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Zhao J, Luo Z, Fu R, Zhou J, Chen S, Wang J, Chen D, Xie X. Disulfidptosis-related signatures for prognostic and immunotherapy reactivity evaluation in hepatocellular carcinoma. Eur J Med Res 2023; 28:571. [PMID: 38057871 DOI: 10.1186/s40001-023-01535-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common cancers in the world and a nonnegligible health concern on a worldwide scale. Disulfidptosis is a novel mode of cell death, which is mainly caused by the collapse of the actin skeleton. Although many studies have demonstrated that various types of cell death are associated with cancer treatment, the relationship between disulfidptosis and HCC has not been elucidated. METHODS Here, we mainly applied bioinformatics methods to construct a disulfidptosis related risk model in HCC patients. Specifically, transcriptome data and clinical information were downloaded from the Gene Expression Omnibus (GEO), International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) database. A total of 45 co-expressed genes were extracted between the disulfidptosis-related genes (DRGs) and the differential expression genes (DEGs) of liver hepatocellular carcinoma (LIHC) in the TCGA database. The LIHC cohort was divided into two subgroups with different prognosis by k-mean consensus clustering and functional enrichment analysis was performed. Subsequently, three hub genes (CDCA8, SPP2 and RDH16) were screened by Cox regression and LASSO regression analysis. In addition, a risk signature was constructed and the HCC cohort was divided into high risk score and low risk score subgroups to compare the prognosis, clinical features and immune landscape between the two subgroups. Finally, the prognostic model of independent risk factors was constructed and verified. CONCLUSIONS High DRGs-related risk score in HCC individuals predict poor prognosis and are associated with poor immunotherapy response, which indicates that risk score assessment model can be utilized to guide clinical treatment strategy.
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Affiliation(s)
- Jiajing Zhao
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Zeminshan Luo
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Ruizhi Fu
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Jinghong Zhou
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Shubiao Chen
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Jianjie Wang
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Dewang Chen
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Xiaojun Xie
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China.
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2
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Wang Z, Ren H, Zhu G, Zhang L, Cao H, Chen B. High expression of CCDC69 is correlated with immunotherapy response and protective effects on breast cancer. BMC Cancer 2023; 23:974. [PMID: 37828454 PMCID: PMC10571395 DOI: 10.1186/s12885-023-11411-2] [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: 10/24/2022] [Accepted: 09/16/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND As a molecule controlling the assembly of central spindles and recruitment of midzone component, coiled-coil domain-containing protein 69 (CCDC69) plays an important role in multiple cancers. Currently, the relationships between CCDC69 and immune infiltration or immunotherapy in breast cancer remain unclear. METHODS The expression and prognostic significance of CCDC69 in breast cancer were comprehensively analyzed by quantitative real-time PCR, immunohistochemical staining and various databases. The data source of differentially expressed genes, gene set enrichment analysis, and immune cell infiltration analysis came from The Cancer Genome Atlas (TCGA) database. Single-cell analysis based on IMMUcan database was used. The protein-protein interaction network was developed applying STRING, Cytoscape, CytoHubba, and GeneMANIA. TISIDB was employed in analyzing the CCDC69 co-expressed immune related genes. The correlations between CCDC69 and immunotherapy or immune-related scores were analyzed by CAMOIP and TISMO. Ctr-db was also used to conduct drug sensitivity analysis. RESULTS The mRNA of CCDC69 was downregulated in breast cancer tissues compared with normal tissues. Higher CCDC69 expression was associated with a better breast cancer prognosis. Enrichment analysis showed that the co-expression genes of CCDC69 were mainly related to immune-related pathways. The expression of CCDC69 was found to be positively correlated with multiple tumor-suppression immune infiltration cells, especially T cells and dendritic cells. Meanwhile, high CCDC69 expression can predict better immunotherapy responses when compared with low CCDC69 expression. After the interferon-gamma treatment, the CCDC69 expression was elevated in vitro. CCDC69 expression was a reliable predictor for the response status of two therapeutic strategies in breast cancer. CONCLUSIONS Our research revealed the clinical significance of CCDC69 in breast cancer and validated the critical roles of CCDC69 in the tumor immune infiltration and immunotherapy responses.
