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Zhang Y, Sun J, Li M, Hou L, Wang Z, Dong H, Xu W, Jiang R, Geng Y, Guan C, Zhu Z, Wang H, Gong Q, Zhang G. Identification and validation of a disulfidptosis-related genes prognostic signature in lung adenocarcinoma. Heliyon 2024; 10:e23502. [PMID: 38223725 PMCID: PMC10784160 DOI: 10.1016/j.heliyon.2023.e23502] [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: 06/17/2023] [Revised: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 01/16/2024] Open
Abstract
Disulfidptosis, a newly revealed form of cell death, regulated by numerous genes that has been recently identified. The exact role of disulfidptosis in lung adenocarcinoma (LUAD) still uncertain. Objective of this study was to explore potential prognostic markers among disulfidptosis genes in LUAD. By combining transcriptomic information from Gene Expression Omnibus databases and The Cancer Genome Atlas, we identified differentially expressed and prognostic disulfidptosis genes. By conducting least absolute shrinkage and selection operator with multivariate Cox regression, four disulfidptosis genes were selected to create the prognostic signature. The implementation of the signature separated the training and validation cohorts into groups with high- and low-risk. Subsequently, the model was verified by conducting an independent analysis of receiver operating characteristic (ROC) curves. Further comparisons were made between the two risk-divided groups with regards the tumor microenvironment, immune cell infiltration, immunotherapy response, and drug sensitivity. The signature was constructed using four disulfidptosis-related genes: SLC7A11, SLC3A2, NCKAP1, and GYS1. According to ROC curves, the signature was effective for predicting LUAD prognosis. In addition, the prognostic signature correlated with sensitivity to chemotherapeutic agents and the efficacy of immunotherapy in LUAD. Finally, through external validation, we showed that NCKAP1 are correlated with tumor migration, proliferation, and invasion of LUAD cells. GYS1 affects immune cell, especially M2 macrophage infiltration in the tumor microenvironment. The disulfidptosis four-gene model can reliably predict the prognosis of patients diagnosed with LUAD, thereby providing valuable information for clinical applications and immunotherapy.
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Affiliation(s)
- Yanpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingyang Sun
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Meng Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Liren Hou
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhiyu Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huanhuan Dong
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wenjun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rongxuan Jiang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuhan Geng
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Chungen Guan
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Zijiang Zhu
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Hongyi Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qiuyu Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Guangjian Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Comparative RNA-Sequencing Analysis Reveals High Complexity and Heterogeneity of Transcriptomic and Immune Profiles in Hepatocellular Carcinoma Tumors of Viral (HBV, HCV) and Non-Viral Etiology. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58121803. [PMID: 36557005 PMCID: PMC9785216 DOI: 10.3390/medicina58121803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Background and Objectives: Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is the leading cause of cancer-related mortality. It arises and progresses against fibrotic or cirrhotic backgrounds mainly due to infection with hepatitis viruses B (HBV) or C (HCV) or non-viral causes that lead to chronic inflammation and genomic changes. A better understanding of molecular and immune mechanisms in HCC subtypes is needed. Materials and Methods: To identify transcriptional changes in primary HCC tumors with or without hepatitis viral etiology, we analyzed the transcriptomes of 24 patients by next-generation sequencing. Results: We identified common and unique differentially expressed genes for each etiological tumor group and analyzed the expression of SLC, ATP binding cassette, cytochrome 450, cancer testis, and heat shock protein genes. Metascape functional enrichment analysis showed mainly upregulated cell-cycle pathways in HBV and HCV and upregulated cell response to stress in non-viral infection. GeneWalk analysis identified regulator, hub, and moonlighting genes and highlighted CCNB1, ACTN2, BRCA1, IGF1, CDK1, AURKA, AURKB, and TOP2A in the HCV group and HSF1, HSPA1A, HSP90AA1, HSPB1, HSPA5, PTK2, and AURKB in the group without viral infection as hub genes. Immune infiltrate analysis showed that T cell, cytotoxic, and natural killer cell markers were significantly more highly expressed in HCV than in non-viral tumors. Genes associated with monocyte activation had the highest expression levels in HBV, while high expression of genes involved in primary adaptive immune response and complement receptor activity characterized tumors without viral infection. Conclusions: Our comprehensive study underlines the high degree of complexity of immune profiles in the analyzed groups, which adds to the heterogeneous HCC genomic landscape. The biomarkers identified in each HCC group might serve as therapeutic targets.
