1
|
Scimeca M, Rovella V, Caporali S, Shi Y, Bischof J, Woodsmith J, Tisone G, Sica G, Amelio I, Melino G, Mauriello A, Bove P. Genetically driven predisposition leads to an unusually genomic unstable renal cell carcinoma. Discov Oncol 2024; 15:80. [PMID: 38512353 PMCID: PMC10957849 DOI: 10.1007/s12672-024-00894-5] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Renal cell carcinoma originates from the lining of the proximal convoluted renal tubule and represents the most common type of kidney cancer. Risk factors and comorbidities might be associated to renal cell carcinoma, while a small fraction of 2-3% emerges from patients with predisposing cancer syndromes, typically associated to hereditary mutations in VHL, folliculin, fumarate hydratase or MET genes. Here, we report a case of renal cell carcinoma in patient with concurrent germline mutations in BRCA1 and RAD51 genes. This case displays an unusual high mutational burden and chromosomal aberrations compared to the typical profile of renal cell carcinoma. Mutational analysis on whole genome sequencing revealed an enrichment of the MMR2 mutational signature, which is indicative of impaired DNA repair capacity. Overall, the tumor displayed a profile of unusual high genomic instability which suggests a possible origin from germline predisposing mutations in the DNA repair genes BRCA1 and RAD51. While BRCA1 and RAD51 germline mutations are well-characterised in breast and ovarian cancer, their role in renal cell carcinoma is still largely unexplored. The genomic instability detected in this case of renal cell carcinoma, along with the presence of unusual mutations, might offer support to clinicians for the development of patient-tailored therapies.
Collapse
Affiliation(s)
- Manuel Scimeca
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Valentina Rovella
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Sabrina Caporali
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, Suzhou, 215000, China
| | - Julia Bischof
- Indivumed GmbH, Falkenried, 88 Building D, 20251, Hamburg, Germany
| | | | - Giuseppe Tisone
- Department of Surgery, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Giuseppe Sica
- Department of Surgery, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Ivano Amelio
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Pierluigi Bove
- Department of Surgery, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| |
Collapse
|
2
|
Zheng P, Tan Y, Liu Q, Wu C, Kang J, Liang S, Zhu L, Yan K, Zeng L, Chen B. Deciphering the molecular and clinical characteristics of TREM2, HCST, and TYROBP in cancer immunity: A comprehensive pan-cancer study. Heliyon 2024; 10:e26993. [PMID: 38468942 PMCID: PMC10926084 DOI: 10.1016/j.heliyon.2024.e26993] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Background Hematopoietic cell signal transducer (HCST) and tyrosine kinase-binding protein (TYROBP) are triggering receptors expressed on myeloid cells 2 (TREM2), which are pivotal in the immune response to disease. Despite growing evidence underscoring the significance of TREM2, HCST, and TYROBP in certain forms of tumorigenesis, a comprehensive pan-cancer analysis of these proteins is lacking. Methods Multiple databases were synthesized to investigate the relationship between TREM2, HCST, TYROBP, and various cancer types. These include prognosis, methylation, regulation by long non-coding RNAs and transcription factors, immune signatures, pathway activity, microsatellite instability (MSI), tumor mutational burden (TMB), single-cell transcriptome profiling, and drug sensitivity. Results TREM2, HCST, and TYROBP displayed extensive somatic changes across numerous tumors, and their mRNA expression and methylation levels influenced patient outcomes across multiple cancer types. long non-coding RNA (lncRNA) -messenger RNA (mRNA) and TF-mRNA regulatory networks involving TREM2, HCST, and TYROBP were identified, with lncRNA MEG3 and the transcription factor SIP1 emerging as potential key regulators. Further immune analyses indicated that TREM2, HCST, and TYROBP play critical roles in immune-related pathways and macrophage differentiation, and may be significantly associated with TGF-β and SMAD9. Furthermore, the expression of TREM2, HCST, and TYROBP correlated with the immunotherapy markers TMB and MSI, and influenced sensitivity to immune-targeted drugs, thereby indicating their potential as predictors of immunotherapy outcomes. Conclusion This study offers valuable insights into the roles of TREM2, HCST, and TYROBP in tumor immunotherapy, suggesting their potential as prognostic markers and therapeutic targets for various cancers.
