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Han J, Lyu L. Identification of the biological functions and chemo-therapeutic responses of ITGB superfamily in ovarian cancer. Discov Oncol 2024; 15:198. [PMID: 38814534 PMCID: PMC11139846 DOI: 10.1007/s12672-024-01047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Patients with ovarian cancer (OC) tend to face a poor prognosis due to a lack of typical symptoms and a high rate of recurrence and chemo-resistance. Therefore, identifying representative and reliable biomarkers for early diagnosis and prediction of chemo-therapeutic responses is vital for improving the prognosis of OC. METHODS Expression levels, IHC staining, and subcellular distribution of eight ITGBs were analyzed using The Cancer Genome Atlas (TCGA)-Ovarian Serous Cystadenocarcinoma (OV) database, GEO DataSets, and the HPA website. PrognoScan and Univariate Cox were used for prognostic analysis. TIDE database, TIMER database, and GSCA database were used to analyze the correlation between immune functions and ITGBs. Consensus clustering analysis was performed to subtype OC patients in the TCGA database. LASSO regression was used to construct the predictive model. The Cytoscape software was used for identifying hub genes. The 'pRRophetic' R package was applied to predict chemo-therapeutic responses of ITGBs. RESULTS ITGBs were upregulated in OC tissues except ITGB1 and ITGB3. High expression of ITGBs correlated with an unfavorable prognosis of OC except ITGB2. In OC, there was a strong correlation between immune responses and ITGB2, 6, and 7. In addition, the expression matrix of eight ITGBs divided the TCGA-OV database into two subgroups. Subgroup A showed upregulation of eight ITGBs. The predictive model distinguishes OC patients from favorable prognosis to poor prognosis. Chemo-therapeutic responses showed that ITGBs were able to predict responses of common chemo-therapeutic drugs for patients with OC. CONCLUSIONS This article provides evidence for predicting prognosis, immuno-, and chemo-therapeutic responses of ITGBs in OC and reveals related biological functions of ITGBs in OC.
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Affiliation(s)
- Jiawen Han
- Department of Nutrition, Jinshan Hospital, Fudan University, 1508 Longhang Road, Jinshan District, Shanghai, 201508, China
| | - Lin Lyu
- Department of Nutrition, Jinshan Hospital, Fudan University, 1508 Longhang Road, Jinshan District, Shanghai, 201508, China.
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Wang J, Jiang L, Shang Z, Ye Z, Yuan D, Cui X. A Prognostic Model for Prostate Cancer Patients Based on Two DNA Damage Response Mutation-Related Immune Genes. Cancer Biother Radiopharm 2024; 39:306-317. [PMID: 37610864 DOI: 10.1089/cbr.2023.0033] [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: 08/25/2023] Open
Abstract
Background: DNA damage response (DDR) mutation-related genes and composition of immune cells are core factors affecting the effectiveness of immune checkpoint inhibitor therapy. The aim of this study is to combine DDR with immune-related genes to screen the prognostic signature for prostate cancer (PCa). Methods: Gene expression profile and somatic mutation were downloaded from The Cancer Genome Atlas (TCGA). DDR-related genes were obtained from published study. After identification of prognostic-related DDR genes, samples were divided into mutation and nonmutation groups. Differentially expressed genes between these two groups were screened, followed by selection of immune-related DDR genes. Univariate and multivariate Cox analyses were performed to screen genes for constructing prognostic model. Nomogram model was also developed. The expression level of signature was detected by quantitative real-time PCR (qPCR). Results: Two genes (MYBBP1A and PCDHA9) were screened to construct the prognostic model, and it showed good risk prediction of PCa prognosis. Survival analysis showed that patients in high-risk group had worse overall survival than those in low-risk group. Cox analyses indicated that risk score could be used as an independent prognostic factor for PCa. qPCR results indicated that MYBBP1A was upregulated, whereas PCDHA9 was downregulated in PCa cell lines. Conclusions: A prognostic model based on DDR mutation-related genes for PCa was established, which serves as an effective tool for prognostic differentiation in patients with PCa.
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Affiliation(s)
- Jian Wang
- Department of Urology Surgery, The First People's Hospital of Foshan, Affiliated Hospital of Sun Yat-sen University, Foshan City, China
| | - Li Jiang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhenhua Shang
- Department of Urology, Xuan Wu Hospital Capital Medical University, Beijing, China
| | - Zhaohua Ye
- Department of Urology Surgery, The People's Hospital of Dongguan, Dongguan City, China
| | - Dan Yuan
- Department of Urology, Jiangmen Central Hospital, Jiangmen, China
| | - Xin Cui
- Department of Urology, Xuan Wu Hospital Capital Medical University, Beijing, China
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Mao X, Chen X, Xu Z, Ding L, Luo W, Lin Y, Wang R, Xia L, Wang M, Li G. The identification of a N 6-methyladenosin-modifed immune pattern to predict immunotherapy response and survival in urothelial carcinoma. Aging (Albany NY) 2024; 16:7774-7798. [PMID: 38696324 PMCID: PMC11131986 DOI: 10.18632/aging.205782] [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: 09/14/2023] [Accepted: 03/29/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND Dysregulation of the immune system and N6-methyladenosine (m6A) contribute to immune therapy resistance and cancer progression in urothelial carcinoma (UC). This study aims to identify immune-related molecules, that are m6A-modified, and that are associated with tumor progression, poor prognosis, and immunotherapy response. METHODS We identified prognostic immune genes (PIGs) using Cox analysis and random survival forest variable hunting algorithm (RSF-VH) on immune genes retrieved from the Immunology Database and Analysis Portal database (ImmPort). The RM2Target database and MeRIP-seq analysis, combined with a hypergeometric test, assessed m6A methylation in these PIGs. We analyzed the correlation between the immune pattern and prognosis, as well as their association with clinical factors in multiple datasets. Moreover, we explored the interplay between immune patterns, tumor immune cell infiltration, and m6A regulators. RESULTS 28 PIGs were identified, of which the 10 most significant were termed methylated prognostic immune genes (MPIGs). These MPIGs were used to create an immune pattern score. Kaplan-Meier and Cox analyses indicated this pattern as an independent risk factor for UC. We observed significant associations between the immune pattern, tumor progression, and immune cell infiltration. Differential expression analysis showed correlations with m6A regulators expression. This immune pattern proved effective in predicting immunotherapy response in UC in real-world settings. CONCLUSION The study identified a m6A-modified immune pattern in UC, offering prognostic and therapeutic response predictions. This emphasizes that immune genes may influence tumor immune status and progression through m6A modifications.
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Affiliation(s)
- Xudong Mao
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xianjiong Chen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Zhehao Xu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Lifeng Ding
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Wenqin Luo
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Yudong Lin
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruyue Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Mingchao Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
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Ibrahim OM, Kalinski P. Breaking Barriers: Modulation of Tumor Microenvironment to Enhance Bacillus Calmette-Guérin Immunotherapy of Bladder Cancer. Cells 2024; 13:699. [PMID: 38667314 PMCID: PMC11049012 DOI: 10.3390/cells13080699] [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: 02/16/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The clinical management of bladder cancer continues to present significant challenges. Bacillus Calmette-Guérin (BCG) immunotherapy remains the gold standard of treatment for non-muscle invasive bladder cancer (NMIBC), but many patients develop recurrence and progression to muscle-invasive disease (MIBC), which is resistant to BCG. This review focuses on the immune mechanisms mobilized by BCG in bladder cancer tumor microenvironments (TME), mechanisms of BCG resistance, the dual role of the BCG-triggered NFkB/TNFα/PGE2 axis in the regulation of anti-tumor and tumor-promoting aspects of inflammation, and emerging strategies to modulate their balance. A better understanding of BCG resistance will help develop new treatments and predictive biomarkers, paving the way for improved clinical outcomes in bladder cancer patients.
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Affiliation(s)
- Omar M. Ibrahim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Pawel Kalinski
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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Alberca-del Arco F, Prieto-Cuadra D, Santos-Perez de la Blanca R, Sáez-Barranquero F, Matas-Rico E, Herrera-Imbroda B. New Perspectives on the Role of Liquid Biopsy in Bladder Cancer: Applicability to Precision Medicine. Cancers (Basel) 2024; 16:803. [PMID: 38398192 PMCID: PMC10886494 DOI: 10.3390/cancers16040803] [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: 01/14/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bladder cancer (BC) is one of the most common tumors in the world. Cystoscopy and tissue biopsy are the standard methods in screening and early diagnosis of suspicious bladder lesions. However, they are invasive procedures that may cause pain and infectious complications. Considering the limitations of both procedures, and the recurrence and resistance to BC treatment, it is necessary to develop a new non-invasive methodology for early diagnosis and multiple evaluations in patients under follow-up for bladder cancer. In recent years, liquid biopsy has proven to be a very useful diagnostic tool for the detection of tumor biomarkers. This non-invasive technique makes it possible to analyze single tumor components released into the peripheral circulation and to monitor tumor progression. Numerous biomarkers are being studied and interesting clinical applications for these in BC are being presented, with promising results in early diagnosis, detection of microscopic disease, and prediction of recurrence and response to treatment.
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Affiliation(s)
- Fernardo Alberca-del Arco
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
| | - Daniel Prieto-Cuadra
- Departamento de Anatomía Patológica, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain;
- Unidad de Gestion Clinica de Anatomia Patologica, IBIMA, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- SYNLAB Pathology, 29007 Málaga, Spain
| | - Rocio Santos-Perez de la Blanca
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
| | - Felipe Sáez-Barranquero
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
| | - Elisa Matas-Rico
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
- Departamento de Biología Celular, Genética y Fisiología, Universidad de Málaga (UMA), 29071 Málaga, Spain
| | - Bernardo Herrera-Imbroda
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Universidad de Málaga (UMA), 29071 Málaga, Spain
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Cui Y, Wu S, Liu K, Zhao H, Ma B, Gong L, Zhou Q, Li X. Extra villous trophoblast-derived PDL1 can ameliorate macrophage inflammation and promote immune adaptation associated with preeclampsia. J Reprod Immunol 2024; 161:104186. [PMID: 38134680 DOI: 10.1016/j.jri.2023.104186] [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: 08/31/2023] [Revised: 10/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
INTRODUCTION Severe preeclampsia (sPE) is a systemic syndrome that may originate from chronic inflammation. Maintaining maternal-fetal hemostasis by the co-inhibitory molecule programmed death ligand 1 (PDL1) can be favorable for ameliorating inflammation from immune cells. Apart from programmed death 1 (PD1) expression, decidual macrophages (dMs) produce inflammatory cytokines, in response to cells which express PDL1. However, strong evidence is lacking regarding whether the PDL1/PD1 interaction between trophoblasts and decidual macrophages affects inflammation during sPE development. METHODS To determine whether the trophoblast-macrophage crosstalk via the PDL1/PD1 axis modulates the inflammatory response in sPE-like conditions, at first, maternal-fetal tissues from sPE and normal patients were collected, and the PDL1/PD1 distribution was analyzed by Western blot, immunohistochemistry/ immunofluorescence and flow cytometry. Next, a coculture system was established and flow cytometry was used to identify how PDL1 was involved in macrophage-related inflammation under hypoxic stress. Transcriptional analysis was performed to clarify the inflammation-associated pathway induced by the PDL1/PD1 interaction. Finally, the Nω-nitro-L-arginine methyl ester hydrochloride (L-NAME) mouse model was used to examine the effect of PDL1 on macrophage-related inflammation by measuring PE-like symptoms. RESULTS In maternal-fetal tissue from sPE patients, placental extravillous trophoblasts (EVTs) and dMs had a surprisingly increase of PDL1 and PD1 expression, respectively, accompanied by a higher percentage of CD68 +CD86 + dMs. In vitro experiments showed that trophoblast-derived PDL1 under hypoxia interacted with PD1 on CD14 +CD80 +macrophages, leading to suppression of inflammation through the TNFα-p38/NFκB pathway. Accordingly, the PE-like mouse model showed a reversal of PE-like symptoms and a reduced F4/80 + CD86 + macrophage percentage in the uterus in response to recombinant PDL1 protein administration, indicating the protective effect of PDL1. DISCUSSION Our results initially explained an immunological adaptation of trophoblasts under placental hypoxia, although this protection was insufficient. Our findings suggest the possible capacity of modulating PDL1 expression as a potential therapeutic strategy to target the inflammatory response in sPE.
