Progress 07/01/23 to 06/30/24
Outputs
Target Audience:Academic Community Poultry Science Researchers.The invited talk at the University of Georgia and the presentation at the Plant and Animal Genome Meetings directly targeted researchers specializing inpoultry science, specifically those interested in geneomics,muscle biology and/ordisease. Broader Scientific Community.The publication inScientific Reportsand the presentation at the Plant and Animal Genome Meetings reached a wider audience within the scientific community, including researchers in fields such as animal science, veterinary medicine, animal genetics and genomics, and muscle disease. Students Graduate Students.The invited talk at the University of Georgia specifically addressed graduate students in the Department of Poultry Science. Industry Professionals Poultry Industry.The research findings, disseminated through publications and presentations, are relevant to the poultry industry, those involved in poultry breeding and genetics,broiler chicken production and animal health. This information can potentially inform breeding programs, improve feed formulations, and develop strategies to mitigate the impact of Wooden Breast. General Public Increased Reach.The publication inScientific Reportsand the University of Delaware article (https://www.udel.edu/udaily/2024/may/poultry-wooden-breast-syndrome-human-health-behnam-abasht-erin-brannick/) broaden the reach to the general public interested in animal health, food production, and potentially human health implications of Wooden Breast syndrome. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? This project provided a platform for the professional development ofPhD student Ziqing Wangwho successfully completed her dissertation research based on its findings. Through this work, she gained extensive hands-on experience in advanced research methodologies (spatial transcriptomics and metabolomics) data analysis techniques, scientific writing, presentation skills, and collaborative research. How have the results been disseminated to communities of interest?The results of this project have been disseminated to the scientific community throughpeer-reviewed publications, invited talks,presentations at national and international conferences, submitting data to online repositories:SRA;National Library of Medicine. What do you plan to do during the next reporting period to accomplish the goals?Identification of DNA Variants in Target Genomic Regions Gene Expression Analysis Metabolomics Analysis Variant-Trait Association Analysis
Impacts
What was accomplished under these goals?
We conducted aspatial transcriptomics study to characterize the cell-type-specific expression profile associated with the microscopic features observed in Wooden Breast myopathy. 1 cm3muscle sample was dissected from the cranial part of the right pectoralis major muscle from three randomly sampled broiler chickens at 23 days post-hatch and processed with Visium Spatial Gene Expression kits (10X Genomics), followed by high-resolution imaging and sequencing on the Illumina Nextseq 2000 system. WB classification was based on histopathologic features identified. Sequence reads were aligned to the chicken reference genome (Galgal6) and mapped to histological images. Unsupervised K-means clustering and Seurat integrative analysis differentiated histologic features and their specific gene expression pattern, including lipid laden macrophages (LLM), unaffected myofibers, myositis and vasculature. In particular, LLM exhibited reprogramming of lipid metabolism with up-regulated lipid transporters and genes in peroxisome proliferator-activated receptors pathway, possibly through P. Moreover, overexpression of fatty acid binding protein 5 could enhance fatty acid uptake in adjacent veins. In myositis regions, increased expression of cathepsins may play a role in muscle homeostasis and repair by mediating lysosomal activity and apoptosis. A better knowledge of different cell-type interactions at early stages of WB is essential in developing a comprehensive understanding.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Wang, Z., Khondowe, P., Brannick, E. and Abasht, B., 2024. Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens. Scientific Reports, 14(1), p.3450.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Velleman, S.G., Coy, C.S. and Abasht, B., 2024. Research Note: Chicken breast muscle satellite cell function: effect of expression of CNN1 and PHRF1. Poultry Science, 103(7), p.103781.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Abasht B. Integrative Analysis of Spatial Transcriptomic Data Provide Novel Insight into Wooden Breast in Broiler Chickens. Poultry Workshop, Plant and Animal Genome Meetings, Jan 2024
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Wang Z, Khondowe P, Brannick EM, Abasht B. Spatial Transcriptomics Study Revealed Alterations in Lipid Metabolism of Lipid Laden Macrophages in Broiler Chickens with Wooden Breast. In Poultry Science Association 2023 Annual Meeting (pp. 176-176).