Collapse
Affiliation(s)
- Piao Zheng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yejun Tan
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Mathematics, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Qing Liu
- The department of neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Changwu Wu
- The department of neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Kang
- Department of rheumatology and immunology, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuzhi Liang
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Lemei Zhu
- Academician Workstation, Changsha Medical University, Changsha, Hunan, China
| | - Kuipo Yan
- Department of cardiology, The First Affiliated Hospital of Henan University of CM, Zhengzhou, Henan, China
| | - Lingfeng Zeng
- Academician Workstation, Changsha Medical University, Changsha, Hunan, China
| | - Bolin Chen
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| |
Collapse
|
3
|
Li Z, Li ZY, Maimaiti Z, Yang F, Fu J, Hao LB, Chen JY, Xu C. Identification of immune infiltration and immune-related biomarkers of periprosthetic joint infection. Heliyon 2024; 10:e26062. [PMID: 38370241 PMCID: PMC10867348 DOI: 10.1016/j.heliyon.2024.e26062] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
Background The immune response associated with periprosthetic joint infection (PJI) is an emerging but relatively unexplored topic. The aim of this study was to investigate immune cell infiltration in periprosthetic tissues and identify potential immune-related biomarkers. Methods The GSE7103 dataset from the GEO database was selected as the data source. Differentially expressed genes (DEGs) and significant modular genes in weighted correlation network analysis (WGCNA) were identified. Functional enrichment analysis and transcription factor prediction were performed on the overlapping genes. Next, immune-related genes from the ImmPort database were matched. The protein-protein interaction (PPI) analysis was performed to identify hub genes. CIBERSORTx was used to evaluate the immune cell infiltration pattern. Spearman correlation analysis was used to evaluate the relationship between hub genes and immune cells. Results A total of 667 DEGs were identified between PJI and control samples, and 1847 PJI-related module genes were obtained in WGCNA. Enrichment analysis revealed that the common genes were mainly enriched in immune and host defense-related terms. TFEC, SPI1, and TWIST2 were the top three transcription factors. Three hub genes, SDC1, MMP9, and IGF1, were identified in the immune-related PPI network. Higher levels of plasma cells, CD4+ memory resting T cells, follicular helper T cells, resting mast cells, and neutrophils were found in the PJI group, while levels of M0 macrophages were lower. Notably, the expression of all three hub genes correlated with the infiltration levels of seven types of immune cells. Conclusion The present study revealed immune infiltration signatures in the periprosthetic tissues of PJI patients. SDC1, MMP9, and IGF1 were potential immune-related biomarkers for PJI.
Collapse
Affiliation(s)
- Zhuo Li
- Medical School of Chinese PLA, Beijing, China
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhi-Yuan Li
- Medical School of Chinese PLA, Beijing, China
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zulipikaer Maimaiti
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Fan Yang
- Medical School of Chinese PLA, Beijing, China
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Jun Fu
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Orthopedics, The Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Li-Bo Hao
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Orthopedics, The Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Ji-Ying Chen
- Medical School of Chinese PLA, Beijing, China
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Chi Xu
- Department of Orthopedics, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Orthopedics, The Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
4
|
Chen J, Epstein MP, Schildkraut JM, Kar SP. Mapping inherited genetic variation with opposite effects on autoimmune disease and cancer identifies candidate drug targets associated with the anti-tumor immune response. medRxiv 2023:2023.12.23.23300491. [PMID: 38234717 PMCID: PMC10793537 DOI: 10.1101/2023.12.23.23300491] [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] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Germline alleles near genes that encode certain immune checkpoints (CTLA4, CD200) are associated with autoimmune/autoinflammatory disease and cancer but in opposite directions. This motivates a systematic search for additional germline alleles which demonstrate this pattern with the aim of identifying potential cancer immunotherapeutic targets using human genetic evidence. Methods Pairwise fixed effect cross-disorder meta-analyses combining genome-wide association studies (GWAS) for breast, prostate, ovarian and endometrial cancers (240,540 cases/317,000 controls) and seven autoimmune/autoinflammatory diseases (112,631 cases/895,386 controls) coupled with in silico follow-up. To ensure detection of alleles with opposite effects on cancer and autoimmune/autoinflammatory disease, the signs on the beta coefficients in the autoimmune/autoinflammatory GWAS were reversed prior to meta-analyses. Results Meta-analyses followed by linkage disequilibrium clumping identified 312 unique, independent lead variants with Pmeta<5x10-8 associated with at least one of the cancer types at Pcancer<10-3 and one of the autoimmune/autoinflammatory diseases at Pauto<10-3. At each lead variant, the allele that conferred autoimmune/autoinflammatory disease risk was protective for cancer. Mapping each lead variant to its nearest gene as its putative functional target and focusing on genes with established immunological effects implicated 32 of the nearest genes. Tumor bulk RNA-Seq data highlighted that the tumor expression of 5/32 genes (IRF1, IKZF1, SPI1, SH2B3, LAT) were each strongly correlated (Spearman's ρ>0.5) with at least one intra-tumor T/myeloid cell infiltration marker (CD4, CD8A, CD11B, CD45) in every one of the cancer types. Tumor single-cell RNA-Seq data from all cancer types showed that the five genes were more likely to be expressed in intra-tumor immune versus malignant cells. The five lead SNPs corresponding to these genes were linked to them via expression quantitative trait locus mechanisms and at least one additional line of functional evidence. Proteins encoded by the genes were predicted to be druggable. Conclusion We provide population-scale germline genetic and functional genomic evidence to support further evaluation of the proteins encoded by IRF1, IKZF1, SPI1, SH2B3, and LAT as possible targets for cancer immunotherapy.
Collapse
Affiliation(s)
- Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Joellen M Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Siddhartha P Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Ovarian Cancer Programme, Cancer Research UK Cambridge Centre, Cambridge, UK
| |
Collapse
|