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Affiliation(s)
- Yutong Cui
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - Suwen Wu
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - Ketong Liu
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - Huanqiang Zhao
- Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Bo Ma
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - Lili Gong
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - Qiongjie Zhou
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Fudan University, Shanghai, China.
| | - Xiaotian Li
- Department Obstetrics, Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China; Department of Obstetrics, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China.
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7
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Xu D, Li P, Zhang C, Shen Y, Cai J, Wei Q, Cao M, Xu Z, Wu D, Wang H, Bi X, Wang B, Li K. Development of an m6A-Related lncRNAs Signature Predicts Tumor Stemness and Prognosis for Low-Grade Glioma Patients. Stem Cells Int 2024; 2024:2062283. [PMID: 38229597 PMCID: PMC10791469 DOI: 10.1155/2024/2062283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
Background Growing evidence has revealed that m6A modification of long noncoding RNAs (lncRNAs) dynamically controls tumor stemness and tumorigenesis-related processes. However, the prognostic significance of m6A-related lncRNAs and their associations with stemness in low-grade glioma (LGG) remain to be clarified. Methods A multicenter transcriptome analysis of lncRNA expression in 1,247 LGG samples was performed in this study. The stemness landscape of LGG tumors was presented and associations with clinical features were revealed. The m6A-related lncRNAs were identified between stemness groups and were further prioritized via least absolute shrinkage and selection operator Cox regression analysis. A risk score model based on m6A-related lncRNAs was constructed and validated in external LGG datasets. Results Based on the expression of LINC02984, PFKP-DT, and CRNDE, a risk model and nomogram were constructed; they successfully predicted the survival of patients and were extended to external datasets. Significant correlations were observed between the risk score and tumor stemness. Moreover, patients in different risk groups exhibited distinct tumor immune microenvironments and immune signatures. We finally provided several potential compounds suitable for specific risk groups, which may aid in LGG treatment. Conclusions This novel signature presents noteworthy value in the prediction of prognosis and stemness status for LGG patients and will foster future research on the development of clinical regimens.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Peihu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Chunrui Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100020, China
| | - Yutong Shen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Jiale Cai
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Qingchen Wei
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Meng Cao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Zhizhou Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Deng Wu
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Bo Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou 571199, China
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Cui S, Chen T, Zhao Y, Xiao Z, Liu M, Huang X, Cao S, Zhou R, Li Y, Huo X, Wang N. Identification of ATM Mutation as a Potential Prognostic Biomarker for Immune Checkpoint Inhibitors Therapy. Curr Cancer Drug Targets 2024; 24:501-509. [PMID: 38804343 DOI: 10.2174/0115680096250376231025062652] [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: 02/22/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 05/29/2024]
Abstract
BACKGROUND Ataxia telangiectasia mutated (ATM), an apical DNA damage response gene, is a commonly mutated gene in tumors, and its mutation could strengthen tumor immunogenicity and alter the expression of PD-L1, which potentially contributes to immune checkpoint inhibitors (ICIs) therapy. METHODS The characteristics of ATM mutation and its relationship with the ICIs-treated clinical prognosis have been analyzed comprehensively in this paper. The overall frequency of ATM mutations has been found to be 4% (554/10953) in the cancer genome atlas (TCGA) cohort. RESULTS Both the TMB and MSI levels in patients with ATM mutations were significantly higher than those in patients without mutations (P < 0.0001). The median TMB was positively correlated with the frequency of ATM mutations (r = 0.54, P = 0.003). In the TCGA cohort, patients with ATM mutations had better clinical benefits in terms of overall survival (OS, hazard ratio (HR) = 0.736, 95% CI = 0.623 - 0.869), progression-free survival (PFS, HR = 0.761, 95% CI = 0.652 - 0.889), and disease-free survival (DFS, HR = 0.686, 95% CI = 0.512 - 0.919)] than patients without ATM mutations. Subsequently, the verification results showed ATM mutations to be significantly correlated with longer OS in ICIs-treated patients (HR = 0.710, 95% CI = 0.544 - 0.928). Further exploration indicated ATM mutation to be significantly associated with regulated anti-tumor immunity (P < 0.05). CONCLUSION Our findings highlight the value of ATM mutation as a promising biomarker to predict ICIs therapy in multiple tumors.
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Affiliation(s)
- Saijin Cui
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Tianyu Chen
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yaning Zhao
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhuoyun Xiao
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Meitong Liu
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xi Huang
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shiru Cao
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Rongmiao Zhou
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - You Li
- Hospital Infection Control Division, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiangran Huo
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Na Wang
- Molecular Biology Laboratory, Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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9
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Peng M, Chu X, Peng Y, Li D, Zhang Z, Wang W, Zhou X, Xiao D, Yang X. Targeted therapies in bladder cancer: signaling pathways, applications, and challenges. MedComm (Beijing) 2023; 4:e455. [PMID: 38107059 PMCID: PMC10724512 DOI: 10.1002/mco2.455] [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: 03/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Bladder cancer (BC) is one of the most prevalent malignancies in men. Understanding molecular characteristics via studying signaling pathways has made tremendous breakthroughs in BC therapies. Thus, targeted therapies including immune checkpoint inhibitors (ICIs), antibody-drug conjugates (ADCs), and tyrosine kinase inhibitor (TKI) have markedly improved advanced BC outcomes over the last few years. However, the considerable patients still progress after a period of treatment with current therapeutic regimens. Therefore, it is crucial to guide future drug development to improve BC survival, based on the molecular characteristics of BC and clinical outcomes of existing drugs. In this perspective, we summarize the applications and benefits of these targeted drugs and highlight our understanding of mechanisms of low response rates and immune escape of ICIs, ADCs toxicity, and TKI resistance. We also discuss potential solutions to these problems. In addition, we underscore the future drug development of targeting metabolic reprogramming and cancer stem cells (CSCs) with a deep understanding of their signaling pathways features. We expect that finding biomarkers, developing novo drugs and designing clinical trials with precisely selected patients and rationalized drugs will dramatically improve the quality of life and survival of patients with advanced BC.
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Affiliation(s)
- Mei Peng
- Department of PharmacyXiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Xuetong Chu
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Yan Peng
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Duo Li
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Zhirong Zhang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Weifan Wang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Xiaochen Zhou
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Di Xiao
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Xiaoping Yang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
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10
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Ma YT, Hua F, Zhong XM, Xue YJ, Li J, Nie YC, Zhang XD, Ma JW, Lin CH, Zhang HZ, He W, Sha D, Zhao MQ, Yao ZG. Clinicopathological characteristics, molecular landscape, and biomarker landscape for predicting the efficacy of PD-1/PD-L1 inhibitors in Chinese population with mismatch repair deficient urothelial carcinoma: a real-world study. Front Immunol 2023; 14:1269097. [PMID: 38022513 PMCID: PMC10657814 DOI: 10.3389/fimmu.2023.1269097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Urothelial carcinoma (UC) with deficient mismatch repair (dMMR) is a specific subtype of UC characterized by the loss of mismatch repair (MMR) proteins and its association with Lynch syndrome (LS). However, comprehensive real-world data on the incidence, clinicopathological characteristics, molecular landscape, and biomarker landscape for predicting the efficacy of PD-1/PD-L1 inhibitors in the Chinese patients with dMMR UC remains unknown. We analyzed 374 patients with bladder urothelial carcinoma (BUC) and 232 patients with upper tract urothelial carcinoma (UTUC) using tissue microarrays, immunohistochemistry, and targeted next-generation sequencing. Results showed the incidence of dMMR UC was higher in the upper urinary tract than in the bladder. Genomic analysis identified frequent mutations in KMT2D and KMT2C genes and LS was confirmed in 53.8% of dMMR UC cases. dMMR UC cases displayed microsatellite instability-high (MSI-H) (PCR method) in 91.7% and tumor mutational burden-high (TMB-H) in 40% of cases. The density of intratumoral CD8+ T cells correlated with better overall survival in dMMR UC patients. Positive PD-L1 expression was found in 20% cases, but some patients positively responded to immunotherapy despite negative PD-L1 expression. Our findings provide valuable insights into the characteristics of dMMR UC in the Chinese population and highlights the relevance of genetic testing and immunotherapy biomarkers for treatment decisions.
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Affiliation(s)
- Yu-Ting Ma
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Fang Hua
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, United States
| | - Xiu-Ming Zhong
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ying-Jie Xue
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Jia Li
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yi-Cong Nie
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xue-Dong Zhang
- Department of Pathology, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Ji-Wei Ma
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Cun-Hu Lin
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Hao-Zhuang Zhang
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Wei He
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Dan Sha
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Miao-Qing Zhao
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Zhi-Gang Yao
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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11
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Borgsmüller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues. CELL GENOMICS 2023; 3:100380. [PMID: 37719146 PMCID: PMC10504633 DOI: 10.1016/j.xgen.2023.100380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 09/19/2023]
Abstract
Cell lineages accumulate somatic mutations during organismal development, potentially leading to pathological states. The rate of somatic evolution within a cell population can vary due to multiple factors, including selection, a change in the mutation rate, or differences in the microenvironment. Here, we developed a statistical test called the Poisson Tree (PT) test to detect varying evolutionary rates among cell lineages, leveraging the phylogenetic signal of single-cell DNA sequencing (scDNA-seq) data. We applied the PT test to 24 healthy and cancer samples, rejecting a constant evolutionary rate in 11 out of 15 cancer and five out of nine healthy scDNA-seq datasets. In six cancer datasets, we identified subclonal mutations in known driver genes that could explain the rate accelerations of particular cancer lineages. Our findings demonstrate the efficacy of scDNA-seq for studying somatic evolution and suggest that cell lineages often evolve at different rates within cancer and healthy tissues.
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Affiliation(s)
- Nico Borgsmüller
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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12
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Xu G, Deng Y, Shi H. Identification of DNA Damage Repair Gene Signature as a Novel Prognostic Marker in Glioblastoma Multiforme. World Neurosurg 2023; 176:e598-e609. [PMID: 37270097 DOI: 10.1016/j.wneu.2023.05.107] [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: 04/28/2023] [Accepted: 05/28/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND The efficacy of treatment of glioblastoma multiforme (GBM) is limited. The effect of DNA damage repair is an important factor. METHODS Expression data were downloaded from The Cancer Genome Atlas (training dataset) and the Gene Expression Omnibus (validation dataset) databases. Univariate Cox regression analysis and the least absolute shrinkage and selection operator were used to construct a DNA damage response (DDR) gene signature. Receiver operating characteristic curve analysis and Kaplan-Meier curve analysis were used to estimate the prognostic value of the risk signature. Moreover, consensus clustering analysis was used to investigate the potential subtypes of GBM according to DDR expression. RESULTS We constructed a 3-DDR-related gene signature through the survival analysis. The Kaplan-Meier curve analysis suggested that patients in the low-risk group have significantly better survival outcomes compared with the high-risk group in the training and external validation datasets. The results from the receiver operating characteristic curve analysis indicated that the risk model has high prognostic value in the training and external validation datasets. Moreover, 3 stable molecular subtypes were identified and validated in the Gene Expression Omnibus and The Cancer Genome Atlas databases according to the expression of the DNA repair gene. The microenvironment and immunity of GBM were further investigated and showed that cluster 2 had higher immunity and a higher immune score compared with clusters 1 and 3. CONCLUSIONS The DNA damage repair-related gene signature was an independent and powerful prognostic biomarker in GBM. Knowledge of the GBM subtypes could have important implications in the subclassification of GBM.
