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Gola C, Maniscalco L, Iussich S, Morello E, Olimpo M, Martignani E, Accornero P, Giacobino D, Mazzone E, Modesto P, Varello K, Aresu L, De Maria R. Hypoxia-associated markers in the prognosis of oral canine melanoma. Vet Pathol 2024; 61:721-731. [PMID: 38613423 DOI: 10.1177/03009858241244853] [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: 04/15/2024]
Abstract
Canine oral malignant melanoma (COMM) is the most common neoplasm in the oral cavity characterized by local invasiveness and high metastatic potential. Hypoxia represents a crucial feature of the solid tumor microenvironment promoting cancer progression and drug resistance. Hypoxia-inducible factor-1α (HIF-1α) and its downstream effectors, vascular endothelial growth factor A (VEGF-A), glucose transporter isoform 1 (GLUT1), C-X-C chemokine receptor type 4 (CXCR4), and carbonic anhydrase IX (CAIX), are the main regulators of the adaptive response to low oxygen availability. The prognostic value of these markers was evaluated in 36 COMMs using immunohistochemistry. In addition, the effects of cobalt chloride-mediated hypoxia were evaluated in 1 primary COMM cell line. HIF-1α expression was observed in the nucleus, and this localization correlated with the presence or enhanced expression of HIF-1α-regulated genes at the protein level. Multivariate analysis revealed that in dogs given chondroitin sulfate proteoglycan-4 (CSPG4) DNA vaccine, COMMs expressing HIF-1α, VEGF-A, and CXCR4 were associated with shorter disease-free intervals (DFI) compared with tumors that were negative for these markers (P = .03), suggesting hypoxia can influence immunotherapy response. Western blotting showed that, under chemically induced hypoxia, COMM cells accumulate HIF-1α and smaller amounts of CAIX. HIF-1α induction and stabilization triggered by hypoxia was corroborated by immunofluorescence, showing its nuclear translocation. These findings reinforce the role of an hypoxic microenvironment in tumor progression and patient outcome in COMM, as previously established in several human and canine cancers. In addition, hypoxic markers may represent promising prognostic markers, highlighting opportunities for their use in therapeutic strategies for COMMs.
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Affiliation(s)
- Cecilia Gola
- University of Surrey, Guildford, UK
- University of Turin, Grugliasco, Turin, Italy
| | | | | | | | | | | | | | | | | | - Paola Modesto
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Turin, Italy
| | - Katia Varello
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Turin, Italy
| | - Luca Aresu
- University of Turin, Grugliasco, Turin, Italy
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Nan K, Zhang M, Geng Z, Zhang Y, Liu L, Yang Z, Xu P. Exploring Unique Extracellular Vesicles Associated Signatures: Prognostic Insights, Immune Microenvironment Dynamics, and Therapeutic Responses in Pancreatic Adenocarcinoma. Mediators Inflamm 2024; 2024:2825971. [PMID: 39220187 PMCID: PMC11366062 DOI: 10.1155/2024/2825971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/09/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Extracellular vesicles play an important role in the progression of pancreatic adenocarcinoma (PAAD) through the transfer of proteins, mRNAs, and long noncoding RNAs (lncRNAs). However, the intricate interplay between extracellular vesicles-related lncRNAs and the tumor microenvironment (TME) remains poorly elucidated. Consequently, our investigation aimed to delineate the association between extracellular vesicles-related lncRNAs and the PAAD microenvironment. Initially, we identified differentially expressed lncRNAs (DELs) from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project datasets. Subsequently, we validated the expression of these DELs within extracellular vesicles and assessed their prognostic implications in PAAD using the GSE133684 and TCGA datasets. Multiomics data were analyzed comprehensively, including genomic landscape, functional annotation, immune profiles, and therapeutic responses. Differential expression of selected lncRNAs in both cellular and exosomal fractions of PAAD was further confirmed through quantitative polymerase chain reaction (qPCR). Eight DELs were identified from TCGA and GTEx datasets, and two exosomal lncRNAs exhibited a significant correlation with overall survival, warranting further investigation. Specifically, elevated expression of LINC00996 correlated positively with immune infiltration and enhanced response to immunotherapy. Conversely, heightened expression of TRHED-AS1 was associated with compromised immune cell infiltration and diminished responsiveness to immunotherapy. Our study establishes a compelling link between two extracellular vesicles-related gene signatures, prognosis, and immune infiltration in PAAD. Notably, these signatures serve as robust prognostic indicators for PAAD patients, offering valuable insights for the strategic selection of immunotherapeutic interventions.