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Affiliation(s)
- Zhen Wang
- Department of Breast and Thyroid Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Huiyang Ren
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Guolian Zhu
- Department of Breast Surgery, The Fifth People's Hospital of Shenyang, Shenyang, China
| | - Lei Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China.
| | - Hongyi Cao
- Department of Pathology, The First Hospital of China Medical University and College of Basic Medical Sciences, Shenyang, China.
| | - Bo Chen
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, China.
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Lin X, Dong Y, Gu Y, Kapoor A, Peng J, Su Y, Wei F, Wang Y, Yang C, Gill A, Neira SV, Tang D. Taxifolin Inhibits Breast Cancer Growth by Facilitating CD8+ T Cell Infiltration and Inducing a Novel Set of Genes including Potential Tumor Suppressor Genes in 1q21.3. Cancers (Basel) 2023; 15:3203. [PMID: 37370814 DOI: 10.3390/cancers15123203] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/27/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Taxifolin inhibits breast cancer (BC) via novel mechanisms. In a syngeneic mouse BC model, taxifolin suppressed 4T-1 cell-derived allografts. RNA-seq of 4T-1 tumors identified 36 differentially expressed genes (DEGs) upregulated by taxifolin. Among their human homologues, 19, 7, and 2 genes were downregulated in BCs, high-proliferative BCs, and BCs with high-fatality risks, respectively. Three genes were established as tumor suppressors and eight were novel to BC, including HNRN, KPRP, CRCT1, and FLG2. These four genes exhibit tumor suppressive actions and reside in 1q21.3, a locus amplified in 70% recurrent BCs, revealing a unique vulnerability of primary and recurrent BCs with 1q21.3 amplification with respect to taxifolin. Furthermore, the 36 DEGs formed a multiple gene panel (DEG36) that effectively stratified the fatality risk in luminal, HER2+, and triple-negative (TN) equivalent BCs in two large cohorts: the METABRIC and TCGA datasets. 4T-1 cells model human TNBC cells. The DEG36 most robustly predicted the poor prognosis of TNBCs and associated it with the infiltration of CD8+ T, NK, macrophages, and Th2 cells. Of note, taxifolin increased the CD8+ T cell content in 4T-1 tumors. The DEG36 is a novel and effective prognostic biomarker of BCs, particularly TNBCs, and can be used to assess the BC-associated immunosuppressive microenvironment.
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Affiliation(s)
- Xiaozeng Lin
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Ying Dong
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yan Gu
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Jingyi Peng
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yingying Su
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Fengxiang Wei
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital of Shenzhen City, Shenzhen 518174, China
| | - Yanjun Wang
- Jilin Jianwei Songkou Biotechnology Co., Ltd., Changchun 510664, China
| | - Chengzhi Yang
- Benda International INC., Ottawa, ON K1X 0C1, Canada
| | - Armaan Gill
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Sandra Vega Neira
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
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Lin YC, Sahoo BK, Gau SS, Yang RB. The biology of SCUBE. J Biomed Sci 2023; 30:33. [PMID: 37237303 PMCID: PMC10214685 DOI: 10.1186/s12929-023-00925-3] [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: 02/20/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The SCUBE [Signal peptide-Complement C1r/C1s, Uegf, Bmp1 (CUB)-Epithelial growth factor domain-containing protein] family consists of three proteins in vertebrates, SCUBE1, 2 and 3, which are highly conserved in zebrafish, mice and humans. Each SCUBE gene encodes a polypeptide of approximately 1000 amino acids that is organized into five modular domains: (1) an N-terminal