1
|
Qu X, Huang Q, Li H, Lou F. Comparative transcriptomics revealed the ecological trap effect of linearly polarized light on Oratosquilla oratoria. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101234. [PMID: 38631126 DOI: 10.1016/j.cbd.2024.101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
Although polarized light can assist many animals in performing special visual tasks, current polarized light pollution (PLP) caused by urban construction has been shown to induce maladaptive behaviors of PL-sensitive animals and change ecological interactions. However, the underlying mechanisms remain unclear. Our previous work hypothesized that linearly polarized light (LPL) is an ecological trap for Oratosquilla oratoria, a common Stomatopoda species in the China Sea. Here we explored the underlying negative effects of artificially LPL on O. oratoria based on comparative transcriptomics. We identified 3616 differentially expressed genes (DEGs) in O. oratoria compound eyes continuous exposed to natural light (NL) and LPL scenarios. In comparison with the NL scenario, a total of 1972 up- and 1644 down- regulated genes were obtained from the O. oratoria compound eyes under LPL scenario, respectively. Furthermore, we performed functional annotation of those DEGs described above and identified 65 DEGs related to phototransduction, reproduction, immunity, and synapse. Based on the functional information, we suspected that continuous LPL exposure could block the light transmission, disrupt the reproductive process, and lead to the progressive failure of the immune response of O. oratoria. In conclusion, this study is the first to systematically describe the negative effects of artificial LPL exposure on O. oratoria at the genetic level, and it can improve the biological conservation theory behind PLP.
Collapse
Affiliation(s)
- Xiuyu Qu
- School of Ocean, Yantai University, Yantai 264003, Shandong, China
| | - Qi Huang
- School of Food Science and Bioengineering, Yantai Institute of Technology, Yantai 264003, Shandong, China
| | - Huanjun Li
- Shandong Marine Resource and Environment Research Institute, Yantai 264003, Shandong, China
| | - Fangrui Lou
- School of Ocean, Yantai University, Yantai 264003, Shandong, China.
| |
Collapse
|
2
|
Dong B, Wu Y, Zhang J, Gu Y, Xie R, He X, Pang X, Wang X, Cui Y. A novel immunogenic cell death-related subtype classification and risk signature for predicting prognosis and immunotherapy efficacy in gastric cancer. Front Immunol 2023; 14:1162876. [PMID: 37215130 PMCID: PMC10196197 DOI: 10.3389/fimmu.2023.1162876] [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: 02/10/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
The majority of gastric cancer (GC) patients are in a progressive stage at the initial stage of treatment, and the overall response rate to immunotherapy remains unsatisfactory largely due to the lack of effective prognostic biomarkers. Immunogenic cell death (ICD) was identified as a new form of regulated cell death that can activate adaptive immune responses and further promote immunotherapy efficacy. Therefore, we attempted to characterize the ICD-associated signature to stratify patients who could benefit from immunotherapy. In our study, two subgroups of patients were identified based on the data of 34 ICD-related genes extracted from The Cancer Genome Atlas database via consensus clustering. The estimated scores, stromal scores, immune scores, tumor purity, and survival rate showed significant differences between the low and high ICD groups. Then, we constructed an ICD-related risk signature, including IFNB1, IL6, LY96, and NT5E, using least absolute shrinkage and selection operator Cox regression analysis; then, high- and low-risk groups could be clearly distinguished. Notably, the risk score is a reliable predictor of the prognosis and immunotherapy outcome in GC, which was further validated in an immunohistochemistry assay. These results suggest that ICD is closely associated with the prognosis and tumor immune microenvironment in GC. Taken together, this study first constructed and validated a prognostic ICD-related signature to predict the survival and effect of immunotherapy in GC, which provided new insight for potent individualized immunotherapy strategies.
Collapse
Affiliation(s)
- Bingqi Dong
- Department of General Surgery, Peking University First Hospital, Beijing, China
| | - Yingchao Wu
- Department of General Surgery, Peking University First Hospital, Beijing, China
| | - Junling Zhang
- Department of General Surgery, Peking University First Hospital, Beijing, China
| | - Yanlun Gu
- Department of Pharmacy, Peking University First Hospital, Beijing, China
- Institute of Clinical Pharmacology, Peking University, Beijing, China
| | - Ran Xie
- Department of Pharmacy, Peking University First Hospital, Beijing, China
- Institute of Clinical Pharmacology, Peking University, Beijing, China
| | - Xu He
- Department of Pharmacy, Peking University First Hospital, Beijing, China
- Institute of Clinical Pharmacology, Peking University, Beijing, China
| | - Xiaocong Pang
- Department of Pharmacy, Peking University First Hospital, Beijing, China
- Institute of Clinical Pharmacology, Peking University, Beijing, China
| | - Xin Wang
- Department of General Surgery, Peking University First Hospital, Beijing, China
| | - Yimin Cui
- Department of Pharmacy, Peking University First Hospital, Beijing, China
- Institute of Clinical Pharmacology, Peking University, Beijing, China
| |
Collapse
|
3
|
Perini F, Cendron F, Wu Z, Sevane N, Li Z, Huang C, Smith J, Lasagna E, Cassandro M, Penasa M. Genomics of Dwarfism in Italian Local Chicken Breeds. Genes (Basel) 2023; 14:genes14030633. [PMID: 36980905 PMCID: PMC10047989 DOI: 10.3390/genes14030633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.
