1
|
Navrazhina K, Renert-Yuval Y, Khattri S, Hamade H, Meariman M, Andrews E, Kim M, NandyMazumdar M, Gour DS, Bose S, Williams SC, Garcet S, Correa da Rosa J, Gottlieb AB, Krueger JG, Guttman-Yassky E. Tape strips detect molecular alterations and cutaneous biomarkers in skin of patients with hidradenitis suppurativa. J Am Acad Dermatol 2024; 90:749-758. [PMID: 38049071 DOI: 10.1016/j.jaad.2023.11.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) has a high unmet need for better treatments. Biopsies are considered the gold standard for studying molecular alterations in skin. A reproducible, minimally invasive approach is needed for longitudinal monitoring in trials and in pediatric populations. OBJECTIVE To determine whether skin tape strips can detect molecular alterations in HS and identify biomarkers of disease activity. METHODS We performed RNA sequencing on tape strips collected from lesional and healthy-appearing (nonlesional) HS skin (n = 22) and healthy controls (n = 21). We correlated the expression of skin biomarkers between tape strips and a previously published gene-signature of HS biopsies. RESULTS Tape strips detected upregulation of known HS biomarkers (eg, Interleukin[IL]-17A) in nonlesional and/or lesional skin and also identified novel clinically actionable targets, including OX40 and JAK3. The expression of Th17 and tumor necrosis factor-α pathways were highly correlated between tape strips and biopsies. HS clinical severity was significantly associated with expression of biomarkers (eg tumor necrosis factor-α , IL-17 A/F, OX40, JAK1-3, IL-4R) in HS lesional and/or nonlesional skin. LIMITATIONS Sample size. Tape stripping is limited in depth. CONCLUSION This study validates tape strips as a minimally-invasive approach to identify cutaneous biomarkers in HS. This provides a novel avenue for monitoring treatment efficacy and a potential step toward individualized therapy in HS.
Collapse
Affiliation(s)
- Kristina Navrazhina
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York; Laboratory for Investigative Dermatology, Rockefeller University, New York, New York
| | - Yael Renert-Yuval
- Laboratory for Investigative Dermatology, Rockefeller University, New York, New York; Pediatric Dermatology Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saakshi Khattri
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hassan Hamade
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marguerite Meariman
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elizabeth Andrews
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Madeline Kim
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Monali NandyMazumdar
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Digpal S Gour
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Swaroop Bose
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samuel C Williams
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sandra Garcet
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joel Correa da Rosa
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alice B Gottlieb
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - James G Krueger
- Laboratory for Investigative Dermatology, Rockefeller University, New York, New York
| | - Emma Guttman-Yassky
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York.
| |
Collapse
|
2
|
Andrews KR, New DD, Gour DS, Francetich K, Minnich SA, Robison BD, Hovde CJ. Author Correction: Genomic surveillance identifies potential risk factors for SARS-CoV-2 transmission at a mid-sized university in a small rural town. Sci Rep 2023; 13:9874. [PMID: 37336957 DOI: 10.1038/s41598-023-36764-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Affiliation(s)
- Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA.
| | - Daniel D New
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Digpal S Gour
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | | | - Scott A Minnich
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, 83844, USA
| | - Barrie D Robison
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Carolyn J Hovde
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, 83844, USA
| |
Collapse
|
3
|
Andrews KR, New DD, Gour DS, Francetich K, Minnich SA, Robison BD, Hovde CJ. Genomic surveillance identifies potential risk factors for SARS-CoV-2 transmission at a mid-sized university in a small rural town. Sci Rep 2023; 13:7902. [PMID: 37193760 PMCID: PMC10185956 DOI: 10.1038/s41598-023-34625-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
Understanding transmission dynamics of SARS-CoV-2 in institutions of higher education (IHEs) is important because these settings have potential for rapid viral spread. Here, we used genomic surveillance to retrospectively investigate transmission dynamics throughout the 2020-2021 academic year for the University of Idaho ("University"), a mid-sized IHE in a small rural town. We generated genome assemblies for 1168 SARS-CoV-2 samples collected during the academic year, representing 46.8% of positive samples collected from the University population and 49.8% of positive samples collected from the surrounding community ("Community") at the local hospital during this time. Transmission dynamics differed for the University when compared to the Community, with more infection waves that lasted shorter lengths of time, potentially resulting from high-transmission congregate settings along with mitigation efforts implemented by the University to combat outbreaks. We found evidence for low transmission rates between the University and Community, with approximately 8% of transmissions into the Community originating from the University, and approximately 6% of transmissions into the University originating from the Community. Potential transmission risk factors identified for the University included congregate settings such as sorority and fraternity events and residences, holiday travel, and high caseloads in the surrounding community. Knowledge of these risk factors can help the University and other IHEs develop effective mitigation measures for SARS-CoV-2 and similar pathogens.