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Affiliation(s)
- Guizhi Xu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Neurosurgery, The Second Hospital of Heilongjiang Province, Harbin, China
| | - Yuhui Deng
- Division of Medical Imaging, Heilongjiang Provincial Hospital, Harbin Institute of Technology, Harbin, China
| | - Huaizhang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
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13
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Koti M, Bivalacqua T, Black PC, Cathomen T, Galsky MD, Gulley JL, Ingersoll MA, Kamat AM, Kassouf W, Siemens DR, Gao J. Adaptive Immunity in Genitourinary Cancers. Eur Urol Oncol 2023; 6:263-272. [PMID: 37069029 DOI: 10.1016/j.euo.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 04/19/2023]
Abstract
CONTEXT While urothelial and renal cell cancers have exhibited modest responses to novel immune checkpoint inhibitors targeting the programmed death ligand 1 and its receptor, response rates in patients with prostate cancer have remained poor. The factors underlying suboptimal outcomes observed in patients treated with novel immunotherapies are still to be resolved. OBJECTIVE To review the literature and describe the key adaptive immune physiological events associated with cancer progression and therapeutic response in genitourinary (GU) cancers. EVIDENCE ACQUISITION We performed a nonsystematic, collaborative narrative review to highlight recent advancements leading to the current state of knowledge on the critical mediators of antitumor adaptive immunity to GU cancers. Further, we discuss the findings on the pre- and post-treatment immunological events that either are unique to each of the three cancer types or exhibit overlapping clinical associations. EVIDENCE SYNTHESIS Aging-associated immune function decline is a major factor underlying poor outcomes observed in patients treated with both conventional and novel immunotherapies. Other cancer immunobiological aspects associated with suboptimal responses in GU cancers include the overall tumor mutational burden, mutations in specific tumor suppressor/DNA damage repair genes (KDM6A, PTEN, STAG2, TP53, ATM, and BRCA2), and abundance of multiple functional states of adaptive immune cells and their spatiotemporal localization within the tumor immune microenvironment. Understanding these mechanisms may potentially lead to the development of prognostic and predictive biomarkers such as immune cell infiltration profiles and tertiary lymphoid structures (TLSs) that associate with variable clinical outcomes depending on the nature of the novel immunotherapeutic approach. Implementation of newer immune-monitoring technologies and improved preclinical modeling systems will augment our understanding of the host and tumor intrinsic factors contributing to the variability of responses to immunotherapies. CONCLUSIONS Despite the tremendous progress made in the understanding of dynamic and static adaptive immune elements within the tumor immune landscape, several knowledge gaps remain. A comprehensive knowledge thus gained will lead to precision immunotherapy, improved drug sequencing, and a therapeutic response. PATIENT SUMMARY We performed a collaborative review by a diverse group of experts in the field to examine our understanding of the events and crosstalk between cancer cells and the patient's immune system that are associated with responses to novel immunotherapies. An evolving understanding of tumor-intrinsic and host-related immune alterations, both before and after therapy, will aid in the discovery of promising markers of responses to immunotherapy as well as the development of unique therapeutic approaches for the management of genitourinary cancers.
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Affiliation(s)
- Madhuri Koti
- Department of Biomedical and Molecular Sciences, Cancer Research Institute, Queen's University, Kingston, ON, Canada.
| | - Trinity Bivalacqua
- Department of Urology, Perelman Center for Advanced Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Faculty of Medicine & Medical Center - University of Freiburg, Freiburg, Germany
| | - Matthew D Galsky
- Division of Hematology/Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James L Gulley
- Center for Immuno-Oncology, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Molly A Ingersoll
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, 75014, France; Mucosal Inflammation and Immunity, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Ashish M Kamat
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wassim Kassouf
- Division of Urology, McGill University Health Center, Montreal, QC, Canada
| | - D Robert Siemens
- Department of Urology, Queen's University School of Medicine, Kingston, ON, Canada
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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14
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Olson BM, Chaudagar K, Bao R, Saha SS, Hong C, Li M, Rameshbabu S, Chen R, Thomas A, Patnaik A. BET Inhibition Sensitizes Immunologically Cold Rb-Deficient Prostate Cancer to Immune Checkpoint Blockade. Mol Cancer Ther 2023; 22:751-764. [PMID: 37014264 PMCID: PMC10239341 DOI: 10.1158/1535-7163.mct-22-0369] [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: 05/25/2022] [Revised: 01/09/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
Non-T-cell-inflamed immunologically "cold" tumor microenvironments (TME) are associated with poor responsiveness to immune checkpoint blockade (ICB) and can be sculpted by tumor cell genomics. Here, we evaluated how retinoblastoma (Rb) tumor-suppressor loss-of-function (LOF), one of the most frequent alterations in human cancer and associated with lineage plasticity, poor prognosis, and therapeutic outcomes, alters the TME, and whether therapeutic strategies targeting the molecular consequences of Rb loss enhance ICB efficacy. We performed bioinformatics analysis to elucidate the impact of endogenous Rb LOF on the immune TME in human primary and metastatic tumors. Next, we used isogenic murine models of Rb-deficient prostate cancer for in vitro and in vivo mechanistic studies to examine how Rb loss and bromodomain and extraterminal (BET) domain inhibition (BETi) reprograms the immune landscape, and evaluated in vivo therapeutic efficacy of BETi, singly and in combination with ICB and androgen deprivation therapy. Rb loss was enriched in non-T-cell-inflamed tumors, and Rb-deficient murine tumors demonstrated decreased immune infiltration in vivo. The BETi JQ1 increased immune infiltration into the TME through enhanced tumor cell STING/NF-κB activation and type I IFN signaling within tumor cells, resulting in differential macrophage and T-cell-mediated tumor growth inhibition and sensitization of Rb-deficient prostate cancer to ICB. BETi can reprogram the immunologically cold Rb-deficient TME via STING/NF-κB/IFN signaling to sensitize Rb-deficient prostate cancer to ICB. These data provide the mechanistic rationale to test combinations of BETi and ICB in clinical trials of Rb-deficient prostate cancer.
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Affiliation(s)
- Brian M. Olson
- Department of Hematology and Medical Oncology; Emory University, Atlanta, GA
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
| | - Kiranj Chaudagar
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
| | - Riyue Bao
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
- Center for Research Informatics, University of Chicago, Chicago, IL
- Cancer Bioinformatics Services, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Sweta Sharma Saha
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
- Department of Pediatrics, University of Chicago, Chicago, IL; Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
| | - Christina Hong
- Department of Hematology and Medical Oncology; Emory University, Atlanta, GA
| | - Marguerite Li
- Department of Hematology and Medical Oncology; Emory University, Atlanta, GA
| | - Srikrishnan Rameshbabu
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
| | - Raymond Chen
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
| | - Alison Thomas
- Department of Hematology and Medical Oncology; Emory University, Atlanta, GA
| | - Akash Patnaik
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL
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15
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Tang Q, Li S, Huang G, Liu H. Research progress on PD-1 and PD-L1 inhibitors in the treatment of metastatic urothelial carcinoma. Int Immunopharmacol 2023; 119:110158. [PMID: 37062259 DOI: 10.1016/j.intimp.2023.110158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/18/2023]
Abstract
Urothelial carcinoma (UC) is a very common malignant tumor. In the past few decades, platinum-based chemotherapy has been regarded as the standard recommended regimen for patients with metastatic urothelial carcinoma (mUC) who can receive either cisplatin or carboplatin. The emergence of immune checkpoint inhibitors (ICIs) brought some hope for possible treatments for mUC patients who were unfit for platinum therapy. ICIs drugs have emerged as new potential weapons to overcome UC in our lifetime. ICIs block the binding of programmed death-1 (PD-1) to programmed death-ligand 1 (PD-L1), leading to enhancement of the immune function of antitumor T cells. In the treatment of UC, ICIs show an apparent ascendancy and effectively enhance survival rates. With good tolerability and remarkable effects, ICIs have given thousands of patients hope. This article mainly shows the application of PD-1 and PD-L1 inhibitors in mUC.
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Affiliation(s)
- Quanqing Tang
- Department of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Shihao Li
- Department of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Gaozhen Huang
- Department of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Hongwei Liu
- Department of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China.
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16
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Li T, Jiang N, Bai Y, Liu T, Zhao Z, Xu X, Zhang Y, Wei F, Sun R, Liu S, Li J, Guo H, Yang R. Prediction of immune infiltration and prognosis for patients with urothelial bladder cancer based on the DNA damage repair-related genes signature. Heliyon 2023; 9:e13661. [PMID: 36873527 PMCID: PMC9976330 DOI: 10.1016/j.heliyon.2023.e13661] [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: 05/22/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Objectives To analyze the correlations between the expression and effect of DNA damage repair genes and the immune status and clinical outcomes of urothelial bladder cancer (BLCA) patients. In addition, we evaluate the efficacy and value of utilizing the DNA damage repair genes signature as a prognosis model for BLCA. Methods Two subtype groups (C1 and C2) were produced based on the varied expression of DNA damage repair genes. Significantly differentiated genes and predicted enriched gene pathways were obtained between the two subtypes. Seven key genes were obtained from the DNA damage repair-related genes and a 7-gene signature prognosis model was established based on the key genes. The efficacy and accuracy of this model in prognosis prediction was evaluated and verified in two independent databases. Also, the difference in biological functions, drug sensitivity, immune infiltration and affinity between the high-risk group and low-risk group was analyzed. Results The DNA damage repair gene signature could significantly differentiate the BLCA into two molecular subgroups with varied genetic expression and enriched gene pathways. Seven key genes were screened out from the 232 candidate genes for prognosis prediction and a 7-gene signature prognosis model was established based on them. Two independent patient cohorts (TCGA cohort and GEO cohort) were utilized to validate the efficacy of the prognosis model, which demonstrated an effective capability to differentiate and predict the overall survival of BLCA patients. Also, the high-risk group and low-risk group derived from the 7-gene model exhibited significantly differences in drug sensitivity, immune infiltration status and biological pathways enrichment. Conclusions Our established 7-gene signature model based on the DNA damage repair genes could serve as a novel prognosis predictive tool for BLCA. The differentiation of BLCA patients based on the 7-gene signature model may be of great value for the appropriate selection of specific chemotherapy agents and immune-checkpoint blockade therapy administration.
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Affiliation(s)
- Tianhang Li
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Ning Jiang
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China
| | - Yuhao Bai
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China
| | - Tianyao Liu
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zihan Zhao
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Xinyan Xu
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yulin Zhang
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Fayun Wei
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Rui Sun
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Siyang Liu
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Jiazheng Li
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongqian Guo
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Rong Yang
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
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17
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Lin L, Zhang W, Chen Y, Ren W, Zhao J, Ouyang W, He Z, Su W, Yao H, Yu Y. Immune gene patterns and characterization of the tumor immune microenvironment associated with cancer immunotherapy efficacy. Heliyon 2023; 9:e14450. [PMID: 36950600 PMCID: PMC10025929 DOI: 10.1016/j.heliyon.2023.e14450] [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: 09/27/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
Although immunotherapy has revolutionized cancer management, most patients do not derive benefits from it. Aiming to explore an appropriate strategy for immunotherapy efficacy prediction, we collected 6251 patients' transcriptome data from multicohort population and analyzed the data using a machine learning algorithm. In this study, we found that patients from three immune gene clusters had different overall survival when treated with immunotherapy (P < 0.001), and that these clusters had differential states of hypoxia scores and metabolism functions. The immune gene score showed good immunotherapy efficacy prediction (AUC was 0.737 at 20 months), which was well validated. The immune gene score, tumor mutation burden, and long non-coding RNA score were further combined to build a tumor immune microenvironment signature, which correlated more strongly with overall survival (AUC, 0.814 at 20 months) than when using a single variable. Thus, we recommend using the characterization of the tumor immune microenvironment associated with immunotherapy efficacy via a multi-omics analysis of cancer.
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Key Words
- AUC, Area under the curve
- CIs, Confidence intervals
- CTL, Cytotoxic T-lymphocyte infiltration
- Cancer
- GEO, Gene Expression Omnibus
- GO, Gene Ontology
- GSEA, Gene set enrichment analysis
- GSVA, Gene set variation analysis
- HLAs, Human leukocyte antigens
- HRs, Hazard ratios
- Immunotherapy
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LASSO, Penalized logistic least absolute shrinkage and selector operation
- Machine learning
- NSCLC, Non-small cell lung cancer
- OS, Overall survival
- PCA, Principal componentanalysis
- PD-L1, Programmed death ligand-1
- PFS, Profession-free survival
- RNA-seq, Transcriptome RNA sequencing
- ROC, receiver operating characteristic curves
- TCGA, The Cancer Genome Atlas
- TMB, Tumor mutation burden
- TME, Tumor immunemicroenvironment
- Tumor immune microenvironment
- WGCNA, Weighted gene co-expression network analysis
- lncRNA, Long non-coding RNA
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Affiliation(s)
- Lili Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenda Zhang
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Yongjian Chen
- Department of Medical Oncology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Ren
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jianli Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenhao Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zifan He
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weifeng Su
- Division of Science and Technology, Beijing Normal University-Hong Kong Baptist University United International College, Hong Kong Baptist University, Zhuhai, China
- Corresponding author.