Collapse
Affiliation(s)
- Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | - Zhou Wu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid, Avenida Puerta de Hierro, 28040 Madrid, Spain
| | - Zhiqiang Li
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- College of Animal Science and Technology, Chengdu Campus, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunhua Huang
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- College of Animal Science and Technology, Chengdu Campus, Sichuan Agricultural University, Chengdu 611130, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- Correspondence: ; Tel.: +39-075-58517102
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
- Federazione delle Associazioni Nazionali di Razza e Specie, 00187 Roma, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| |
Collapse
|
4
|
He XY, Wang XQ, Xiao QL, Liu D, Xu QR, Liu S. Long non-coding RNA NCK1-AS1 functions as a ceRNA to regulate cell viability and invasion in esophageal squamous cell carcinoma via microRNA-133b/ENPEP axis. Cell Cycle 2023; 22:596-609. [PMID: 36412985 PMCID: PMC9928473 DOI: 10.1080/15384101.2022.2138416] [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] [Received: 02/07/2021] [Revised: 01/04/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
This study is designed to explore the role of long non-coding RNAs (lncRNAs) NCK1-AS1 in proliferative and invasive activities of esophageal squamous cell carcinoma (ESCC) cells by binding to microRNA-133b (miR-133b) to regulate ENPEP. Differentially expressed lncRNAs, miRs, genes and their targeting relationships were screened on ESCC-related gene expression datasets GSE17351 and GSE6188. The targeting relationships among NCK1-AS1, miR-133b, and ENPEP were verified using functional assays. Loss- and gain- of function assays were carried out to examine the roles of NCK1-AS1, miR-133b, and ENPEP in ESCC cell proliferative, invasive, migrative and apoptotic abilities as well as tumorigenesis in vivo. Elevated NCK1-AS1 and ENPEP but reduced miR-133b expression were found in ESCC. NCK1-AS1 knockdown or miR-133b overexpression inhibited the malignant properties of ESCC cells as well as tumorigenesis in vivo. NCK1-AS1 regulated the ENPEP expression by competitively binding to miR-133b. ENPEP overexpression reversed inhibition of NCK1-AS1 knockdown on the function of ESCC cells. This study provides evidence that silencing NCK1-AS1 inhibits expression of ENPEP by sponging miR-133b, thereby suppressing ESCC.
Collapse
Affiliation(s)
- Xiang-Yuan He
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Xiu-Qi Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Qi-Lu Xiao
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Duan Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Qi-Rong Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Sheng Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| |
Collapse
|
5
|
Modulation of the tumour microenvironment in hepatocellular carcinoma by tyrosine kinase inhibitors: from modulation to combination therapy targeting the microenvironment. Cancer Cell Int 2022; 22:73. [PMID: 35148789 PMCID: PMC8840552 DOI: 10.1186/s12935-021-02435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/28/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer deaths worldwide. Tyrosine kinase inhibitors (TKIs) remain the backbone of systematic therapy for advanced hepatocellular carcinoma. Sorafenib and lenvatinib are currently approved as first-line therapeutic drugs, and regorafenib and cabozantinib are applied as second-line treatments. With inhibition of angiogenesis as the main target, TKIs exert a profound effect on the tumour microenvironment (TME). The TME is a complex mixture of cellular and noncellular components surrounding the tumour mass, and is associated with tumour progression partially through the epithelial-mesenchymal transition. Specifically, the TME of HCC is characterized by profound extracellular matrix remodelling and an immunosuppressive microenvironment. The purpose of this review is to provide a summary of TME remodelling mediated by four Food and Drug Administration approved TKIs in HCC and thus summarize the rationale and potential targets for combination therapy. The modulatory effect of TKIs on the TME of HCC was reported to enhance the antitumour effect of TKIs through pyroptosis of macrophages and subsequent natural killer cell activation, T cell activation, regulatory T cell reduction in HCC. Meanwhile, TKIs also induce drug resistance via M2 polarization and accumulation, recruitment of tumour-associated neutrophils, and induction of the epithelial-mesenchymal transition. In conclusion, the effect of TKIs on TME can enhance its antitumour effect, but might also partially contribute to the drug resistance that hinders the progression of TKIs as treatment for HCC. Additionally, the effect of TKIs also provides the rationale for combination therapy, including combining TKIs with immune checkpoint inhibitors, to facilitate increased drug efficacy of TKIs.
Collapse
|