signal peptide sequence, (2) nine tandem epidermal growth factor (EGF)-like repeats, (3) a large spacer region, (4) three cysteine-rich (CR) motifs, and (5) a CUB domain at the C-terminus. Murine Scube genes are expressed individually or in combination during the development of various tissues, including those in the central nervous system and the axial skeleton. The cDNAs of human SCUBE orthologs were originally cloned from vascular endothelial cells, but SCUBE expression has also been found in platelets, mammary ductal epithelium and osteoblasts. Both soluble and membrane-associated SCUBEs have been shown to play important roles in physiology and pathology. For instance, upregulation of SCUBEs has been reported in acute myeloid leukemia, breast cancer and lung cancer. In addition, soluble SCUBE1 is released from activated platelets and can be used as a clinical biomarker for acute coronary syndrome and ischemic stroke. Soluble SCUBE2 enhances distal signaling by facilitating the secretion of dual-lipidated hedgehog from nearby ligand-producing cells in a paracrine manner. Interestingly, the spacer regions and CR motifs can increase or enable SCUBE binding to cell surfaces via electrostatic or glycan-lectin interactions. As such, membrane-associated SCUBEs can function as coreceptors that enhance the signaling activity of various serine/threonine kinase or tyrosine kinase receptors. For example, membrane-associated SCUBE3 functions as a coreceptor that promotes signaling in bone morphogenesis. In humans, SCUBE3 mutations are linked to abnormalities in growth and differentiation of both bones and teeth. In addition to studies on human SCUBE function, experimental results from genetically modified mouse models have yielded important insights in the field of systems biology. In this review, we highlight novel molecular discoveries and critical directions for future research on SCUBE proteins in the context of cancer, skeletal disease and cardiovascular disease.
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Affiliation(s)
- Yuh-Charn Lin
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Binay K Sahoo
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shiang-Shin Gau
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan.
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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Li X, Huang W, Xu X, Zhang HY, Shi Q. Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network. Front Genet 2023; 14:1202409. [PMID: 37303949 PMCID: PMC10248005 DOI: 10.3389/fgene.2023.1202409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Spatially resolved transcriptomics (SRT) provides an unprecedented opportunity to investigate the complex and heterogeneous tissue organization. However, it is challenging for a single model to learn an effective representation within and across spatial contexts. To solve the issue, we develop a novel ensemble model, AE-GCN (autoencoder-assisted graph convolutional neural network), which combines the autoencoder (AE) and graph convolutional neural network (GCN), to identify accurate and fine-grained spatial domains. AE-GCN transfers the AE-specific representations to the corresponding GCN-specific layers and unifies these two types of deep neural networks for spatial clustering via the clustering-aware contrastive mechanism. In this way, AE-GCN accommodates the strengths of both AE and GCN for learning an effective representation. We validate the effectiveness of AE-GCN on spatial domain identification and data denoising using multiple SRT datasets generated from ST, 10x Visium, and Slide-seqV2 platforms. Particularly, in cancer datasets, AE-GCN identifies disease-related spatial domains, which reveal more heterogeneity than histological annotations, and facilitates the discovery of novel differentially expressed genes of high prognostic relevance. These results demonstrate the capacity of AE-GCN to unveil complex spatial patterns from SRT data.