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Tang S, Huang X, Jiang H, Qin S. Identification of a Five-Gene Prognostic Signature Related to B Cells Infiltration in Pancreatic Adenocarcinoma. Int J Gen Med 2021; 14:5051-5068. [PMID: 34511988 PMCID: PMC8416334 DOI: 10.2147/ijgm.s324432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
Background Pancreatic adenocarcinoma (PAAD) is an extremely malignant cancer. Immunotherapy is a promising avenue to increase the survival time of patients with PAAD. Methods RNA sequencing and clinical data for PAAD were downloaded from the TCGA database. The ssGSEA method and weighted gene co-expression network analysis were used to calculate the relative abundance of tumor-infiltrating immune cells and identify the related modules. Least absolute shrinkage and selection operator (LASSO) and Cox regression analyses were used to construct a prognostic model. MCPcounter and EPIC were also used to assess immune cell components using gene expression profiles. Results The B cells closely related module was identified, and five genes, including ARID5A, CLEC2B, MICAL1, MZB1, and RAPGEF1, were ultimately selected to establish a prognostic signature to calculate the risk scores of PAAD patients. Kaplan–Meier curves showed worse survival in the high-risk patients (p < 0.05), and the area under the receiver operating characteristic (ROC) curves of risk score for 1-year and 3-year survival were 0.78 and 0.80, respectively, based on the training set. Similar results were verified using the validated and combined sets. Interestingly, the low-risk group presented significantly elevated immune and stromal scores, proportion of B cells, and associations between these five genes and B cells were identified using multiple methods including ssGSEA, MCPcounter, and EPIC. Conclusion This is the first attempt to study a B cells-related prognostic signature, which is instrumental in the exploration of novel prognostic biomarkers in PAAD.
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Affiliation(s)
- Shaomei Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xiaoliang Huang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, People's Republic of China
| | - Haixing Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Shanyu Qin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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Noordam L, Ge Z, Özturk H, Doukas M, Mancham S, Boor PPC, Campos Carrascosa L, Zhou G, van den Bosch TPP, Pan Q, IJzermans JNM, Bruno MJ, Sprengers D, Kwekkeboom J. Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13102499. [PMID: 34065388 PMCID: PMC8160719 DOI: 10.3390/cancers13102499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary High recurrence rates after resection of liver cancer (hepatocellular carcinoma) with curative intent impair clinical outcomes of patients diagnosed with liver cancer. Cancer/testis antigens (CTAs) are expressed in cancer and can serve as therapeutic targets. We identified 12 CTAs expressed in 80% of liver cancer patients, and each one individually in at least 10%. Furthermore, we found that patients with expression of CTAs in macroscopically tumor-free liver tissue, experience more tumor recurrence and poor survival after surgical tumor removal. The increased risk of tumor recurrence in patients with CTA expression in tumor-free liver suggests that these patients already have micro-metastasis at the time of operation. These CTA-expressing (pre-)malignant cells may thus be a source of liver cancer recurrence, reflecting the relevance of targeting these to prevent liver cancer recurrence. Abstract High recurrence rates after resection of hepatocellular carcinoma (HCC) with curative intent impair clinical outcomes of HCC. Cancer/testis antigens (CTAs) are suitable targets for cancer immunotherapy if selectively expressed in tumor cells. The aims were to identify CTAs that are frequently and selectively expressed in HCC-tumors, and to investigate whether CTAs could serve as biomarkers for occult metastasis. Tumor and paired tumor-free liver (TFL) tissues of HCC-patients and healthy tissues were assessed for mRNA expression of 49 CTAs by RT-qPCR and protein expression of five CTAs by immunohistochemistry. Twelve CTA-mRNAs were expressed in ≥10% of HCC-tumors and not in healthy tissues except testis. In tumors, mRNA and protein of ≥ 1 CTA was expressed in 78% and 71% of HCC-patients, respectively. In TFL, CTA mRNA and protein was found in 45% and 30% of HCC-patients, respectively. Interestingly, CTA-expression in TFL was an independent negative prognostic factor for post-resection HCC-recurrence and survival. We established a panel of 12 testis-restricted CTAs expressed in tumors of most HCC-patients. The increased risk of HCC-recurrence in patients with CTA expression in TFL, suggests that CTA-expressing (pre-)malignant cells may be a source of HCC-recurrence, reflecting the relevance of targeting these to prevent HCC-recurrence.
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Affiliation(s)
- Lisanne Noordam
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Zhouhong Ge
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Hadiye Özturk
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Michail Doukas
- Department of Pathology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.D.); (T.P.P.v.d.B.)
| | - Shanta Mancham
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Patrick P. C. Boor
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Lucia Campos Carrascosa
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Guoying Zhou
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Thierry P. P. van den Bosch
- Department of Pathology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.D.); (T.P.P.v.d.B.)
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Jan N. M. IJzermans
- Department of Surgery, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands;
| | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Dave Sprengers
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Jaap Kwekkeboom
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
- Correspondence: ; Tel.: +31-(0)10-703-5942
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