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Corresponding author.
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Division of Science and Technology, Beijing Normal University-Hong Kong Baptist University United International College, Hong Kong Baptist University, Zhuhai, China
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao, PR China
- Corresponding author. Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Centre, Phase I Clinical Trial Centre, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China.
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Papadopoulou K, Koliou GA, Tsimiliotis D, Kotoula V, Foukas P, Goussia A, Tsiatas M, Visvikis A, Chatzopoulos K, Nifora M, Charchanti A, Koumarianou A, Christodoulou C, Pectasides D, Psyrri A, Fostira F, Fountzilas G, Samantas E. Investigation of prognostic biomarkers in patients with urothelial carcinoma treated with platinum-based regimens. Urol Oncol 2022; 40:538.e15-538.e24. [PMID: 36041976 DOI: 10.1016/j.urolonc.2022.07.007] [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: 05/11/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Bladder cancer (BC) is a heterogeneous malignancy with dismal outcome. PATIENTS AND METHODS Mutations in genes, altered or linked to platinum sensitivity in BC, were examined in 66 patients' tumors along with tumor infiltrating lymphocytes (TILs) density and MMR, PD-L1 and CD8 protein expression, as well as basal and luminal subtypes, defined by protein expression of markers, including CK5/6 and GATA3 or CK20, respectively. RESULTS 41 tumors harbored mutations, mainly in TP53 (38%), ARID1A (17%) and the DNA damage response and repair (DDR) genes ERCC2 (17%) and BRCA2 (15%). Mutations in other DDR relevant genes were also present. Age showed unfavorable prognosis for overall survival (HR=1.07, P = 0.026); no benefit was seen for patients with TP53, ARID1A, ERCC2 or BRCA2 mutations or mutations in 1 or more DDR genes. PD-L1 status positively correlated with stromal (rho=0.46, P < 0.001) and intratumoral (rho=0.53, P < 0.001) CD8 expression or TILs (rho=0.29, P = 0.018); none associated with overall survival (OS). A statistically significant difference was observed between PD-L1 status and immunohistochemistry (IHC)‑based subtypes, with tumors classified as luminal (GATA3+ and/or CK20+ and CK5/6-) showing lower PD-L1 expression relative to basal (CK5/6+ and GATA3- and/or CK20-) (median value 0 vs. 2.5, P = 0.029). Concerning OS, no statistically significant difference was seen among patients with basal or luminal tumors. CONCLUSION No association was seen herein between DDR mutations, TILs, PD-L1, CD8 expression or IHC-based subtypes and patient survival; these observations warrant validation within a larger cohort.
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Affiliation(s)
- Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | | | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Periklis Foukas
- Second Department of Pathology, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital, Haidari, Greece
| | - Anna Goussia
- Department of Pathology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Marinos Tsiatas
- Department of Oncology, Athens Medical Center, Marousi, Greece
| | - Anastasios Visvikis
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Kyriakos Chatzopoulos
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Martha Nifora
- Second Department of Pathology, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital, Haidari, Greece
| | - Antonia Charchanti
- Department of Anatomy-Histology-Embryology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Anna Koumarianou
- Hematology Oncology Unit, Fourth Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Section of Medical Oncology, Athens, Greece
| | - Amanda Psyrri
- Attikon University Hospital, Faculty of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece; Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Medical Oncology, German Oncology Center, Limassol, Cyprus
| | - Epaminontas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
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Role of PARP Inhibitors in Cancer Immunotherapy: Potential Friends to Immune Activating Molecules and Foes to Immune Checkpoints. Cancers (Basel) 2022; 14:cancers14225633. [PMID: 36428727 PMCID: PMC9688455 DOI: 10.3390/cancers14225633] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) induce cytotoxic effects as single agents in tumors characterized by defective repair of DNA double-strand breaks deriving from BRCA1/2 mutations or other abnormalities in genes associated with homologous recombination. Preclinical studies have shown that PARPi-induced DNA damage may affect the tumor immune microenvironment and immune-mediated anti-tumor response through several mechanisms. In particular, increased DNA damage has been shown to induce the activation of type I interferon pathway and up-regulation of PD-L1 expression in cancer cells, which can both enhance sensitivity to Immune Checkpoint Inhibitors (ICIs). Despite the recent approval of ICIs for a number of advanced cancer types based on their ability to reinvigorate T-cell-mediated antitumor immune responses, a consistent percentage of treated patients fail to respond, strongly encouraging the identification of combination therapies to overcome resistance. In the present review, we analyzed both established and unexplored mechanisms that may be elicited by PARPi, supporting immune reactivation and their potential synergism with currently used ICIs. This analysis may indicate novel and possibly patient-specific immune features that might represent new pharmacological targets of PARPi, potentially leading to the identification of predictive biomarkers of response to their combination with ICIs.
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20
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Tong Y, Zhang X, Zhou Y. Integrated Analysis of Multi-Omics Data to Establish a Hypoxia-Related Prognostic Model in Osteosarcoma. Evol Bioinform Online 2022; 18:11769343221128537. [PMID: 36325183 PMCID: PMC9618759 DOI: 10.1177/11769343221128537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Osteosarcoma (OS) is the most common malignant bone tumor in clinical practice, and currently, the ability to predict prognosis in the diagnosis of OS is limited. There is an urgent need to find new diagnostic methods and treatment strategies for OS. Material and methods: We downloaded the multi-omics data for OS from the TARGET database. Prognosis-associated methylation sites were used to identify clustered subtypes of OS, and OS was classified into 3 subtypes (C1, C2, C3). Survival analysis showed significant differences between the C3 subtype and the other subtypes. Subsequently, differentially expressed genes (DEGs) across subtypes were screened and subjected to pathway enrichment analysis. Results: A total of 249 DEGs were screened from C3 subtype to other subtypes. Metabolic pathway enrichment analysis showed that DEGs were significantly enriched to the hypoxic pathway. Based on univariate and multivariate COX regression analysis, 12 genes from the hypoxia pathway were further screened and used to construct hypoxia-related prognostic model (HRPM). External validation of the HRPM was performed on the GSE21257 dataset. Finally, differences in survival and immune infiltration between high and low risk score groups were compared. Conclusion: In summary, we proposed a hypoxia-associated risk model based on a 12-gene expression signature, which is potentially valuable for prognostic diagnosis of patients with OS.
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Affiliation(s)
- Ye Tong
- Department of Orthopaedics, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui, China
| | - Xiaoqing Zhang
- Department of Laboratory, Bozhou People’s Hospital, Bozhou, Anhui, China
| | - Ye Zhou
- Department of Orthopaedics, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui, China,Ye Zhou, Department of Orthopaedics, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui 234000, China.
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21
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Shi C, Qin K, Lin A, Jiang A, Cheng Q, Liu Z, Zhang J, Luo P. The role of DNA damage repair (DDR) system in response to immune checkpoint inhibitor (ICI) therapy. J Exp Clin Cancer Res 2022; 41:268. [PMID: 36071479 PMCID: PMC9450390 DOI: 10.1186/s13046-022-02469-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
As our understanding of the mechanisms of cancer treatment has increased, a growing number of studies demonstrate pathways through which DNA damage repair (DDR) affects the immune system. At the same time, the varied response of patients to immune checkpoint blockade (ICB) therapy has prompted the discovery of various predictive biomarkers and the study of combination therapy. Here, our investigation explores the interactions involved in combination therapy, accompanied by a review that summarizes currently identified and promising predictors of response to immune checkpoint inhibitors (ICIs) that are useful for classifying oncology patients. In addition, this work, which discusses immunogenicity and several components of the tumor immune microenvironment, serves to illustrate the mechanism by which higher response rates and improved efficacy of DDR inhibitors (DDRi) in combination with ICIs are achieved.
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22
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Yu Y, Zeng H, Jin K, You R, Liu Z, Zhang H, Liu C, Su X, Yan S, Chang Y, Liu L, Xu L, Xu J, Zhu Y, Wang Z. Immune inactivation by neuropilin-1 predicts clinical outcome and therapeutic benefit in muscle-invasive bladder cancer. Cancer Immunol Immunother 2022; 71:2117-2126. [DOI: 10.1007/s00262-022-03153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/07/2022] [Indexed: 10/19/2022]
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THEM6: A Novel Molecular Biomarker Predicts Tumor Microenvironment, Molecular Subtype, and Prognosis in Bladder Cancer. DISEASE MARKERS 2022; 2022:7147279. [PMID: 35909893 PMCID: PMC9334031 DOI: 10.1155/2022/7147279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022]
Abstract
Background Thioesterase superfamily member 6 (THEM6) has been implicated in the development and progression of various cancers. However, prior research emphasized on its regulatory role merely, we aim to investigate the effect of THEM6 gene on the immunological role and its relationship with molecular subtype in bladder cancer (BLCA). Methods Through pan-cancer analysis, we explored the THEM6 expression pattern and immunological role using The Cancer Genome Atlas (TCGA) database. In addition, we performed a correlation of THEM6 and its immunological functions, including immunomodulators, immune checkpoints, cancer immunity cycles, T cell inflamed score, and tumor-infiltrating immune cells in the BLCA tumor microenvironment (TME) based on TCGA and BLCA microarray cohort from Xiangya Hospital. We also assessed the accuracy of THEM6 in predicting the molecular subtype and its response to different interventions in BLCA. Finally, we computed and validated a prediction model established by THEM6-related different expressed immune-related genes that might help in BLCA prognosis. Results THEM6 led to immunosuppression in BLCA TME. Furthermore, there was a downregulation in the immunological functions. Besides, THEM6 could effectively distinguish BLCA molecular subtypes, and THEM6 low expression implied basal subtype that was more effective to several interventions, such as immune checkpoint blockade (ICB) therapies, neoadjuvant chemotherapy, and radiotherapy. While THEM6 high expression indicated luminal subtype, hyperprogression and better response to targeted therapies, such as blocking THEM6 and several immune-inhibited oncogenic pathways. Conclusions THEM6 may be with potential immune-modulating properties and may become a potential new immunotherapy target for BLCA. THEM6 could accurately predict the molecular subtype of BLCA, which was helpful for guiding the treatment. Simultaneously, the prediction model may exhibit an excellent predictive value in patients with BLCA.
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Zhou J, Wang J, Kong W, Zhang J, Wu X, Huang J, Zheng J, Chen Y, Zhai W, Xue W. VHL and DNA damage repair pathway alterations as potential clinical biomarkers for first-line TKIs in metastatic clear cell renal cell carcinomas. Cell Oncol (Dordr) 2022; 45:677-687. [PMID: 35834099 PMCID: PMC9424144 DOI: 10.1007/s13402-022-00691-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 11/12/2022] Open
Abstract
Purpose Vascular endothelial growth factor receptor tyrosine kinase inhibitors (VEGFR-TKIs) are being used for the first-line treatment of metastatic clear cell renal cell carcinoma (mccRCC). Here, we set out to explore associations between genomic statuses, gene expression clusters and clinical outcomes of mccRCCs upon the application of VEGFR-TKIs. Methods A retrospective study of 56 patients with mccRCC who received first-line VEGFR-TKIs and who underwent genomic profiling and whole transcriptome sequencing was conducted. Survival analysis was carried out using log-rank tests and Cox regression analyses, and Kaplan–Meier curves were plotted. Clustering was performed using the K-means method. Results Among the 56 patients tested, 17 harbored DNA Damage and Repair (DDR) pathway alterations and 35 VHL mutations. The median progression-free survival (PFS) rates for the DDR and VHL alteration groups were 18 and 18 months, respectively, compared with 14 and 10 months for the nonmutant groups. DDR mutations, VHL mutations and co-mutations were identified as prognostic biomarkers of a longer PFS (p = 0.017, 0.04, 0.014). K-means clustering of expressed transcripts revealed three clusters of 40 patients: C_1, C_2 and C_3. The C_1 cluster exhibited the best PFS and objective response rate (ORR) to TKI therapy, with the highest proportion of DDR and VHL mutations. Further analysis of the tumor immune environment revealed that the C_1 cluster was enriched in activated CD8 T cells and effector CD4 T cells, whereas the C_2 cluster was enriched in eosinophils, mast cells and DC cells and, thus, in immunosuppressive cells. Conclusions We found that patients with mccRCC harboring DDR and VHL alterations were more likely to benefit from first-line VEGF-TKI systemic therapy than patients with wild-type disease. In addition, we found that a three-cluster prognostic model based on gene expression can predict PFS and ORR, which was well-matched with activated TIL infiltration. Supplementary Information The online version contains supplementary material available at 10.1007/s13402-022-00691-8.