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Jain N, Nagaich U, Pandey M, Chellappan DK, Dua K. Predictive genomic tools in disease stratification and targeted prevention: a recent update in personalized therapy advancements. EPMA J 2022; 13:561-580. [PMID: 36505888 PMCID: PMC9727029 DOI: 10.1007/s13167-022-00304-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/01/2022] [Indexed: 11/15/2022]
Abstract
In the current era of medical revolution, genomic testing has guided the healthcare fraternity to develop predictive, preventive, and personalized medicine. Predictive screening involves sequencing a whole genome to comprehensively deliver patient care via enhanced diagnostic sensitivity and specific therapeutic targeting. The best example is the application of whole-exome sequencing when identifying aberrant fetuses with healthy karyotypes and chromosomal microarray analysis in complicated pregnancies. To fit into today's clinical practice needs, experimental system biology like genomic technologies, and system biology viz., the use of artificial intelligence and machine learning is required to be attuned to the development of preventive and personalized medicine. As diagnostic techniques are advancing, the selection of medical intervention can gradually be influenced by a person's genetic composition or the cellular profiling of the affected tissue. Clinical genetic practitioners can learn a lot about several conditions from their distinct facial traits. Current research indicates that in terms of diagnosing syndromes, facial analysis techniques are on par with those of qualified therapists. Employing deep learning and computer vision techniques, the face image assessment software DeepGestalt measures resemblances to numerous of disorders. Biomarkers are essential for diagnostic, prognostic, and selection systems for developing personalized medicine viz. DNA from chromosome 21 is counted in prenatal blood as part of the Down's syndrome biomarker screening. This review is based on a detailed analysis of the scientific literature via a vigilant approach to highlight the applicability of predictive diagnostics for the development of preventive, targeted, personalized medicine for clinical application in the framework of predictive, preventive, and personalized medicine (PPPM/3 PM). Additionally, targeted prevention has also been elaborated in terms of gene-environment interactions and next-generation DNA sequencing. The application of 3 PM has been highlighted by an in-depth analysis of cancer and cardiovascular diseases. The real-time challenges of genome sequencing and personalized medicine have also been discussed.
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Affiliation(s)
- Neha Jain
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, 201303 UP India
| | - Upendra Nagaich
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, 201303 UP India
| | - Manisha Pandey
- Department of Pharmaceutical Sciences, Central University of Haryana, Mahendergarh, 123031 India
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007 Australia
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007 Australia
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7
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Shen Y, Ren H, Davshilt T, Tian S, Wang X, Yi M, Ulaangerel T, Li B, Dugarjav M, Bou G. The transcriptome landscapes of allantochorion and vitelline-chorion in equine day 30 conceptus. Front Cell Dev Biol 2022; 10:958205. [PMID: 35990610 PMCID: PMC9386053 DOI: 10.3389/fcell.2022.958205] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
During equine early gestation, trophectoderm forms chorion tissue, which is composed of two parts that one is covering allantoin, called allantochorion (AC) and another is covering yolk sac, which here we call vitelline-chorion (VC). Given that little is known about the equine trophoblast-derived chorion differentiation at an early stage, we first compared the transcriptome of AC and VC of day 30 equine conceptus based on RNA-sequencing. As a result, we found that compared to VC, there are 484 DEGs, including 305 up- and 179 down-regulated genes in AC. GO and KEGG analysis indicated that up-regulated genes in AC are mainly cell proliferation and cell adhesion-related genes, participating in allantois expansion and allantochorionic-placenta formation; dominant genes in VC are extracellular exosome and other cell adhesion-related genes implicated in direct and indirect conceptus-maternal communication. Additionally, as for the progenitor chorion tissue of equine chorionic gonadotropin secreting endometrium cup-the chorionic girdle (CG), which locates at the junction of the dilating AC and regressing VC, we revealed its unique gene expression pattern and the gene regulation during its further differentiation in vitro. Collectively, this study sheds light on the molecular events regarding the trophoblast differentiation and function at an early stage of the equine preimplantation conceptus.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Manglai Dugarjav
