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Muhuitijiang B, Zhou J, Zhou R, Zhang Z, Yan G, Zheng Z, Zeng X, Zhu Y, Wu H, Gao R, Zhu T, Shi X, Tan W. Development and experimental validation of an M2 macrophage and platelet-associated gene signature to predict prognosis and immunotherapy sensitivity in bladder cancer. Cancer Sci 2024; 115:1417-1432. [PMID: 38422408 DOI: 10.1111/cas.16113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Platelets and M2 macrophages both play crucial roles in tumorigenesis, but their relationship and the prognosis value of the relative genes in bladder cancer (BLCA) remain obscure. In the present study, we found that platelets stimulated by BLCA cell lines could promote M2 macrophage polarization, and platelets were significantly associated with the infiltration of M2 macrophages in BLCA samples. Through the bioinformatic analyses, A2M, TGFB3, and MYLK, which were associated with platelets and M2 macrophages, were identified and verified in vitro and then included in the predictive model. A platelet and M2 macrophage-related gene signature was constructed to evaluate the prognosis and immunotherapeutic sensitivity, helping to guide personalized treatment and to disclose the underlying mechanisms.
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Affiliation(s)
| | - Jiawei Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ranran Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiyong Zhang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guang Yan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zaosong Zheng
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiangbo Zeng
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuanchao Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haowei Wu
- The First Clinical Medical College of Southern Medical University, Guangzhou, Guangdong, China
| | - Ruxi Gao
- The First Clinical Medical College of Southern Medical University, Guangzhou, Guangdong, China
| | - Tianhang Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaojun Shi
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Iqbal MA, Hadlich F, Reyer H, Oster M, Trakooljul N, Murani E, Perdomo‐Sabogal A, Wimmers K, Ponsuksili S. RNA-Seq-based discovery of genetic variants and allele-specific expression of two layer lines and broiler chicken. Evol Appl 2023; 16:1135-1153. [PMID: 37360029 PMCID: PMC10286233 DOI: 10.1111/eva.13557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/28/2023] Open
Abstract
Recent advances in the selective breeding of broilers and layers have made poultry production one of the fastest-growing industries. In this study, a transcriptome variant calling approach from RNA-seq data was used to determine population diversity between broilers and layers. In total, 200 individuals were analyzed from three different chicken populations (Lohmann Brown (LB), n = 90), Lohmann Selected Leghorn (LSL, n = 89), and Broiler (BR, n = 21). The raw RNA-sequencing reads were pre-processed, quality control checked, mapped to the reference genome, and made compatible with Genome Analysis ToolKit for variant detection. Subsequently, pairwise fixation index (F ST) analysis was performed between broilers and layers. Numerous candidate genes were identified, that were associated with growth, development, metabolism, immunity, and other economically significant traits. Finally, allele-specific expression (ASE) analysis was performed in the gut mucosa of LB and LSL strains at 10, 16, 24, 30, and 60 weeks of age. At different ages, the two-layer strains showed significantly different allele-specific expressions in the gut mucosa, and changes in allelic imbalance were observed across the entire lifespan. Most ASE genes are involved in energy metabolism, including sirtuin signaling pathways, oxidative phosphorylation, and mitochondrial dysfunction. A high number of ASE genes were found during the peak of laying, which were particularly enriched in cholesterol biosynthesis. These findings indicate that genetic architecture as well as biological processes driving particular demands relate to metabolic and nutritional requirements during the laying period shape allelic heterogeneity. These processes are considerably affected by breeding and management, whereby elucidating allele-specific gene regulation is an essential step towards deciphering the genotype to phenotype map or functional diversity between the chicken populations. Additionally, we observed that several genes showing significant allelic imbalance also colocalized with the top 1% of genes identified by the FST approach, suggesting a fixation of genes in cis-regulatory elements.
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Affiliation(s)
| | - Frieder Hadlich
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Henry Reyer
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Michael Oster
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Nares Trakooljul
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Eduard Murani
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | | | - Klaus Wimmers
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
- Faculty of Agricultural and Environmental SciencesUniversity RostockRostockGermany
| | - Siriluck Ponsuksili
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
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Ponsuksili S, Hadlich F, Perdomo-Sabogal A, Reyer H, Oster M, Trakooljul N, Iqbal MA, Schmucker S, Stefanski V, Roth C, Silva AC, Huber K, Sommerfeld V, Rodehutscord M, Wimmers K. The dynamics of molecular, immune and physiological features of the host and the gut microbiome, and their interactions before and after onset of laying in two hen strains. Poult Sci 2022; 102:102256. [PMID: 36335740 PMCID: PMC9640326 DOI: 10.1016/j.psj.2022.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Aggregation of data, including deep sequencing of mRNA and miRNA data in jejunum mucosa, abundance of immune cells, metabolites, or hormones in blood, composition of microbiota in digesta and duodenal mucosa, and production traits collected along the lifespan, provides a comprehensive picture of lifelong adaptation processes. Here, respective data from two laying hen strains (Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL) collected at 10, 16, 24, 30, and 60 wk of age were analyzed. Data integration revealed strain- and stage-specific biosignatures, including elements indicative of molecular pathways discriminating the strains. Although the strains performed the same, they differed in the activity of immunological and metabolic functions and pathways and showed specific gut-microbiota-interactions in different production periods. The study shows that both strains employ different strategies to acquire and maintain their capabilities under high performance conditions, especially during the transition phase. Furthermore, the study demonstrates the capacity of such integrative analyses to elucidate molecular pathways that reflect functional biodiversity. The bioinformatic reduction of the multidimensional data provides good guidance for further manual review of the data.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany,Corresponding author:
| | - Frieder Hadlich
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany
| | - Alvaro Perdomo-Sabogal
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany
| | - Michael Oster
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany
| | - Muhammad Arsalan Iqbal
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany
| | - Sonja Schmucker
- University of Hohenheim, Institute of Animal Science, 70599 Stuttgart, Germany,University Rostock, Faculty of Agricultural and Environmental Sciences, 18059 Rostock, Germany
| | - Volker Stefanski
- University of Hohenheim, Institute of Animal Science, 70599 Stuttgart, Germany
| | - Christoph Roth
- University of Hohenheim, Institute of Animal Science, 70599 Stuttgart, Germany
| | | | - Korinna Huber
- University of Hohenheim, Institute of Animal Science, 70599 Stuttgart, Germany
| | - Vera Sommerfeld
- University of Hohenheim, Institute of Animal Science, 70599 Stuttgart, Germany
| | - Markus Rodehutscord
- University of Hohenheim, Institute of Animal Science, 70599 Stuttgart, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 Dummerstorf, Germany,University Rostock, Faculty of Agricultural and Environmental Sciences, 18059 Rostock, Germany
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