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Affiliation(s)
- Kai Nan
- Department of Joint SurgeryHongHui HospitalXi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Ming Zhang
- Department of General PracticeHonghui HospitalXi'an Jiao Tong University, Xi'an 710054, Shaanxi, China
| | - Zilong Geng
- Department of OrthopaedicsThe Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Yuankai Zhang
- Department of OrthopaedicsThe Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Lin Liu
- Department of Joint SurgeryHongHui HospitalXi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Zhi Yang
- Department of Joint SurgeryHongHui HospitalXi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Peng Xu
- Department of Joint SurgeryHongHui HospitalXi'an Jiaotong University, Xi'an 710054, Shaanxi, China
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Yu K, Wang J, Wang Y, He J, Hu S, Kuai S. Consensus clustering and development of a risk signature based on trajectory differential genes of cancer-associated fibroblast subpopulations in colorectal cancer. J Cancer Res Clin Oncol 2024; 150:388. [PMID: 39120743 PMCID: PMC11315798 DOI: 10.1007/s00432-024-05906-z] [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: 04/03/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) play a crucial role in the progression of colorectal cancer (CRC). However, the impact of CAF subpopulation trajectory differentiation on CRC remains unclear. METHODS In this study, we first explored the trajectory differences of CAFs subpopulations using bulk and integrated single-cell sequencing data, and then performed consensus clustering of CRC samples based on the trajectory differential genes of CAFs subpopulations. Subsequently, we analyzed the heterogeneity of CRC subtypes using bioinformatics. Finally, we constructed relevant prognostic signature using machine learning and validated them using spatial transcriptomic data. RESULTS Based on the differential genes of CAFs subpopulation trajectory differentiation, we identified two CRC subtypes (C1 and C2) in this study. Compared to C1, C2 exhibited worse prognosis, higher immune evasion microenvironment and high CAF characteristics. C1 was primarily associated with metabolism, while C2 was primarily associated with cell metastasis and immune regulation. By combining 101 combinations of 10 machine learning algorithms, we developed a High-CAF risk signatures (HCAFRS) based on the C2 characteristic gene. HCAFRS was an independent prognostic factor for CRC and, when combined with clinical parameters, significantly predicted the overall survival of CRC patients. HCAFRS was closely associated with epithelial-mesenchymal transition, angiogenesis, and hypoxia. Furthermore, the risk score of HCAFRS was mainly derived from CAFs and was validated in the spatial transcriptomic data. CONCLUSION In conclusion, HCAFRS has the potential to serve as a promising prognostic indicator for CRC, improving the quality of life for CRC patients.