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
| | - Gerelchimeg Bou
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
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8
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Yi Y, Xu T, Tan Y, Lv W, Zhao C, Wu M, Wu Y, Zhang Q. CCDC69 is a prognostic marker of breast cancer and correlates with tumor immune cell infiltration. Front Surg 2022; 9:879921. [PMID: 35910470 PMCID: PMC9334777 DOI: 10.3389/fsurg.2022.879921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Breast cancer (BC) is the most common malignancy and the leading cause of cancer-related death among women worldwide. Early detection, treatment, and metastasis monitoring are very important for the prognosis of BC patients. Therefore, effective biomarkers need to be explored to help monitor the prognosis of BC patients and guide treatment decisions. Methods In this study, the relationship between CCDC69 expression levels and tumor clinical characteristics were analyzed using RNA-seq information in BC samples from the TCGA database. Kaplan-Meier survival analysis was performed to analyze the prognostic value of CCDC69 in BC patients. Besides, gene enrichment analysis in BC samples was used to confirm the main function of CCDC69 in BC. The correlation between the expression of CCDC69 and the number of tumor-infiltrating lymphocytes was confirmed by interaction analysis of TIMER and GEPIA. Results The results showed that CCDC69 expression was significantly lower in cancer samples than in normal tissues, and was significantly lower in highly invasive BC than in carcinoma in situ. Meanwhile, low levels of CCDC69 were associated with a further poor prognosis. CDCC69 expression was positively correlated with the amount of different tumor-infiltrating lymphocytes. Mechanically, it could be presumed that the low expression of CCDC69 in BC might be caused by hypermethylation of the promoter region. Conclusions Summarily, CDCC69 could be used as a potential biomarker to predict the prognosis of BC and the sensitivity to immunotherapy such as PD-1/PD-L1 checkpoint inhibitors.
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Affiliation(s)
- Yi Yi
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Xu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yufang Tan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenchang Lv
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chongru Zhao
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Correspondence: Yiping Wu Qi Zhang
| | - Qi Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Correspondence: Yiping Wu Qi Zhang
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9
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Qi L, Xu R, Ren X, Zhang W, Yang Z, Tu C, Li Z. Comprehensive Profiling Reveals Prognostic and Immunogenic Characteristics of Necroptosis in Soft Tissue Sarcomas. Front Immunol 2022; 13:877815. [PMID: 35663937 PMCID: PMC9159500 DOI: 10.3389/fimmu.2022.877815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/14/2022] [Indexed: 12/31/2022] Open
Abstract
Soft tissue sarcomas (STSs) are heterogeneous malignancies derived from mesenchymal cells. Due to its rarity, heterogeneity, and limited overall response to chemotherapy, STSs represent a therapeutic challenge. Necroptosis is a novel therapeutic strategy for enhancing immunotherapy of cancer. Nevertheless, no research has explored the relationship between necroptosis-related genes (NRGs) and STSs. In this study, differentially expressed NRGs were identified using The Cancer Genome Atlas (TCGA) and The Cancer Genotype-Tissue Expression (GTEx) project. The expression levels of 34 NRGs were significantly different. Several key NRGs were validated using RT-qPCR and our own sequencing data. Patients with STSs were divided into two clusters using consensus cluster analysis, and significant differences were observed in their survival (p=0.002). We found the differentially expressed genes (DEGs) between the two clusters and carried out subsequent analysis. The necroptosis-related gene signatures with 10 key DEGs were identified with a risk score constructed. The prognosis of TCGA-SARC cohort with low necroptosis-related risk score was better (p<0.001). Meanwhile, the low-risk group had a significantly increased immune infiltration. Using the data of GSE17118 and another immunotherapy cohort as external validations, we observed significant survival differences between the two risk groups (p=0.019). The necroptosis-related risk score proved to be an independent prognostic factor, and a nomogram was further established and integrated with other clinical features. Notably, the necroptosis-related gene signature could also act as the prognostic indicator in other malignancies based on pan-cancer analysis. In summary, the study outlines NRGs in STSs and their potential role in prognosis and will be one of the important directions for future research.