Collapse
Affiliation(s)
- Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA.
| | - Daniel D New
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Digpal S Gour
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | | | - Scott A Minnich
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, 83844, USA
| | - Barrie D Robison
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Carolyn J Hovde
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, 83844, USA
| |
Collapse
|
4
|
Barbosa S, Andrews KR, Goldberg AR, Gour DS, Hohenlohe PA, Conway CJ, Waits LP. The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. Mol Ecol 2021; 30:4673-4694. [PMID: 34324748 DOI: 10.1111/mec.16096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/10/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus - NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both theinter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.
Collapse
Affiliation(s)
- Soraia Barbosa
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Kimberly R Andrews
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA
| | - Amanda R Goldberg
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Digpal S Gour
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Paul A Hohenlohe
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA.,Department of Biological Sciences, College of Science, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-3051, USA
| | - Courtney J Conway
- U.S. Geological Survey, Idaho Cooperative Fish & Wildlife Research Unit, Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, 83844-1141, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| |
Collapse
|
5
|
Goldberg AR, Conway CJ, Tank DC, Andrews KR, Gour DS, Waits LP. Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival. Ecol Evol 2020; 10:7627-7643. [PMID: 32760553 PMCID: PMC7391308 DOI: 10.1002/ece3.6488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 01/18/2023] Open
Abstract
In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.
Collapse
Affiliation(s)
- Amanda R. Goldberg
- Idaho Cooperative Fish and Wildlife Research UnitDepartment of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Courtney J. Conway
- U.S. Geological SurveyIdaho Cooperative Fish and Wildlife Research UnitUniversity of IdahoMoscowIDUSA
| | - David C. Tank
- Department of Biological Sciences and Stillinger HerbariumUniversity of IdahoMoscowIDUSA
| | - Kimberly R. Andrews
- Department of Fish & Wildlife Sciences and Institute for Bioinformatics and Evolutionary Studies (IBEST)University of IdahoMoscowIDUSA
| | - Digpal S. Gour
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| |
Collapse
|
6
|
Gour DS, Reddy PA. Genetic monitoring critical in low-density and poorly studied tiger ( Panthera tigris) habitats in India. A comment by D.S. Gour & P.A. Reddy. ETHOL ECOL EVOL 2016. [DOI: 10.1080/03949370.2015.1119195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Digpal S. Gour
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- Escuela de Ingeniería en Alimentos, Biotecnología y Agronomía, Instituto Tecnológico y de Estudios Superiores de Monterrey, Querétaro 76130, México
| | - Patlolla Anuradha Reddy
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| |
Collapse
|
7
|
Kumar D, Sharma R, Pandey AK, Gour DS, Malik G, Ahlawat SPS, Jain A. Genetic diversity and bottleneck analysis of Indian bellary sheep by microsatellite markers. Genetika 2007; 43:1198-1208. [PMID: 17990518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Bellary sheep population variability and structure was investigated genetically utilizing FAO recommended microsatellite markers. Genetic variation at 20 microsatellite loci, population structure, and genetic bottleneck hypothesis were examined. Estimates of genetic variability such as effective number of alleles and gene diversities revealed substantial genetic variation frequently displayed by microsatellite markers. A total of 133 alleles were detected. Average polymorphism across the studied loci and expected gene diversity in the population were 1.419 +/- 0.405 and 0.684 +/- 0.140, respectively. No significant genotypic linkage disequilibrium was detected across population, suggesting no evidence of linkage between loci. The population was observed to be significantly differentiated into different groups, showed fairly high level of inbreeding (f = 0.253 +/- 0.050) and global heterozygote deficit. Population structure analysis indicated the intermixing/introduction of unique/rare alleles in these migrating flocks. A normal L-shaped distribution of mode-shift test, non-significant heterozygosity excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests suggested that there was no recent bottleneck. The study revealed that even breed with increasing population trend needs genetic management for the conservation and improvement.
Collapse
Affiliation(s)
- D Kumar
- Small Ruminant Molecular Genetics Laboratory, DNA Fingerprinting Unit, National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, India
| | | | | | | | | | | | | |
Collapse
|