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Affiliation(s)
- Ke Yu
- Wuxi Huishan District People's Hospital, No. 2, Zhan Qian North Road, Luoshe Town, Huishan District, Wuxi City, Jiangsu Province, China
- Affiliated Huishan Hospital of Xinglin College, Nantong University, Wuxi, Jiangsu, China
| | - Jiao Wang
- Wuxi Huishan District People's Hospital, No. 2, Zhan Qian North Road, Luoshe Town, Huishan District, Wuxi City, Jiangsu Province, China
- Affiliated Huishan Hospital of Xinglin College, Nantong University, Wuxi, Jiangsu, China
| | - Yueqing Wang
- Wuxi Huishan District People's Hospital, No. 2, Zhan Qian North Road, Luoshe Town, Huishan District, Wuxi City, Jiangsu Province, China
- Affiliated Huishan Hospital of Xinglin College, Nantong University, Wuxi, Jiangsu, China
| | - Jiayi He
- Wuxi Huishan District People's Hospital, No. 2, Zhan Qian North Road, Luoshe Town, Huishan District, Wuxi City, Jiangsu Province, China
- Affiliated Huishan Hospital of Xinglin College, Nantong University, Wuxi, Jiangsu, China
| | | | - Shougang Kuai
- Wuxi Huishan District People's Hospital, No. 2, Zhan Qian North Road, Luoshe Town, Huishan District, Wuxi City, Jiangsu Province, China.
- Affiliated Huishan Hospital of Xinglin College, Nantong University, Wuxi, Jiangsu, China.
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Yuan R, Xu ZJ, Zhang SK, Cao XY, Dai AG, Song L. New evidence for a role of DANCR in cancers: a comprehensive review. J Transl Med 2024; 22:569. [PMID: 38877534 PMCID: PMC11177382 DOI: 10.1186/s12967-024-05246-z] [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: 03/22/2024] [Accepted: 04/28/2024] [Indexed: 06/16/2024] Open
Abstract
Cancer remains a leading cause of mortality and poses a substantial threat to public health. Studies have revealed that Long noncoding RNA DANCR is a cytoplasmic lncRNA whose aberrant expression plays a pivotal role in various cancer types. Within tumour biology, DANCR exerts regulatory control over crucial processes such as proliferation, invasion, metastasis, angiogenesis, inflammatory responses, cellular energy metabolism reprogramming, and apoptosis. By acting as a competitive endogenous RNA for miRNAs and by interacting with proteins and mRNAs at the molecular level, DANCR contributes significantly to cancer progression. Elevated DANCR levels have also been linked to heightened resistance to anticancer drugs. Moreover, the detection of circulating DANCR holds promise as a valuable biomarker for aiding in the clinical differentiation of different cancer types. This article offers a comprehensive review and elucidation of the primary functions and molecular mechanisms through which DANCR influences tumours.
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Affiliation(s)
- Rong Yuan
- School of Medicine, Hunan University of Chinese Medicine, 300 Xueshi Road, Hanpu Science and Teaching Park, Changsha, 410208, Hunan, China
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, 300 Xueshi Road, Hanpu Science and Teaching Park, Changsha, 410208, Hunan, China
| | - Zhao-Jun Xu
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, 97 Shaoshan Road, Changsha, 410007, Hunan, China
| | - Sheng-Kang Zhang
- Department of Cardiothoracic Surgery, the First Affiliated Hospital, Hunan University of Chinese Medicine, 97 Shaoshan Road, Changsha, 410007, Hunan, China
| | - Xian-Ya Cao
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, 300 Xueshi Road, Hanpu Science and Teaching Park, Changsha, 410208, Hunan, China
- Department of Respiratory Diseases, School of Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Ai-Guo Dai
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, 300 Xueshi Road, Hanpu Science and Teaching Park, Changsha, 410208, Hunan, China.
- Department of Respiratory Diseases, School of Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.
- Department of Respiratory Medicine, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410021, Hunan, China.
| | - Lan Song
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, 300 Xueshi Road, Hanpu Science and Teaching Park, Changsha, 410208, Hunan, China.
- Department of Biochemistry and Molecular Biology, School of Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.