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Affiliation(s)
- Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Ruiling Xu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Wenchao Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Zhimin Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China.,Department of Microbiology, Immunology & Molecular Genetics, UT Health Science Center, University of Texas Long School of Medicine, San Antonio, TX, United States
| | - Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
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Chen L, Dong Y, Pan Y, Zhang Y, Liu P, Wang J, Chen C, Lu J, Yu Y, Deng R. Identification and development of an independent immune-related genes prognostic model for breast cancer. BMC Cancer 2021; 21:329. [PMID: 33785008 PMCID: PMC8011146 DOI: 10.1186/s12885-021-08041-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/15/2021] [Indexed: 01/01/2023] Open
Abstract
Background Breast cancer is one of the main malignant tumors that threaten the lives of women, which has received more and more clinical attention worldwide. There are increasing evidences showing that the immune micro-environment of breast cancer (BC) seriously affects the clinical outcome. This study aims to explore the role of tumor immune genes in the prognosis of BC patients and construct an immune-related genes prognostic index. Methods The list of 2498 immune genes was obtained from ImmPort database. In addition, gene expression data and clinical characteristics data of BC patients were also obtained from the TCGA database. The prognostic correlation of the differential genes was analyzed through Survival package. Cox regression analysis was performed to analyze the prognostic effect of immune genes. According to the regression coefficients of prognostic immune genes in regression analysis, an immune risk scores model was established. Gene set enrichment analysis (GSEA) was performed to probe the biological correlation of immune gene scores. P < 0.05 was considered to be statistically significant. Results In total, 556 immune genes were differentially expressed between normal tissues and BC tissues (p < 0. 05). According to the univariate cox regression analysis, a total of 66 immune genes were statistically significant for survival risk, of which 30 were associated with overall survival (P < 0.05). Finally, a 15 immune genes risk scores model was established. All patients were divided into high- and low-groups. KM survival analysis revealed that high immune risk scores represented worse survival (p < 0.001). ROC curve indicated that the immune genes risk scores model had a good reliability in predicting prognosis (5-year OS, AUC = 0.752). The established risk model showed splendid AUC value in the validation dataset (3-year over survival (OS) AUC = 0.685, 5-year OS AUC = 0.717, P = 0.00048). Moreover, the immune risk signature was proved to be an independent prognostic factor for BC patients. Finally, it was found that 15 immune genes and risk scores had significant clinical correlations, and were involved in a variety of carcinogenic pathways. Conclusion In conclusion, our study provides a new perspective for the expression of immune genes in BC. The constructed model has potential value for the prognostic prediction of BC patients and may provide some references for the clinical precision immunotherapy of patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08041-x.
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Affiliation(s)
- Lin Chen
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Yuxiang Dong
- First Clinical Medical College of Nanjing Medical University, Nanjing, 210029, China
| | - Yitong Pan
- Nanjing Medical University, Nanjing, 211116, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhan Zhang
- First Clinical Medical College of Nanjing Medical University, Nanjing, 210029, China
| | - Ping Liu
- Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Junyi Wang
- Nanjing Medical University, Nanjing, 211116, China
| | - Chen Chen
- Nanjing Medical University, Nanjing, 211116, China
| | - Jianing Lu
- First Clinical Medical College of Nanjing Medical University, Nanjing, 210029, China
| | - Yun Yu
- Nanjing Medical University, Nanjing, 211116, China. .,Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211116, China.
| | - Rong Deng
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China.