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2023
Citation:
Ziqing Wang, HIGH THROUGHPUT SEQUENCING APPLICATIONS IN
STUDYING WOODEN BREAST AND ADIPOSITY IN
COMMERCIAL BROILER CHICKENS
- Type:
Other
Status:
Published
Year Published:
2024
Citation:
UDaily article: https://www.udel.edu/udaily/2024/may/poultry-wooden-breast-syndrome-human-health-behnam-abasht-erin-brannick/
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Invited talk: Abasht. 2023. Spatial Transcriptomic Approach to Study Wooden Breast in Commercial Broilers, Grad Seminar Series, Department of Poultry Science, University of Georgia, Athens, GA
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Progress 07/01/22 to 06/30/23
Outputs
Target Audience:Research results were presented at the Poultry Genomics Workshop at Plant and Animal Genome meeting in Jan 2023 and inPoultry Science Association 2023 Annual Meeting. Additionally,a manuscript published in a peer-reviewed scientism journalin 2023 (Scientific Reports, 13(1), p.474) Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One PhD student (Ziqng Wang) and one Fulbright Visiting Scholar from Zambia (Paul Khondowe) were trained on molecular biology and advanced microscopy techniques. An additional non-thesis MS student was trained on scoring muscle histology specimens for pathologic lesions. How have the results been disseminated to communities of interest?Research results were presented at the Poultry Genomics Workshop at Plant and Animal Genome meeting in Jan 2023 and inPoultry Science Association 2023 Annual Meeting. Additionally a manuscript published in a peer-reviewed scientism journalin 2023 (Scientific Reports, 13(1), p.474) What do you plan to do during the next reporting period to accomplish the goals?For next reporting, research was planned to conduct spatial transcriptomics to identify cellular expression of genes involved in Wooden Breast.
Impacts
What was accomplished under these goals?
We studied the effect ofcandidate genes associated with Wooden Breast on satellite cell proliferation, differentiation, and the synthesis of lipids by satellite cells is unknown. To determine the effect of calponin 1 (CNN1), HRas proto-oncogene (HRAS), enoyl-CoA hydratase 1 (ECH1), glutamic-oxaloacetic transaminase 1 (GOT1), dickkopf 3 (DKK3), and PHD and ring fingers domains 1 (PHRF1) on satellite cell activity, their expression was knocked during proliferation or differentiation using small interfering RNA. Satellite cells isolated from a commercial Ross 708 broilers and a Randombred chicken (RBch) line were used in the current study. Of the genes studied,CNN1andPHRF1had the greatest effect on satellite cell activity and lipid accumulation in both lines. Proliferation was reduced in the Ross 708 and RBch lines by knocking the expression of both genes and differentiation was affected with a line and treatment interaction when gene expression was reduced at the beginning of proliferation. Expression ofCNN1andPHRF1during proliferation is needed for the formation of multinucleated myotubes. During differentiation lipid accumulation was decreased with knocking down the expression ofCNN1andPHRF1. Both CNN1 and PHRF1 have not been reported in skeletal muscle and further research is required to determine their effect on satellite cell-mediated growth and regeneration of the breast muscle. We also conductedintegrative study of transcriptomics and metabolomics aimed to further characterize the candidate gene functions and their roles in metabolism. The Joint Pathway Analysis was applied on 119 metabolites and 3444 genes exhibiting differential abundance or expression between WB affected and unaffected chickens. Mitochondrial dysfunctions in WB was suggested by higher levels of monoacylglycerols and down-regulated genes involved in lipid production, fatty acid beta oxidation, and oxidative phosphorylation. Lower levels of carnosine and anserine, along with down-regulated carnosine synthase 1 suggested decreased carnosine synthesis and hence impaired antioxidant capacity in WB. Additionally, Weighted Gene Co-expression Network Analysis results indicated that abundance of inosine monophosphate, significantly lower in WB muscle, was correlated with mRNA expression levels of numerous genes related to focal adhesion, extracellular matrix and intercellular signaling, implying its function in connecting and possibly regulating multiple key biological pathways. Overall, this studied provided insight into the interconnection between gene expression and metabolic functions and help understand the roles of some candidate genes in development of Wooden Breast disease.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Wang Z., Brannick E.M., Abasht B. 2023. Integrative Transcriptomic and Metabolomic Analysis Reveals Alterations in Energy Metabolism and Mitochondrial Functionality in Broiler Chickens with Wooden Breast. Scientific Reports, 13(1), p.4747.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2023