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Chen X, Sun B, Li S. Downregulation of HIGD1B induces mitochondria-mediated apoptosis in gastric cancer cells by inactivating Akt and ERK pathways. Drug Dev Res 2024; 85:e22221. [PMID: 38863387 DOI: 10.1002/ddr.22221] [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: 03/03/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/13/2024]
Abstract
Gastric cancer (GC) is one of the most common malignancies worldwide. Hypoxia-inducible domain (HIGD) family members (e.g., HIGD1A) have been linked to tumor progression. However, the role of HIGD1B (another HIGD family member) in GC has yet to be fully understood. Based on data from TCGA_GC, GSE65801, and GSE65801 data sets, HIGD1B levels were evaluated in normal and GC tissues. Next, HIGD1B levels were validated by reverse transcription-quantitative PCR and western blot analysis analyses. Meanwhile, patients with GC in the TCGA_GC cohort were grouped into high- and low-HIGD1B level groups, and overall survival, functional enrichment, and immune infiltration were analyzed. Additionally, gain- and loss-of-function experiments were performed to determine the function of HIGD1B in GC cells. Compared to normal controls, HIGD1B mRNA levels were significantly elevated in GC tissues. Moreover, high HIGD1B levels may be an independent indicator of poor prognosis in patients with GC. Additionally, high HIGD1B levels were correlated with high stromal and ESTIMATE scores and elevated expression of immune checkpoints in patients with GC. Functional analyses showed that HIGD1B deficiency notably suppressed GC cell proliferation, migration, and invasion. Moreover, HIGD1B deficiency significantly induced mitochondria-mediated apoptosis in GC cells by inactivating Akt and ERK pathways. Collectively, HIGD1B may predict the prognosis of patients with GC and may function as an oncogene in GC. These findings suggest that HIGD1B may serve as a prognostic biomarker and potential therapeutic target in GC.
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Affiliation(s)
- Xiangyu Chen
- The Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Binghua Sun
- The Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuai Li
- The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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Sun P, Wang Y, Liu X, Li Z, Cui D, Li Q, Wang Q, Wang J. Methylation-driven mechanisms of allergic rhinitis during pollen and non-pollen seasons using integrated bioinformatics analysis. Front Genet 2024; 15:1242974. [PMID: 38699230 PMCID: PMC11063319 DOI: 10.3389/fgene.2024.1242974] [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: 06/20/2023] [Accepted: 03/25/2024] [Indexed: 05/05/2024] Open
Abstract
Background Allergic rhinitis (AR) is a widespread allergic airway disease that results from a complex interplay between genetic and environmental factors and affects approximately 10%-40% of the global population. Pollen is a common allergen, and exposure to pollen can cause epigenetic changes. However, the mechanism underlying pollen-induced DNA methylation changes and their potential effects on the allergic march are still unclear. The purpose of this study was to explore the methylation-driven mechanisms of AR during the pollen and non-pollen seasons using bioinformatics analysis and to investigate their relationship with asthma. Methods We downloaded DNA methylation and gene expression data from the GEO database (GSE50387: GSE50222, GSE50101) and identified differentially methylated positions (DMPs) and differentially expressed genes (DEGs) during the pollen and non-pollen seasons using the CHAMP and limma packages. Through correlation analysis, we identified methylation-driven genes and performed pathway enrichment analysis to annotate their functions. We incorporated external data on AR combined with asthma (GSE101720) for analysis to identify key CpGs that promote the transformation of AR to asthma. We also utilized external data on olive pollen allergy (GSE54522) for analysis to validate the methylation-driven genes. Weighted correlation network analysis (WGCNA) was employed to identify gene modules significantly correlated with pollen allergy. We extracted genes related to the key methylation-driven gene ZNF667-AS1 from the significant module and performed pathway intelligent clustering using KOBAS-i. We also utilized gene set enrichment analysis to explore the potential function of ZNF667-AS1. Results We identified 20 and 24 CpG-Gene pairings during the pollen and non-pollen seasons. After incorporating external data from GSE101720, we found that ZNF667-AS1 is a key gene that may facilitate the transformation of AR into asthma during the pollen season. This finding was further validated in another external dataset, GSE54522, which is associated with pollen allergy. WGCNA identified 17 modules, among which the blue module showed significant correlation with allergies. ZNF667-AS1 was located in the blue module. We performed pathway analysis on the genes correlated with ZNF667-AS1 extracted from the blue module and identified a prominent cluster of pathways in the KOBAS-i results, including Toll-like receptor (TLR) family, MyD88, MAPK, and oxidative stress. Gene set enrichment analysis around cg05508084 (paired with ZNF667-AS1) also indicated its potential involvement in initiating and modulating allergic inflammation from the perspective of TLR and MAPK signaling. Conclusion We identified methylation-driven genes and their related pathways during the pollen and non-pollen seasons in patients with AR and identified key CpGs that promote the transformation of AR into asthma due to pollen exposure. This study provides new insights into the underlying molecular mechanisms of the transformation of AR to asthma.
