecting the body from the environment and perceiving external stimuli, creating an evolved balance between skin and the environment. We compare skin gene expression in humans with psoriasis to humans and non-human primates without psoriasis to better understand human-specific evolutionary changes in the skin. Our results suggest important evolutionary links between skin perception, human-specific skin development and immune response.
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Affiliation(s)
- Izzy Starr
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Kristina Seiffert-Sinha
- Department of Dermatology, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Animesh A Sinha
- Department of Dermatology, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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Lee JS, Kim J, Cui B, Kim SK, Cho SA, An S, Cho SW. Hybrid skin chips for toxicological evaluation of chemical drugs and cosmetic compounds. LAB ON A CHIP 2022; 22:343-353. [PMID: 34904990 DOI: 10.1039/d1lc00550b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Development of drugs and cosmetics for topical application require safety tests in skin models. However, current skin models, such as skin cell sheets and artificial tissue-engineered skin, do not allow sophisticated toxicological evaluations (e.g., sensory irritation, hepatotoxicity). Animal models are prohibited worldwide for testing cosmetics. Therefore, reliable human skin models that recapitulate physiological events in skin tissue need to be established under in vitro settings. In this study, hybrid human skin models that enable delicate toxicological evaluations of drugs and cosmetic compounds are demonstrated. To recapitulate skin cornification, keratinocytes in the top layer of a vertical microfluidic chip were cultured at the air-liquid interface. For the skin-nerve hybrid model, differentiated neural stem cells in 3D collagen were positioned adjacent to and right below the skin layer. This model enables real-time quantitative skin sensitization analysis following chemical treatments by detecting alterations in neuronal activity in combination with a calcium imaging technique. For the skin-liver model, hepatic cells derived from pluripotent stem cells were cultured in 3D collagen distant from the skin layer. Potential hepatotoxicity of cutaneously applied chemicals in this model can be evaluated by quantification of glutathione and reactive oxygen species. Our study suggests that 3D hybrid skin chips would provide useful human skin models in pharmaceutical and cosmetic industries.
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Affiliation(s)
- Jong Seung Lee
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jin Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Baofang Cui
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Su Kyeom Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Sun-A Cho
- Safety & Microbiology Lab, Amorepacific Co. R&D Unit, Yongin 17038, Republic of Korea
| | - Susun An
- Safety & Microbiology Lab, Amorepacific Co. R&D Unit, Yongin 17038, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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