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Affiliation(s)
- Jiale Zhou
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junyun Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101, China
| | - Wen Kong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jin Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaorong Wu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jiwei Huang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junhua Zheng
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonghui Chen
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Wei Zhai
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Urology, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Wei Xue
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Urology, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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25
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Liu Z, Zeng H, Jin K, Yu Y, You R, Zhang H, Liu C, Su X, Yan S, Chang Y, Liu L, Xu L, Xu J, Zhu Y, Wang Z. TIGIT and PD-1 expression atlas predicts response to adjuvant chemotherapy and PD-L1 blockade in muscle-invasive bladder cancer. Br J Cancer 2022; 126:1310-1317. [PMID: 35039625 PMCID: PMC9042924 DOI: 10.1038/s41416-022-01703-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/11/2021] [Accepted: 01/06/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND TIGIT and PD-1 are checkpoint receptors that could regulate the functional status of immune cells through independent pathways. However, the clinical significance of immune classification based on TIGIT and PD-1 expression remains unclear in muscle-invasive bladder cancer (MIBC). METHODS Patients with MIBC from four independent cohorts were categorised into three clusters. Survival analysis conducted through Kaplan-Meier curves and Cox regression model. Immune contexture was measured by immunohistochemistry and CIBERSORT algorithm. Twenty-five fresh tumour tissue samples were utilised to evaluate functional state of CD8+ T cells by flow cytometry. RESULTS Cluster I (TIGITlowPD-1low) contained widely poor immune infiltrates with higher FGFR3 mutation, Cluster II (TIGITlowPD-1high) exhibited a highly infiltrated contexture with increased cytolytic CD8+ T cells and had the best prognosis, Cluster III (TIGIThigh) presented a suppressive tumour microenvironment (TME) featured by exhausted CD8+ T cells and basal molecular subtype. Patients of Cluster III had the worst survival but could benefit more from adjuvant chemotherapy and anti-PD-L1 immunotherapy, and also presented limited FGFR3 signalling signature but activated immunotherapeutic and EGFR-associated pathway. CONCLUSIONS TIGIT/PD-1-based risk stratification with distinct immune and molecular features could be served as a predictor for systematic therapeutic response including adjuvant chemotherapy and immunotherapy in MIBC patients.
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Affiliation(s)
- Zhaopei Liu
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Han Zeng
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kaifeng Jin
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yanze Yu
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Runze You
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hongyi Zhang
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chunnan Liu
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaohe Su
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Sen Yan
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuan Chang
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Li Liu
- grid.413087.90000 0004 1755 3939Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Le Xu
- grid.16821.3c0000 0004 0368 8293Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiejie Xu
- grid.8547.e0000 0001 0125 2443Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yu Zhu
- grid.452404.30000 0004 1808 0942Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zewei Wang
- grid.413087.90000 0004 1755 3939Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
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Wang L, Lu J, Song Y, Bai J, Sun W, Yu J, Cai M, Fu S. Analysis of DNA Repair-Related Prognostic Function and Mechanism in Gastric Cancer. Front Cell Dev Biol 2022; 10:897096. [PMID: 35656545 PMCID: PMC9152153 DOI: 10.3389/fcell.2022.897096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
DNA repair mechanisms have been proven to be essential for cells, and abnormalities in DNA repair could cause various diseases, such as cancer. However, the diversity and complexity of DNA repair mechanisms obscure the functions of DNA repair in cancers. In addition, the relationships between DNA repair, the tumor mutational burden (TMB), and immune infiltration are still ambiguous. In the present study, we evaluated the prognostic values of various types of DNA repair mechanisms and found that double-strand break repair through single-strand annealing (SSA) and nonhomologous end-joining (NHEJ) was the most prognostic DNA repair processes in gastric cancer (GC) patients. Based on the activity of these two approaches and expression profiles, we constructed a HR-LR model, which could accurately divide patients into high-risk and low-risk groups with different probabilities of survival and recurrence. Similarly, we also constructed a cancer-normal model to estimate whether an individual had GC or normal health status. The prognostic value of the HR-LR model and the accuracy of the cancer-normal model were validated in several independent datasets. Notably, low-risk samples, which had higher SSA and NHEJ activities, had more somatic mutations and less immune infiltration. Furthermore, the analysis found that low-risk samples had higher and lower methylation levels in CpG islands (CGIs) and open sea regions respectively, and had higher expression levels of programmed death-ligand 1 (PD-L1) and lower methylation levels in the promoter of the gene encoding PD-L1. Moreover, low-risk samples were characterized primarily by higher levels of CD4+ memory T cells, CD8+ naive T cells, and CD8+ TEM cells than those in high-risk samples. Finally, we proposed a decision tree and nomogram to help predict the clinical outcome of an individual. These results provide an improved understanding of the complexity of DNA repair, the TMB, and immune infiltration in GC, and present an accurate prognostic model for use in GC patients.
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Affiliation(s)
- Liqiang Wang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ying Song
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jing Bai
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jingcui Yu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Mengdi Cai
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- *Correspondence: Songbin Fu, ; Mengdi Cai,
| | - Songbin Fu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- *Correspondence: Songbin Fu, ; Mengdi Cai,
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Yan S, Zeng H, Jin K, Shao F, Liu Z, Chang Y, Wang Y, Zhu Y, Wang Z, Xu L, Xu J. NKG2A and PD-L1 expression panel predicts clinical benefits from adjuvant chemotherapy and PD-L1 blockade in muscle-invasive bladder cancer. J Immunother Cancer 2022; 10:jitc-2022-004569. [PMID: 35523436 PMCID: PMC9073407 DOI: 10.1136/jitc-2022-004569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2022] [Indexed: 12/11/2022] Open
Abstract
Background Programmed cell death ligand-1 (PD-L1) expression as a single biomarker for immune checkpoint blockade (ICB) was controversial. NKG2A was a PD1/PD-L1 axis-related immunity-dependent factor. NKG2A and PD-L1 expression as a combinatorial biomarker might improve the prediction of PD-L1 in patients with muscle-invasive bladder cancer (MIBC). Methods Three independent cohorts were enrolled in our study. 195 patients with bladder-derived metastatic urothelial carcinoma on PD-L1 inhibitor treatment from the IMvigor210 trial were enrolled. 124 MIBC patients from Zhongshan Hospital and 391 patients with MIBC from The Cancer Genome Atlas database were included in this study. The PD-L1/NKG2A-based risk stratification was validated in three independent cohorts, and its association with response to ICB and adjuvant chemotherapy (ACT), immune contexture and molecular features was evaluated. Histologic staining and genomic algorithm were performed to detect characteristics of NKG2A and PD-L1 expression and infiltration of immune cells. Results We identified NKG2AhiPD-L1hi patients could benefit more from cisplatin-based ACT and PD-L1 inhibitor. Further analyses revealed NKG2A and PD-L1 expression panel was linked to an immune-active tumor microenvironment with highly immune effector cells and effector molecules. In addition, NKG2A and PD-L1 expression panel was intrinsically correlated with genomic alterations related to therapeutic response in MIBC. Conclusions NKG2A and PD-L1 expression panel was associated with an immune inflamed microenvironment and acted as a combinatorial biomarker to predict the therapeutic response to ACT and PD-L1 blockade in MIBC.
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Affiliation(s)
- Sen Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Han Zeng
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kaifeng Jin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Fei Shao
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaopei Liu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yuan Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yiwei Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zewei Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Le Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Yan C, Li K, Meng F, Chen L, Zhao J, Zhang Z, Xu D, Sun J, Zhou M. Integrated immunogenomic analysis of single-cell and bulk tissue transcriptome profiling unravels a macrophage activation paradigm associated with immunologically and clinically distinct behaviors in ovarian cancer. J Adv Res 2022; 44:149-160. [PMID: 36725186 PMCID: PMC9936412 DOI: 10.1016/j.jare.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/14/2022] [Accepted: 04/11/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Increasing evidence demonstrates that the activation states and diverse spectrum of macrophage subtypes display dynamic heterogeneity in the tumor microenvironment, which plays a critical role in a variety of cancer types. OBJECTIVES To investigate the heterogeneity and the homeostasis of different macrophage subtypes, as well as their effect on biological and clinical manifestations of ovarian cancer (OV). METHOD Integrated immunogenomic analysis of single-cell and bulk tissuetranscriptome profiling was performed to systematically investigate the association between macrophage activation and prognostic and therapeutic efficacy. Consensus clustering analysis was used to define novel macrophage subtypes. An artificial neural network was used to simulate the dynamic activation of macrophages. RESULTS The pan-cohort results suggested that high relative infiltration abundance of M0 and M1 macrophages was associated with improved outcome and therapeutic efficacy. However, it was the opposite for M2 macrophages. Unsupervised consensus clustering analysis revealed two OV subgroups characterized by a balance between M0, M1 and M2 macrophages with distinct clinical and immunological behaviors. Finally, a macrophage polarization-derived artificial neural network model was proposed to serve as a robust prognostic factor and predictive biomarker for therapeutic efficacy, which was validated in different independent patient cohorts. CONCLUSION The present study provides a new understanding of macrophage heterogeneity and its association with OV prognosis and underlines the future clinical potential of a macrophage activation model for tumor prevention and treatment.
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Affiliation(s)
- Congcong Yan
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Ke Li
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Fanling Meng
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin 150081, P. R. China
| | - Lu Chen
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Jingting Zhao
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Zicheng Zhang
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Dandan Xu
- School of Basic Medical Sciences, Harbin Medical University, Harbin 150081, P. R. China.
| | - Jie Sun
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China.
| | - Meng Zhou
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, P. R. China.
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Su F, Liu M, Zhang W, Tang M, Zhang J, Li H, Zou L, Zhang R, Liu Y, Li L, Ma J, Zhang Y, Chen M, Xiao F. Bacillus Calmette–Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer. Front Oncol 2022; 12:842182. [PMID: 35311085 PMCID: PMC8930202 DOI: 10.3389/fonc.2022.842182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background Bacillus Calmette–Guérin (BCG) is currently the most effective intravesical therapy for non-muscle-invasive bladder cancer (NMIBC) as it can prevent disease recurrence and progression and lower mortality. However, the response rates to BCG vary widely and are dependent on a multitude of factors. Methods We performed a systematic discovery by analyzing the whole exome sequence, expression profile, and immune repertoire sequence of treatment-naive and 5-year time-serial relapsed tumors from 24 NMIBC patients. Results BCG therapy showed bidirectional effects on tumor evolution and immune checkpoint landscape, along with a significant reduction of the percentage of neoantigen burden. In addition, a remarkable proportion of subclonal mutations were unique to the matched pre- or post-treatment tumors, suggesting the presence of BCG-induced and/or spatial heterogeneity. In the relapsed tumors, we identified and validated a shift in the mutational signatures in which mutations associated with aristolochic acid (AA) exposure were enriched, implying AA may be associated with tumor recurrence. Enhanced expressions of immune checkpoint regulation genes were found in the relapsed tumors, suggesting that the combination of immune checkpoint with BCG treatment may be an effective strategy to treat NMIBC. TCR sequencing revealed treatment-associated changes in the T-cell repertoire in the primary and relapsed tumors. Conclusion Our results provide insight into the genomic and immune dynamics of tumor evolution with BCG treatment, suggest new mechanisms of BCG resistance, and inform the development of clinically relevant biomarkers and trials of potential immune checkpoint inhibitor combination therapies.