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Affiliation(s)
- Pengcheng Sun
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yi Wang
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xing Liu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zhuqing Li
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Diankun Cui
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qianru Li
- Qinghai Golmud Jianqiao Hospital, Golmud, Qinghai, China
| | - Qi Wang
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ji Wang
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
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Zhu W, Wu C, Hu S, Liu S, Zhao S, Zhang D, Qiu G, Cheng X, Huang J. Chemokine- and chemokine receptor-based signature predicts immunotherapy response in female colorectal adenocarcinoma patients. Sci Rep 2023; 13:21358. [PMID: 38049474 PMCID: PMC10695967 DOI: 10.1038/s41598-023-48623-2] [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: 03/17/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
The clinical significance and comprehensive characteristics of chemokines and chemokine receptors in female patients with advanced colorectal adenocarcinoma have not ever been reported. Our study explored the expression profiles of chemokines and chemokine receptors and constructed a chemokine- and chemokine receptor-based signature in female patients with advanced colorectal adenocarcinoma. Four independent cohorts containing 1335 patients were enrolled in our study. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were performed to construct the signature. CIBERSORT was used to evaluate the landscape of immune cell infiltration. Thirty-two pairs of tissue specimens of female advanced colorectal cancer (CRC) patients and two CRC cell lines were used to validate the signature in vitro. Quantitative real-time PCR and western blotting were performed to validate the mRNA and protein expression levels of signature genes. EdU and colony formation assays were performed to examine proliferative ability. Transwell and wound healing assays were used to evaluate cell invasion and migration capacity. During the signature construction and validation process, we found that the signature was more applicable to female patients with advanced colorectal adenocarcinoma. Hence, the subsequent study mainly focused on the particular subgroup. Enrichment analyses revealed that the signature was closely related to immunity. The landscape of immune cell infiltration presented that the signature was significantly associated with T cells CD8 and neutrophils. Gene set enrichment analysis (GSEA) confirmed that the high-risk group was chiefly enriched in the tumor-promoting related pathways and biological processes, whereas the low-risk group was mainly enriched in anti-tumor immune response pathways and biological processes. The signature was closely correlated with CTLA4, PDL1, PDL2, TMB, MSI, and TIDE, indicating that our signature could serve as a robust biomarker for immunotherapy and chemotherapy response. ROC curves verified that our signature had more robust prognostic power than all immune checkpoints and immunotherapy-related biomarkers. Finally, we used 32 pairs of tissue specimens and 2 CRC cell lines to validate our signature in vitro. We first provided a robust prognostic chemokine- and chemokine receptor-based signature, which could serve as a novel biomarker for immunotherapy and chemotherapy response to guide individualized treatment for female patients with advanced colorectal adenocarcinoma.