Citation:
Spatial Transcriptomics and 3UTR sequencing provide novel insights into the Development of Wooden Breast Disease and Adiposity in Commercial Broiler Chickens. Ziqing Wang, 2023
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Wang Z, Khondowe P, Brannick EM, Abasht B.. Spatial Transcriptomics Reveals Cell Types Responsible for Key Metabolic Features of Wooden Breast Disease in Broiler Chickens. Plant and Animal Genome Meetings, San Diego, CA, Jan 2023
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Wang Z, Khondowe P, Brannick EM, Abasht B. Spatial Transcriptomics Study Revealed Alterations in Lipid Metabolism of Lipid Laden Macrophages in Broiler Chickens with Wooden Breast. In Poultry Science Association 2023 Annual Meeting (pp. 176-176).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Wang Z, Khondowe P, Brannick EM, Abasht B. Spatial Transcriptomics Reveals Cell Types Responsible for Key Metabolic Features of Wooden Breast Disease in Broiler Chickens. Plant and Animal Genome Meetings, San Diego, CA, Jan 2023
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Progress 07/01/21 to 06/30/22
Outputs
Target Audience:Scientific community, poultry breeders, students Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided for 8 undergrad and 2 grad students. Student participated in a wide range of activities, including but not restricted to feeding breeders (hens and roosters), collecting eggs, setting eggs in an incubator, candling eggs to identify viable embryos, hatching eggs, raising chicks, tagging chicks (wing-band), recording live weight, routine checking on live chickens, postmortem tissue sample and data collection, tissue sample processing (homogenization) and RNA isolation from tissue samples. RNA quality and quantity checks, blood sample collection and separating plasma from blood cells. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals? Histopathologic Analysis of 567 p. major muscle samples harvested at necropsy Spatial transcriptomic analysis using Visium Spatial Transcriptomic method RNA and DNA isolation from blood and tissue samples RNAi assays for candidate genes to knock-down gene expression in satellite cells in co-PI's lab
Impacts
What was accomplished under these goals?
Live animal experiment: A new experiment was conducted using commercial broiler chickensat the University of Delaware. Cobb Breeders including 30 hens (Cobb500) and 6 roosters (Cobb Vantage)were obtained from abreeders farm in New Holland, PA.Breeders were randomly placed in 2 breeder houses, 15 hens and 3 roosters per house. Egg were collected twice daily and stored in a cold room until incubation.Eggs from one week of egg collection were incubated in an egg incubator at 100 °F, 70% humidity, and checked by candling at embryonic day 11;non-viableeggs were disposed properly.Upon hatching,chickenswere placed in chicken houses at the University of Delawareand raised in accordance with the Animal Care and Use Handbook 2019 of the UD College of Agriculture and Natural Resources. Chicks had free access to feed and water throughout the experiment.Tissue samples were harvested post-euthanasia at day 14 15, 16, 17 post-hatch immediately frozen in liquid nitrogen, and stored in a −80 °C freezer until subsequent analysis.Sex was determined post-euthanasia during necropsy by visual inspection of gonads and will subsequently be confirmed by PCR-based sexing, as we described before (Zhuo et al., 2017). During necropsy, the entire p. major muscle was removed, weighed, and samples from the p. major muscle were taken from the cranial aspect (which is typically the fastest growing part of the muscle) of the left p. major muscle. Two sets of samples, one for histopathologic analysis and another for gene expression analysis were collected from the same sampling location.While this project is focused on the p. major muscle, two important metabolic tissues (liver and adipose) were also collected forpotentialfuture studies.Body weight were recorded and cardiac blood samples were collectedpost-euthanasia. In total, tissue and blood samples were collected from 534 chicks over 5 hatches. Histopathologic Analysis: One set of p. majorsamples harvested at necropsy were placed in 10% neutral buffered formalin for histologic analysis. Tissues were trimmed, embedded transversely and longitudinally in paraffin, sectioned to 4 μm thickness, and autostained with Hematoxylin and Eosin. Slides will be analyzed microscopically in a blinded manner by students trained by the project collaborator Dr. Brannick-board certified veterinary anatomic pathologist screening for lesions of vasculitis/phlebitis, abnormal lipid deposition, and WB (myofiber damage, myositis, regeneration, fibrosis, edema, etc.).
Publications
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