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Affiliation(s)
- Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Min Tang
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinsong Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lihui Zou
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yudong Liu
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Li
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Ma
- Center for Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- State Key Lab of Molecular Oncology, National Cancer Center, Chinese Academy of Medical Sciences Cancer Hospital & Peking Union Medical College, Beijing, China
| | - Yaqun Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yaqun Zhang, ; Meng Chen, ; Fei Xiao,
| | - Meng Chen
- National Cancer Data Center, National Cancer Center, Chinese Academy of Medical Sciences Cancer Hospital & Peking Union Medical College, Beijing, China
- *Correspondence: Yaqun Zhang, ; Meng Chen, ; Fei Xiao,
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yaqun Zhang, ; Meng Chen, ; Fei Xiao,
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Dyugay IA, Lukyanov DK, Turchaninova MA, Serebrovskaya EO, Bryushkova EA, Zaretsky AR, Khalmurzaev O, Matveev VB, Shugay M, Shelyakin PV, Chudakov DM. Accounting for B-cell Behavior and Sampling Bias Predicts Anti-PD-L1 Response in Bladder Cancer. Cancer Immunol Res 2022; 10:343-353. [PMID: 35013004 PMCID: PMC9381118 DOI: 10.1158/2326-6066.cir-21-0489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 01/07/2023]
Abstract
Cancer immunotherapy is predominantly based on T cell-centric approaches. At the same time, the adaptive immune response in the tumor environment also includes clonally produced immunoglobulins and clonal effector/memory B cells that participate in antigen-specific decisions through their interactions with T cells. Here, we investigated the role of infiltrating B cells in bladder cancer via patient dataset analysis of intratumoral immunoglobulin repertoires. We showed that the IgG1/IgA ratio is a prognostic indicator for several subtypes of bladder cancer and for the whole IMVigor210 anti-PD-L1 immunotherapy study cohort. A high IgG1/IgA ratio associated with the prominence of a cytotoxic gene signature, T-cell receptor signaling, and IL21-mediated signaling. Immunoglobulin repertoire analysis indicated that effector B-cell function, rather than clonally produced antibodies, was involved in antitumor responses. From the T-cell side, we normalized a cytotoxic signature against the extent of immune cell infiltration to neutralize the artificial sampling-based variability in immune gene expression. Resulting metrics reflected proportion of cytotoxic cells among tumor-infiltrating immune cells and improved prediction of anti-PD-L1 responses. At the same time, the IgG1/IgA ratio remained an independent prognostic factor. Integration of the B-cell, natural killer cell, and T-cell signatures allowed for the most accurate prediction of anti-PD-L1 therapy responses. On the basis of these findings, we developed a predictor called PRedIctive MolecUlar Signature (PRIMUS), which outperformed PD-L1 expression scores and known gene signatures. Overall, PRIMUS allows for reliable identification of responders among patients with muscle-invasive urothelial carcinoma, including the subcohort with the low-infiltrated "desert" tumor phenotype.
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Affiliation(s)
- Ilya A. Dyugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniil K. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A. Turchaninova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O. Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina A. Bryushkova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Molecular Biology Department, Lomonosov Moscow State University, Moscow, Russia
| | - Andrew R. Zaretsky
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Oybek Khalmurzaev
- Department of Urology, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vsevolod B. Matveev
- Department of Urology, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Mikhail Shugay
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Pavel V. Shelyakin
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Corresponding Author: Dmitriy M. Chudakov, Genomics of Adaptive Immunity, IBCH RAS, Miklukho-Maklaya, 16/10, Moscow 117997, Russia. Phone: 7 (495) 335-01-00; E-mail:
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31
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Maiorano BA, De Giorgi U, Ciardiello D, Schinzari G, Cisternino A, Tortora G, Maiello E. Immune-Checkpoint Inhibitors in Advanced Bladder Cancer: Seize the Day. Biomedicines 2022; 10:biomedicines10020411. [PMID: 35203620 PMCID: PMC8962271 DOI: 10.3390/biomedicines10020411] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 02/05/2023] Open
Abstract
Background: In advanced bladder cancer (BCa), platinum-based chemotherapy represents the first-choice treatment. In the last ten years, immune checkpoint inhibitors (ICIs) have changed the therapeutic landscape of many solid tumors. Our review aims to summarize the main findings regarding the clinical use of ICIs in advanced BCa. Methods: We searched PubMed, Embase, and Cochrane databases, and conference abstracts from international congresses (ASCO, ESMO, ASCO GU) for clinical trials, focusing on ICIs as monotherapy and combinations in metastatic BCa. Results: 18 studies were identified. ICIs targeting PD1 (nivolumab, pembrolizumab), PD-L1 (avelumab, atezolizumab, durvalumab), and CTLA4 (ipilimumab, tremelimumab) were used. Survival outcomes have been improved by second-line ICIs, whereas first-line results are dismal. Avelumab maintenance in patients obtaining disease control with chemotherapy has achieved the highest survival rates. Conclusions: ICIs improve survival after platinum-based chemotherapy. Avelumab maintenance represents a new practice-changing treatment. The combinations of ICIs and other compounds, such as FGFR-inhibitors, antibody-drug conjugates, and anti-angiogenic drugs, represent promising therapeutic approaches. Biomarkers with predictive roles and sequencing strategies are warranted for best patient selection.
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Affiliation(s)
- Brigida Anna Maiorano
- Oncology Unit, IRCCS Foundation Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (D.C.); (E.M.)
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy; (G.S.); (G.T.)
- Correspondence:
| | - Ugo De Giorgi
- Department of Oncology, IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Davide Ciardiello
- Oncology Unit, IRCCS Foundation Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (D.C.); (E.M.)
- Medical Oncology Unit, Department of Precision Medicine, “Luigi Vanvitelli” University of Campania, 80131 Naples, Italy
| | - Giovanni Schinzari
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy; (G.S.); (G.T.)
- Comprehensive Cancer Center, Medical Oncology Unit, IRCCS Foundation “A. Gemelli” Policlinic, 00168 Rome, Italy
| | - Antonio Cisternino
- Urology Unit, IRCCS Foundation Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Giampaolo Tortora
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, 00168 Rome, Italy; (G.S.); (G.T.)
- Comprehensive Cancer Center, Medical Oncology Unit, IRCCS Foundation “A. Gemelli” Policlinic, 00168 Rome, Italy
| | - Evaristo Maiello
- Oncology Unit, IRCCS Foundation Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (D.C.); (E.M.)
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Wen H, Guo QH, Zhou XL, Wu XH, Li J. Genomic Profiling of Chinese Cervical Cancer Patients Reveals Prevalence of DNA Damage Repair Gene Alterations and Related Hypoxia Feature. Front Oncol 2022; 11:792003. [PMID: 35071000 PMCID: PMC8782566 DOI: 10.3389/fonc.2021.792003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Cervical cancer is responsible for 10–15% of cancer-related deaths in women worldwide. In China, it is the most common cancer in the female genital tract. However, the genomic profiles of Chinese cervical cancer patients remain unclear. Materials and Methods A total of 129 cervical cancer patients were enrolled in this study (113 squamous, 12 adenocarcinoma, 2 adenosquamous, and 2 neuroendocrine carcinoma). To classify the clinical features and molecular characteristics of cervical cancer, the genomic alterations of 618 selected genes were analyzed in the samples of these patients, utilizing target next-generation sequencing (NGS) technology. Furthermore, the findings from the Chinese cohort were then compared with the data of Western patients downloaded from The Cancer Genome Atlas (TCGA) database, in terms of gene expression files, mutation data, and clinical information. Results All studied patients had valid somatic gene alterations, and the most frequently altered genes were PIK3C, TP53, FBXW7, ARID1A, ERBB2, and PTEN. Comparison of genomic profiling showed significantly different prevalence of genes, including TP53, KMT2C, and RET, between the Chinese and the TCGA cohorts. Moreover, 57 patients (44.19%) with 83 actionable alterations were identified in our cohort, especially in PI3K and DNA damage repair (DDR) pathways. After an in-depth analysis of cervical cancer data from the TCGA cohort, DDR alteration was found to be associated with extremely higher tumor mutation burden (TMB) (median mutation count: 149.5 vs 66, p <0.0001), and advanced stages (p <0.05). Additionally, DDR alteration, regardless of its function, was positively correlated with hypoxia feature and score. Moreover, patients with a high hypoxia score were positively correlated with a high abundance of mast cell resting, but lower abundance of CD8+ T cells and activated mast cell. Finally, CDHR5 was identified as the hub gene to be involved in the DDR–hypoxia network, which was negatively correlated with both the DDR alteration and hypoxia score. Conclusions Overall, a unique genomic profiling of Chinese patients with cervical cancer was uncovered. Besides, the prevalent actionable variants, especially in PI3K and DDR pathways, would help promote the clinical management. Moreover, DDR alteration exerted the significant influence on the tumor microenvironment in cervical cancer, which could guide the clinical decisions for the treatment. CDHR5 was the first identified hub gene to be negatively correlated with DDR or hypoxia in cervical cancer, which had potential effects on the treatment of immune checkpoint inhibitors (ICIs).
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Affiliation(s)
- Hao Wen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qin-Hao Guo
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiao-Lan Zhou
- Hua-Shan Worldwide Medical Center, Hua-Shan Hospital, Fudan University, Shanghai, China
| | - Xiao-Hua Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jin Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
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Tang Q, Zuo W, Wan C, Xiong S, Xu C, Yuan C, Sun Q, Zhou L, Li X. Comprehensive genomic profiling of upper tract urothelial carcinoma and urothelial carcinoma of the bladder identifies distinct molecular characterizations with potential implications for targeted therapy & immunotherapy. Front Immunol 2022; 13:1097730. [PMID: 36818471 PMCID: PMC9936149 DOI: 10.3389/fimmu.2022.1097730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023] Open
Abstract
Backgrounds Despite the genomic landscape of urothelial carcinomas (UC) patients, especially those with UC of bladder (UCB), has been comprehensively delineated and associated with pathogenetic mechanisms and treatment preferences, the genomic characterization of upper tract UC (UTUC) has yet to be fully elucidated. Materials and methods A total of 131 Chinese UTUC (74 renal pelvis & 57 ureter) and 118 UCB patients were enrolled in the present study, and targeted next-generation sequencing (NGS) of 618 cancer-associated genes were conducted to exhibit the profile of somatic and germline alterations. The COSMIC database, including 30 mutational signatures, were utilized to evaluate the mutational spectrums. Moreover, TCGA-UCB, MSKCC-UCB, and MSKCC-UTUC datasets were retrieved for preforming genomic alterations (GAs) comparison analysis between Western and Chinese UC patients. Results In our cohort, 93.98% and 56.63% of UC patients were identified with oncogenic and actionable somatic alterations, respectively. Meanwhile, 11.24% of Chinese UC patients (of 14.50% and 7.63% of UTUC and UCB cases, respectively) were identified to harbor a total of 32 pathogenic/likely-pathogenic germline variants in 22 genes, with DNA damage repair (DDR)-associated BRCA1 (1.20%) and CHEK2 (1.20%) being the most prevalent. Chinese UTUC and UCB patients possessed distinct somatic genomic characteristics, especially with significantly different prevalence in KMT2D/C/A, GNAQ, ERCC2, RB1, and PPM1D. In addition, we also found notable differences in the prevalence of ELF3, TP53, PMS2, and FAT4 between renal pelvis and ureter carcinomas. Moreover, 22.90% and 33.90% of UTUC and UCB patients, respectively, had at least one deleterious/likely deleterious alteration in DDR related genes/pathways. Subsequently, mutational signature analysis revealed that UC patients with mutational signature 22, irrespective of UTUC or UCB, consistently had the markedly higher level of tumor mutational burden (TMB), which was proved to be positively correlated with the objective complete/partial response rate in the IMvigor210 cohort. By comparison, Chinese and Western UTUC patients also differed regrading GAs in oncogenic-related genes/pathways, especially in TP53, RTK/RAS, and PI3K pathways; besides, more alterations in WNT pathway but less TP53, RTK/RAS, HIPPO, and PI3K pathways were identified in Chinese UCB. Discussions The in-depth analysis of genomic mutational landscapes revealed distinct pathogenetic mechanisms between Chinese UTUC and UCB, and specific genomic characterizations could identify high risk population of UTUC/UCB and provided information regarding the selection of alternative therapeutic regimens.