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Affiliation(s)
- Wenjie Zhu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Changlei Wu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shiqi Hu
- Queen Mary College, Medical Department, Nanchang University, Nanchang, Jiangxi, China
| | - Sicheng Liu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shimin Zhao
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Dongdong Zhang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Guisheng Qiu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiufeng Cheng
- Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jun Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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Mo Y, Adu-Amankwaah J, Qin W, Gao T, Hou X, Fan M, Liao X, Jia L, Zhao J, Yuan J, Tan R. Unlocking the predictive potential of long non-coding RNAs: a machine learning approach for precise cancer patient prognosis. Ann Med 2023; 55:2279748. [PMID: 37983519 DOI: 10.1080/07853890.2023.2279748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
The intricate web of cancer biology is governed by the active participation of long non-coding RNAs (lncRNAs), playing crucial roles in cancer cells' proliferation, migration, and drug resistance. Pioneering research driven by machine learning algorithms has unveiled the profound ability of specific combinations of lncRNAs to predict the prognosis of cancer patients. These findings highlight the transformative potential of lncRNAs as powerful therapeutic targets and prognostic markers. In this comprehensive review, we meticulously examined the landscape of lncRNAs in predicting the prognosis of the top five cancers and other malignancies, aiming to provide a compelling reference for future research endeavours. Leveraging the power of machine learning techniques, we explored the predictive capabilities of diverse lncRNA combinations, revealing their unprecedented potential to accurately determine patient outcomes.
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Affiliation(s)
- Yixuan Mo
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
| | - Joseph Adu-Amankwaah
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
| | - Wenjie Qin
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Tan Gao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Xiaoqing Hou
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Mengying Fan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Xuemei Liao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Liwei Jia
- Department of Pathology, UT Southwestern Medical Center, Dallas, UT, USA
| | - Jinming Zhao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, The First Hospital of China Medical University, Shenyang, China
| | - Jinxiang Yuan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Rubin Tan
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
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Alzamami A. Implications of single-cell immune landscape of tumor microenvironment for the colorectal cancer diagnostics and therapy. Med Oncol 2023; 40:352. [PMID: 37950801 DOI: 10.1007/s12032-023-02226-z] [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: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 11/13/2023]
Abstract
Colorectal cancer (CRC) originates from the polyps lining the colon and is among the most common types of cancer. With the increasing popularity of single-cell sequencing technologies, researchers have been able to better understand the immune landscape of colorectal cancer, by analyzing their expression and interactions in detail with the tumor microenvironment (TME) at single-cell level. Since the tumor-immune cell interactions play a critical part in the advancement as well as treatment response in colorectal cancer, the release of inhibitory factors such as T cells are important for recognizing and destroying cancer cells. Such information is vital to identify immunotherapeutic targets for cure and monitoring response to treatments. Therefore, a comprehensive single-cell studies-based overview of key immunogenic agents regulating the TME of CRC is provided in this review. Tumor-associated macrophages can promote tumor growth and resistance to treatment by releasing factors that inhibit the function of other immune cells. Additionally, colorectal cancer cells can express programmed cell death protein 1 and its ligand, which can also inhibit T-cell function. Researchers have found that certain types of immune cells, prominently T cells, natural killer, and dendritic cells, can have a positive impact on the prognosis of colorectal cancer patients. Treatments like immune checkpoint inhibitors and CAR-T therapies that help to release the inhibitory signals from the cancer cells allow the immune cells to function more effectively.
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Affiliation(s)
- Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Sciences, Shaqra University, 11961, Al-Quwayiyah, Saudi Arabia.