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Li J, Zhang P, Xia Y. Study on <em>CCDC69</em> interfering with the prognosis of patients with breast cancer through PPAR signal pathway. Eur J Histochem 2021; 65. [PMID: 33634680 PMCID: PMC7922363 DOI: 10.4081/ejh.2021.3207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
Coiled-coil domain-containing protein 69 (CCDC69) is a novel gene and limited knowledge in known in breast cancer. In the present study, we aimed to explore the relationship between CCDC69 and breast cancer, demonstrate the clinicopathological significance and prognostic role of CCDC69 in breast cancer, and analyze the possible mechanism of CCDC69 affecting the prognosis of breast cancer. First, from GEO database, TIMER, GEPIA, and OncoLnc, we selected CCDC69 as the potential gene which closely involved in breast cancer progression. Next, by real-time PCR detection, the expression of CCDC69 in breast cancer tissue was notably lower than that in normal breast tissues (p=0.0002). In addition, our immunohistochemistry indicated that the positive expression rate of CCDC69 in the triple-negative breast cancer (TNBC) was lower than that in the non-TNBC (p=0.0362), and it was negatively correlated with the expression of Ki67 (p=0.001). Further enrichment analysis of CCDC69 and the similar genes performed on FunRich3.1.3 revealed that these genes were significantly associated with fat differentiation, and most of them were related to peroxisome proliferator-activated receptor (PPAR) signal pathway. Collectively, our findings suggest that CCDC69 is down regulated in breast cancer tissue especially in TNBC which has higher malignant grade and poorer clinical prognosis.
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Affiliation(s)
- Jinjiao Li
- Department of Breast, Thyroid and Burn Surgery, The People's Hospital of Wenshan Prefecture, Wenshan City, Yunnan.
| | - Panshi Zhang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan.
| | - Yun Xia
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan.
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Fernández LP, Gómez de Cedrón M, Ramírez de Molina A. Alterations of Lipid Metabolism in Cancer: Implications in Prognosis and Treatment. Front Oncol 2020; 10:577420. [PMID: 33194695 PMCID: PMC7655926 DOI: 10.3389/fonc.2020.577420] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 01/06/2023] Open
Abstract
Cancer remains the second leading cause of mortality worldwide. In the course of this multistage and multifactorial disease, a set of alterations takes place, with genetic and environmental factors modulating tumorigenesis and disease progression. Metabolic alterations of tumors are well-recognized and are considered as one of the hallmarks of cancer. Cancer cells adapt their metabolic competences in order to efficiently supply their novel demands of energy to sustain cell proliferation and metastasis. At present, there is a growing interest in understanding the metabolic switch that occurs during tumorigenesis. Together with the Warburg effect and the increased glutaminolysis, lipid metabolism has emerged as essential for tumor development and progression. Indeed, several investigations have demonstrated the consequences of lipid metabolism alterations in cell migration, invasion, and angiogenesis, three basic steps occurring during metastasis. In addition, obesity and associated metabolic alterations have been shown to augment the risk of cancer and to worsen its prognosis. Consequently, an extensive collection of tumorigenic steps has been shown to be modulated by lipid metabolism, not only affecting the growth of primary tumors, but also mediating progression and metastasis. Besides, key enzymes involved in lipid-metabolic pathways have been associated with cancer survival and have been proposed as prognosis biomarkers of cancer. In this review, we will analyze the impact of obesity and related tumor microenviroment alterations as modifiable risk factors in cancer, focusing on the lipid alterations co-occurring during tumorigenesis. The value of precision technologies and its application to target lipid metabolism in cancer will also be discussed. The degree to which lipid alterations, together with current therapies and intake of specific dietary components, affect risk of cancer is now under investigation, and innovative therapeutic or preventive applications must be explored.
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Affiliation(s)
- Lara P Fernández
- Precision Nutrition and Cancer Program, Molecular Oncology Group, IMDEA Food Institute, Campus of International Excellence (CEI) University Autonomous of Madrid (UAM) + CSIC, Madrid, Spain
| | - Marta Gómez de Cedrón
- Precision Nutrition and Cancer Program, Molecular Oncology Group, IMDEA Food Institute, Campus of International Excellence (CEI) University Autonomous of Madrid (UAM) + CSIC, Madrid, Spain
| | - Ana Ramírez de Molina
- Precision Nutrition and Cancer Program, Molecular Oncology Group, IMDEA Food Institute, Campus of International Excellence (CEI) University Autonomous of Madrid (UAM) + CSIC, Madrid, Spain
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