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Affiliation(s)
- Qi Tang
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Wei Zuo
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Chong Wan
- Precision Medicine Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, China
| | - Shengwei Xiong
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Changwei Yuan
- Department of Urology, Peking University First Hospital, Beijing, China
| | | | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, China
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Jiménez-Morales S, Aranda-Uribe IS, Pérez-Amado CJ, Ramírez-Bello J, Hidalgo-Miranda A. Mechanisms of Immunosuppressive Tumor Evasion: Focus on Acute Lymphoblastic Leukemia. Front Immunol 2021; 12:737340. [PMID: 34867958 PMCID: PMC8636671 DOI: 10.3389/fimmu.2021.737340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/27/2021] [Indexed: 01/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a malignancy with high heterogeneity in its biological features and treatments. Although the overall survival (OS) of patients with ALL has recently improved considerably, owing to the application of conventional chemo-therapeutic agents, approximately 20% of the pediatric cases and 40-50% of the adult patients relapse during and after the treatment period. The potential mechanisms that cause relapse involve clonal evolution, innate and acquired chemoresistance, and the ability of ALL cells to escape the immune-suppressive tumor response. Currently, immunotherapy in combination with conventional treatment is used to enhance the immune response against tumor cells, thereby significantly improving the OS in patients with ALL. Therefore, understanding the mechanisms of immune evasion by leukemia cells could be useful for developing novel therapeutic strategies.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Ivan Sammir Aranda-Uribe
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- Departamento de Farmacología, División de Ciencias de la Salud, Universidad de Quintana Roo, Quintana Roo, Mexico
| | - Carlos Jhovani Pérez-Amado
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Julian Ramírez-Bello
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Liu J, Zheng Z, Zhang W, Wan M, Ma W, Wang R, Yan Y, Guo Y, Zhang J, Li W, Yao X. Dysregulation of tumor microenvironment promotes malignant progression and predicts risk of metastasis in bladder cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1438. [PMID: 34733990 PMCID: PMC8506754 DOI: 10.21037/atm-21-4023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/02/2021] [Indexed: 11/12/2022]
Abstract
Background The tumor microenvironment (TME) is not only a key factor in the malignant progression of cancer but also plays an indispensable role in tumor immunotherapy. As an important regulatory factor in the TME, long non-coding RNAs (incRNA) are important for the development of bladder cancer. The purpose of this study was to explore the molecular mechanism of malignant progression of bladder cancer (BCa) from the perspective of immunology, establish a reliable signature, and evaluate its effect on prognosis, metastasis, and the effectiveness of immunotherapy. Methods The TME was assessed by single-sample gene set enrichment analysis (ssGSEA) in 373 patients with muscle invasive bladder cancer (MIBC) in The Cancer Genome Atlas (TCGA). Combining RNA sequence data from 49 BCa patients in our center, we established TME-related prognostic signatures (TMERPS) based on TME-related immune prognosis genes using weighted gene correlation network analysis, selection operator Cox analysis, minimum absolute shrinkage, and survival analysis. Real-Time Quantitative PCR was used for expression level analysis of related genes. Functional enrichment analysis and nomograms were used to explore the potential impact of TMERPS on the immune system, prognosis, and metastasis. Results The ssGSEA proved to be an accurate assessment of immune levels in BCa samples. TMERPS was established based on six TME-associated prognostic lncRNAs and was shown to be closely associated with prognosis, metastasis, and immune levels, and to have a significant stratifying effect on the therapeutic efficacy of immune checkpoint inhibitors. Finally, three TMERPS-based nomograms were shown to be effective in predicting prognosis, lymph node metastasis, and distant metastasis in BCa patients. Conclusions TMERPS can stratify BCa patients into different risk groups with different prognoses, immunotherapy sensitivity, and risk of metastasis. TMERPS-based nomograms can effectively predict prognosis and metastasis in BCa patients.
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Affiliation(s)
- Ji Liu
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Zongtai Zheng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Wentao Zhang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Moxi Wan
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Wenchao Ma
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Ruiliang Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Yang Yan
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Yadong Guo
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Junfeng Zhang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Wei Li
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Institute of Urinary Oncology, School of Medicine, Tongji University, Shanghai, China
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Wang QW, Sun LH, Zhang Y, Wang Z, Zhao Z, Wang ZL, Wang KY, Li GZ, Xu JB, Ren CY, Ma WP, Wang HJ, Li SW, Zhu YJ, Jiang T, Bao ZS. MET overexpression contributes to STAT4-PD-L1 signaling activation associated with tumor-associated, macrophages-mediated immunosuppression in primary glioblastomas. J Immunother Cancer 2021; 9:jitc-2021-002451. [PMID: 34667077 PMCID: PMC8527154 DOI: 10.1136/jitc-2021-002451] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 11/12/2022] Open
Abstract
Background Dysregulated receptor tyrosine kinases, such as the mesenchymal-epidermal transition factor (MET), have pivotal role in gliomas. MET and its interaction with the tumor microenvironment have been previously implicated in secondary gliomas. However, the contribution of MET gene to tumor cells’ ability to escape immunosurveillance checkpoints in primary gliomas, especially in glioblastoma (GBM), which is a WHO grade 4 glioma with the worst overall survival, is still poorly understood. Methods We investigated the relationship between MET expression and glioma microenvironment by using multiomics data and aimed to understand the potential implications of MET in clinical practice through survival analysis. RNA expression data from a total of 1243 primary glioma samples (WHO grades 2–4) were assembled, incorporating The Cancer Genome Atlas, Chinese Glioma Genome Atlas, and GSE16011 data sets. Results Pearson’s correlation test from the three data sets indicated that MET showed a robust correlation with programmed death-ligand 1 (PD-L1) and STAT pathways. Western blot analysis revealed that in GBM cell lines (N33 and LN229), PD-L1 and phosphorylated STAT4 were upregulated by MET activation treatment with hepatocyte growth factor and were downregulated on MET suppression by PLB-1001. Tumor tissue microarray analysis indicated a positive correlation between MET and PD-L1 and macrophage-associated markers. Chromatin immunoprecipitation-PCR assay showed enrichment of STAT4 in the PD-L1 DNA. Transwell co-culture and chemotaxis assays revealed that knockdown of MET in GBM cells inhibited macrophage chemotaxis. Moreover, we performed CIBERSORTx and single-cell RNA sequencing data analysis which revealed an elevated number of macrophages in glioma samples with MET overexpression. Kaplan-Meier survival analysis indicated that activation of the MET/STAT4/PD-L1 pathway and upregulation of macrophages were associated with shorter survival time in patients with primary GBM. Conclusions These data indicated that the MET-STAT4-PD-L1 axis and tumor-associated macrophages might enforce glioma immune evasion and were associated with poor prognosis in GBM samples, suggesting potential clinical strategies for targeted therapy combined with immunotherapy in patients with primary GBM.
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Affiliation(s)
- Qiang-Wei Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li-Hua Sun
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhi-Liang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jian-Bao Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chang-Yuan Ren
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, San Bo Brain Hospital, Capital Medical University, Beijing, China
| | - Wen-Ping Ma
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Hong-Jun Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shou-Wei Li
- Department of Neurosurgery, San Bo Brain Hospital, Capital Medical University, Beijing, China
| | - Yong-Jian Zhu
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhao-Shi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Jiang M, Jia K, Wang L, Li W, Chen B, Liu Y, Wang H, Zhao S, He Y, Zhou C. Alterations of DNA damage response pathway: Biomarker and therapeutic strategy for cancer immunotherapy. Acta Pharm Sin B 2021; 11:2983-2994. [PMID: 34729299 PMCID: PMC8546664 DOI: 10.1016/j.apsb.2021.01.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/25/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Genomic instability remains an enabling feature of cancer and promotes malignant transformation. Alterations of DNA damage response (DDR) pathways allow genomic instability, generate neoantigens, upregulate the expression of programmed death ligand 1 (PD-L1) and interact with signaling such as cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling. Here, we review the basic knowledge of DDR pathways, mechanisms of genomic instability induced by DDR alterations, impacts of DDR alterations on immune system, and the potential applications of DDR alterations as biomarkers and therapeutic targets in cancer immunotherapy.
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Key Words
- ATM, ataxia-telangiectasia mutated
- ATR, ataxia telangiectasia and Rad3 related
- BAP1, BRCA1-associated protein 1
- BER, base excision repair
- BRAF, v-RAF murine sarcoma viral oncogene homologue B
- BRCA, breast cancer susceptibility gene
- CHEK, cell-cycle checkpoint kinase
- CHK1, checkpoint kinase 1
- DAMP, damage-associated molecular patterns
- DDR, DNA damage response
- DNA damage response
- DNA repair
- DR, direct repair
- DSBs, double-strand breaks
- FDA, United State Food and Drug Administration
- GSK3β, glycogen synthase kinase 3β
- Genomic instability
- HMGB1, high mobility group box-1
- HRR, homologous recombination repair
- ICI, immune checkpoint inhibitor
- IFNγ, interferon gamma
- IHC, immunohistochemistry
- IRF1, interferon regulatory factor 1
- Immunotherapy
- JAK, Janus kinase
- MAD1, mitotic arrest deficient-like 1
- MGMT, O6-methylguanine methyltransferase
- MLH1, MutL homolog 1
- MMR, mismatch repair
- MNT, MAX network transcriptional repressor
- MSH2/6, MutS protein homologue-2/6
- MSI, microsatellite instability
- MUTYH, MutY homolog
- MyD88, myeloid differentiation factor 88
- NEK1, NIMA-related kinase 1
- NER, nucleotide excision repair
- NGS, next generation sequencing
- NHEJ, nonhomologous end-joining
- NIMA, never-in-mitosis A
- NSCLC, non-small cell lung cancer
- ORR, objective response rate
- OS, overall survival
- PALB2, partner and localizer of BRCA2
- PARP, poly-ADP ribose polymerase
- PCR, polymerase chain reaction
- PD-1
- PD-1, programmed death 1
- PD-L1
- PD-L1, programmed death ligand 1
- PFS, progression-free survival
- RAD51C, RAD51 homolog C
- RB1, retinoblastoma 1
- RPA, replication protein A
- RSR, replication stress response
- SCNAs, somatic copy number alterations
- STAT, signal transducer and activator of transcription
- STING, stimulator of interferon genes
- TBK1, TANK-binding kinase 1
- TILs, tumor-infiltrating lymphocytes
- TLR4, Toll-like receptor 4
- TMB, tumor mutational burden
- TME, tumor microenvironment
- TP53, tumor protein P53
- TRIF, Toll-interleukin 1 receptor domain-containing adaptor inducing INF-β
- Tumor microenvironment
- XRCC4, X-ray repair cross complementing protein 4
- cGAS, cyclic GMP–AMP synthase
- cGAS–STING
- ssDNA, single-stranded DNA
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Affiliation(s)
- Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Keyi Jia
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Medical School, Tongji University, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
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Wang Y, Jiao X, Li S, Chen H, Wei X, Liu C, Gong J, Zhang X, Wang X, Peng Z, Qi C, Wang Z, Wang Y, Zhuo N, Zou J, Zhang H, Li J, Shen L, Lu Z. Alterations in DNA damage response and repair genes as potential biomarkers for immune checkpoint blockade in gastrointestinal cancer. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0708. [PMID: 34570439 PMCID: PMC9425187 DOI: 10.20892/j.issn.2095-3941.2020.0708] [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] [Indexed: 12/24/2022] Open
Abstract
Objective: Immune checkpoint inhibitors (ICIs) have achieved remarkable results in cancer treatments. However, there is no effective predictive biomarker for gastrointestinal (GI) cancer. Methods: We conducted integrative analyses of the genomic and survival data of ICI-treated GI cancer patients from the Memorial Sloan Kettering Cancer Center cohort (MSK-GI, n = 227), the Janjigian cohort (n = 40), and the Peking University Cancer Hospital & Institute cohort (PUCH, n = 80) to determine the possible associations between DNA damage response and repair (DDR) gene mutations and clinical outcomes. Data from The Cancer Genome Atlas database were analyzed to determine the possible correlations between DDR gene mutations and the tumor microenvironment. Results: In the MSK cohort, the presence of ≥ 2 DDR gene mutations was correlated with prolonged overall survival (OS). The Janjigian and PUCH cohorts further confirmed that subgroups with ≥ 2 DDR gene mutations displayed a prolonged OS and a higher durable clinical benefit. Furthermore, the DDR gene mutation load could be considered as an independent prognostic factor, and exhibited a potential predictive value for survival in GI cancer patients treated with ICIs. Mechanistically, we showed that the presence of ≥ 2 DDR gene mutations was correlated with higher levels of tumor mutation burden, neoantigen, and T cell infiltration. Conclusions: The DDR gene mutation status was correlated with favorable clinical outcomes in GI cancer patients receiving ICIs, which could serve as a potential biomarker to guide patient selection for immunotherapy.