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10
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Kang Z, Chen B, Ma X, Yan F, Wang Z. Immune-related gene-based model predicts the survival of colorectal carcinoma and reflected various biological statuses. Front Mol Biosci 2023; 10:1277933. [PMID: 37920710 PMCID: PMC10619740 DOI: 10.3389/fmolb.2023.1277933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023] Open
Abstract
Bakcground: Prognosis of colorectal cancer (CRC) varies due to complex genetic-microenviromental interactions, and multiple gene-based prognostic models have been highlighted. Material and Method: In this work, the immune-related genes' expression-based model was developed and the scores of each sample were calculated. The correlation between the model and clinical information, immune infiltration, drug response and biological pathways were analyzed. Results: The high-score samples have a significantly longer survival (overall survival and progression-free survival) period than those with a low score, which was validated across seven datasets containing 1,325 samples (GSE17536 (N = 115), GSE17537 (N = 55), GSE33113 (N = 90), GSE37892 (N = 130), GSE38832 (N = 74), GSE39582 (N = 481), and TCGA (N = 380)). The score is significantly associated with clinical indicators, including age and stage, and further associated with PD-1/PD-L1 gene expression. Furthermore, high-score samples have significantly higher APC and a lower MUC5B mutation rate. The high-score samples show more immune infiltration (including CD4+ and CD8+ T cells, M1/M2 macrophages, and NK cells). Enriched pathway analyses showed that cancer-related pathways, including immune-related pathways, were significantly activated in high-score samples and that some drugs have significantly lower IC50 values than those with low score. Conclusion: The model developed based on immune-related genes is robust and reflected various statuses of CRC and may be a potential clinical indicator.
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Affiliation(s)
| | | | | | - Feihu Yan
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zhen Wang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
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Huang L, Zeng X, Liang W, Chen J, Zhong C, Cai W, Wang X, Zhu Z, Su L, Liu Z, Peng H. Dissecting the role of lactate metabolism LncRNAs in the progression and immune microenvironment of osteosarcoma. Transl Oncol 2023; 36:101753. [PMID: 37549606 PMCID: PMC10423928 DOI: 10.1016/j.tranon.2023.101753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/15/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The process of lactate metabolism has been proved to play a critical role in the progression of various cancers and to influence the immune microenvironment, but its potential role in osteosarcoma remains unclear. METHODS We have acquired transcriptomic and clinical data from 84 osteosarcoma samples and 70 normal bone samples from the TARGET and GTEx databases. We identified differentially expressed lactate metabolism-related LncRNAs (LRLs) in osteosarcoma and performed Cox regression and LASSO regression to establish LRLs prognostic signature (LRPS). The reliability of LRPS performance was examined by separate prognostic analysis, viability curves and receiver operating characteristic (ROC) curves. Furthermore, the effects of LRPS on the immune microenvironment of osteosarcoma were investigated, and the functions of the focal genes were experimentally validated. RESULT A total of 856 differentially expressed LRLs were identified and 5 of them were selected to construct LRPS, which was a better prognostic predictor for osteosarcoma compared with other published prognostic signatures (AUC up to 0.947 and 0.839 in the training and test groups, respectively, with adj-p<0.05 for KM curves). We found that LRPS significantly affected the immune infiltration of osteosarcoma, while RP11-472M19.2 significantly promoted the metastasis of osteosarcoma, which was well validated experimentally. Encouragingly, a number of sensitive drugs were identified for LRPS and RP11-472M19.2 high-risk groups. CONCLUSION Our study shows that lactate metabolism plays a crucial role in the development of osteosarcoma and has been well validated experimentally, providing extremely important insights into the clinical treatment and in-depth research of osteosarcoma.
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Affiliation(s)
- Liangkun Huang
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Xiaoshuang Zeng
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Wanting Liang
- Department of Clinical Medicine, Xianyue Hospital of Xiamen Medical College, Xiamen, 310058, China
| | - Junwen Chen
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Changheng Zhong
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Wenxiang Cai
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Xuezhong Wang
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Zhengjie Zhu
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Li Su
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China
| | - Zilin Liu
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China.
| | - Hao Peng
- Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei, 430060, China.
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12
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Shakhpazyan NK, Mikhaleva LM, Bedzhanyan AL, Sadykhov NK, Midiber KY, Konyukova AK, Kontorschikov AS, Maslenkina KS, Orekhov AN. Long Non-Coding RNAs in Colorectal Cancer: Navigating the Intersections of Immunity, Intercellular Communication, and Therapeutic Potential. Biomedicines 2023; 11:2411. [PMID: 37760852 PMCID: PMC10525929 DOI: 10.3390/biomedicines11092411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This comprehensive review elucidates the intricate roles of long non-coding RNAs (lncRNAs) within the colorectal cancer (CRC) microenvironment, intersecting the domains of immunity, intercellular communication, and therapeutic potential. lncRNAs, which are significantly involved in the pathogenesis of CRC, immune evasion, and the treatment response to CRC, have crucial implications in inflammation and serve as promising candidates for novel therapeutic strategies and biomarkers. This review scrutinizes the interaction of lncRNAs with the Consensus Molecular Subtypes (CMSs) of CRC, their complex interplay with the tumor stroma affecting immunity and inflammation, and their conveyance via extracellular vesicles, particularly exosomes. Furthermore, we delve into the intricate relationship between lncRNAs and other non-coding RNAs, including microRNAs and circular RNAs, in mediating cell-to-cell communication within the CRC microenvironment. Lastly, we propose potential strategies to manipulate lncRNAs to enhance anti-tumor immunity, thereby underlining the significance of lncRNAs in devising innovative therapeutic interventions in CRC.
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Affiliation(s)
- Nikolay K. Shakhpazyan
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Liudmila M. Mikhaleva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Arcady L. Bedzhanyan
- Department of Abdominal Surgery and Oncology II (Coloproctology and Uro-Gynecology), Petrovsky National Research Center of Surgery, 119435 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Konstantin Y. Midiber
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexandra K. Konyukova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Andrey S. Kontorschikov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Ksenia S. Maslenkina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexander N. Orekhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, 121096 Moscow, Russia
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Zeng T, Jiang S, Wang Y, Sun G, Cao J, Hu D, Wang G, Liang X, Ding J, Du J. Identification and validation of a cellular senescence-related lncRNA signature for prognostic prediction in patients with multiple myeloma. Cell Cycle 2023; 22:1434-1449. [PMID: 37227248 PMCID: PMC10281485 DOI: 10.1080/15384101.2023.2213926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/01/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023] Open
Abstract
Multiple myeloma (MM) is the second most common hematologic malignancy, which primarily occurs in the elderly. Cellular senescence is considered to be closely associated with the occurrence and progression of malignant tumors including MM, and lncRNA can mediate the process of cellular senescence by regulating key signaling pathways such as p53/p21 and p16/RB. However, the role of cellular senescence related lncRNAs (CSRLs) in MM development has never been reported. Herein, we identified 11 CSRLs (AC004918.5, AC103858.1, AC245100.4, ACBD3-AS1, AL441992.2, ATP2A1-AS1, CCDC18-AS1, LINC00996, TMEM161B-AS1, RP11-706O15.1, and SMURF2P1) to build the CSRLs risk model, which was confirmed to be highly associated with overall survival (OS) of MM patients. We further demonstrated the strong prognostic value of the risk model in MM patients receiving different regimens, especially for those with three-drug combination of bortezomib, lenalidomide, and dexamethasone (VRd) as first-line therapy. Not only that, our risk model also excels in predicting the OS of MM patients at 1, 2, and 3 years. In order to verify the function of these CSRLs in MM, we selected the lncRNA ATP2A1-AS1 which presented the largest expression difference between high-risk groups and low-risk groups for subsequent analysis and validation. Finally, we found that down-regulation of ATP2A1-AS1 can promote cellular senescence in MM cell lines. In conclusion, the CSRLs risk model established in present study provides a novel and more accurate method for predicting MM patients' prognosis and identifies a new target for MM therapeutic intervention.
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Affiliation(s)
- Tanlun Zeng
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Sihan Jiang
- Department of Hematology, Myeloma & Lymphoma Center, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yichuan Wang
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Guanqun Sun
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Jinjin Cao
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Guang Wang
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Xijun Liang
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Juan Du
- Department of Hematology, Myeloma & Lymphoma Center, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
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