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Affiliation(s)
- Yujiao Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xi Jiao
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Shuang Li
- Department of Gastric & Colorectal Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Huan Chen
- Genecast Precision Medicine Technology Institute, Beijing 100192, China
| | - Xin Wei
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chang Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jifang Gong
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaotian Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xicheng Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhi Peng
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Changsong Qi
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhenghang Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yanni Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Na Zhuo
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jianling Zou
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Jian Li
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhihao Lu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
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Pan YH, Zhang JX, Chen X, Liu F, Cao JZ, Chen Y, Chen W, Luo JH. Predictive Value of the TP53/ PIK3CA/ ATM Mutation Classifier for Patients With Bladder Cancer Responding to Immune Checkpoint Inhibitor Therapy. Front Immunol 2021; 12:643282. [PMID: 34421886 PMCID: PMC8371040 DOI: 10.3389/fimmu.2021.643282] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/15/2021] [Indexed: 12/18/2022] Open
Abstract
Background Only a proportion of patients with bladder cancer may benefit from durable response to immune checkpoint inhibitor (ICI) therapy. More precise indicators of response to immunotherapy are warranted. Our study aimed to construct a more precise classifier for predicting the benefit of immune checkpoint inhibitor therapy. Methods This multi-cohort study examined the top 20 frequently mutated genes in five cohorts of patients with bladder cancer and developed the TP53/PIK3CA/ATM mutation classifier based on the MSKCC ICI cohort. The classifier was then validated in a validation set consisting of IMvigor210 cohort and Broad/Dana-Farber cohort. The molecular profile and immune infiltration characteristics in each subgroup as defined by this classifier were explored. Results Among all 881 patients with bladder cancer, the mutation frequency of TP53, PIK3CA, and ATM ranked in the top 20 mutated genes. The TP53/PIK3CA/ATM mutation classifier was constructed based on the Memorial Sloan Kettering Cancer Center (MSKCC) ICI cohort and only showed predictive value for patients with bladder cancer who received ICI therapy (median overall survival: low-risk group, not reached; moderate-risk group, 13.0 months; high-risk group, 8.0 months; P<0.0001). Similar results were found in subgroups of MSKCC ICI cohort defined by tumor mutation burden. Multivariate Cox analysis revealed that the risk group defined by the classifier served as an independent prognostic factor for overall survival in patients with bladder cancer. Efficacy of the classifier was verified in a validation set consisting of IMvigor210 cohort and Broad/Dana-Farber cohort. Lower expression of PD-1/PD-L1 and less tumor immune infiltration were observed in the high-risk group than the other two groups of the TCGA cohort and the IMvigor210 cohort. Conclusion Our study constructed a TP53/PIK3CA/ATM mutation classifier to predict the benefit of immune checkpoint inhibitor therapy for patients with bladder cancer. This classifier can potentially complement the tumor mutation burden and guide clinical ICI treatment decisions according to distinct risk levels.
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Affiliation(s)
- Yi-Hui Pan
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jia-Xing Zhang
- Department of Oncology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xu Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fei Liu
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia-Zheng Cao
- Department of Urology, Jiangmen Hospital, Sun Yat-sen University, Jiangmen, China
| | - Yu Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun-Hang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Gu L, Xu Y, Jian H. Identification of a 15 DNA Damage Repair-Related Gene Signature as a Prognostic Predictor for Lung Adenocarcinoma. Comb Chem High Throughput Screen 2021; 25:1437-1449. [PMID: 34279196 DOI: 10.2174/1386207324666210716104714] [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: 01/27/2021] [Revised: 05/26/2021] [Accepted: 05/30/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Lung Adenocarcinoma (LUAD) is a common malignancy with a poor prognosis due to the lack of predictive markers. DNA Damage Repair (DDR)-related genes are closely related to cancer progression and treatment. INTRODUCTION To identify a reliable DDR-related gene signature as an independent predictor of LUAD. METHODS DDR-related genes were obtained using combined analysis of TCGA-LUAD data and literature information, followed by the identification of DDR-related prognostic genes. The DDR-related molecular subtypes were then screened, followed by Kaplan-Meier analysis, feature gene identification, and pathway enrichment analysis of each subtype. Moreover, Cox and LASSO regression analyses were performed for the feature genes of each subtype to construct a prognostic model. The clinical utility of the prognostic model was confirmed using the validation dataset GSE72094 and nomogram analysis. RESULTS Eight DDR-related prognostic genes were identified from 31 DDR-related genes. Using consensus cluster analysis, three molecular subtypes were screened. Cluster 2 had the best prognosis, while cluster 3 had the worst. Compared to cluster 2, clusters 1 and 3 consisted of more stage 3 - 4, T2-T4, male, and older samples. The feature genes of clusters 1, 2, and 3 were mainly enriched in the cell cycle, arachidonic acid metabolism, and ribosomes. Furthermore, a 15-feature gene signature was identified for improving the prognosis of LUAD patients. CONCLUSION The 15 DDR-related feature gene signature is an independent and powerful prognostic biomarker for LUAD that may improve risk classification and provide supplementary information for a more accurate evaluation and personalized treatment.
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Affiliation(s)
- Linping Gu
- Department of Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Yuanyuan Xu
- Department of Surgery Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Hong Jian
- Department of Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
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Chenard S, Jackson C, Vidotto T, Chen L, Hardy C, Jamaspishvilli T, Berman D, Siemens DR, Koti M. Sexual Dimorphism in Outcomes of Non-muscle-invasive Bladder Cancer: A Role of CD163+ Macrophages, B cells, and PD-L1 Immune Checkpoint. EUR UROL SUPPL 2021; 29:50-58. [PMID: 34337534 PMCID: PMC8317911 DOI: 10.1016/j.euros.2021.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Non-muscle-invasive bladder cancer (NMIBC) is over three times as common in men as it is in women; however, female patients do not respond as well to immunotherapeutic treatments and experience worse clinical outcomes than their male counterparts. Based on the established sexual dimorphism in mucosal immune responses, we hypothesized that the tumor immune microenvironment of bladder cancer differs between the sexes, and this may contribute to discrepancies in clinical outcomes. OBJECTIVE To determine biological sex-associated differences in the expression of immune regulatory genes and spatial organization of immune cells in tumors from NMIBC patients. DESIGN SETTING AND PARTICIPANTS Immune regulatory gene expression levels in tumors from male (n = 357) and female (n = 103) patients were measured using whole transcriptome profiles of tumors from the UROMOL cohort. Multiplexe immunofluorescence was performed to evaluate the density and spatial distribution of immune cells and immune checkpoints in tumors from an independent cohort of patients with NMIBC (n = 259 males and n = 73 females). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Transcriptome sequencing data were analyzed using DESeq2 in R v4.0.1, followed by application of the Kruskal-Wallis test to determine gene expression differences between tumors from males and females. Immunofluorescence data analyses were conducted using R version 3.5.3. Survival analysis was performed using survminer packages. RESULTS AND LIMITATIONS High-grade tumors from female patients exhibited significantly increased expression of B-cell recruitment (CXCL13) and function (CD40)-associated genes and the immune checkpoint genes CTLA4, PDCD1, LAG3, and ICOS. Tumors from female patients showed significantly higher infiltration of PD-L1+ cells and CD163+ M2-like macrophages than tumors from male patients. Increased abundance of CD163+ macrophages and CD79a+ B cells were associated with decreased recurrence-free survival. CONCLUSIONS These novel findings highlight the necessity of considering sexual dimorphism in the design of future immunotherapy trials in NMIBC. PATIENT SUMMARY In this study, we measured the abundance of various immune cell types between tumors from male and female patients with non-muscle-invasive bladder cancer. We demonstrate that tumors from female patients have a significantly higher abundance of immunosuppressive macrophages that express CD163. Higher abundance of tumor-associated CD163-expressing macrophages and B cells is associated with shorter recurrence-free survival in both male and female patients.
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Affiliation(s)
- Stephen Chenard
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
| | - Chelsea Jackson
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Thiago Vidotto
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lina Chen
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Céline Hardy
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Tamara Jamaspishvilli
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - David Berman
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - D. Robert Siemens
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
- Department of Urology, Queen’s University, Kingston, ON, Canada
| | - Madhuri Koti
- Queen’s Cancer Research Institute, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
- Department of Urology, Queen’s University, Kingston, ON, Canada
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Khalifa MK, Bakr NM, Ramadan A, Abd Elwahab KM, Desoky E, Nageeb AM, Swellam M. Implications of targeted next-generation sequencing for bladder cancer: report of four cases. J Genet Eng Biotechnol 2021; 19:91. [PMID: 34152511 PMCID: PMC8217481 DOI: 10.1186/s43141-021-00182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Bladder cancer is considered heterogeneous diseases with two major subgroups: non-muscle- invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC). It is a major healthcare problem, and it is one of the leading causes of mortality worldwide. Genetic mutations are not only a cause for carcinogenesis but are also a way for treatment strategy. The present study aimed to investigate breast cancer (BRCA genes) tumor suppressor gene mutations in bladder cancer tissue and combined blood samples for patients who developed secondary tumor after or during trimodal therapy. Fresh tissue samples and their matched blood samples were collected from four patients with bladder cancer. The objective regions for the examined genes (BRCA1 and BRCA2) were sequenced using next-generation sequencing (NGS); generated BAM files were uploaded to the cloud-based Ionreporter server, and the Oncomine BRCA-specific plugin was used to analyze the paired normal and tumor sample for each patient using the default plugin parameters. RESULTS Intronic BRCA1 mutation c.5050-104 C >T was reported among the four investigated bladder cancer patients, and three somatic mutations were reported as follows: two of them were found to be benign rs1064793056 and rs28897679 on the Clinivar database and one nonsense pathogenic variant rs80357006. BRCA 2 gene mutation reported an exonic synonymous mutation rs397507876 in the tissue and germline DNA. Patients were treated with trimodal; however, three bladder cancer patients who reported BRCA mutations developed secondary tumors. CONCLUSION Identification of mutational BRCA changes in bladder cancer is a promising marker for better treatment strategy. Further studies are encouraged on a large cohort of bladder cancer patients to confirm our findings.
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Affiliation(s)
| | - Noha M Bakr
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
| | - Amal Ramadan
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
| | | | - Esam Desoky
- Urology Department, Zagazig University, Zagazig, Egypt
| | - Amira M Nageeb
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
| | - Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt.
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt.
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Jiang M, Ren L, Chen Y, Wang H, Wu H, Cheng S, Li G, Yu S. Identification of a Hypoxia-Related Signature for Predicting Prognosis and the Immune Microenvironment in Bladder Cancer. Front Mol Biosci 2021; 8:613359. [PMID: 34026819 PMCID: PMC8138130 DOI: 10.3389/fmolb.2021.613359] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/22/2021] [Indexed: 01/19/2023] Open
Abstract
Accumulating evidence indicates that hypoxia is highly associated with bladder cancer genesis, progression, and immune microenvironment. Nevertheless, few studies have identified the role of hypoxia-related genes as a prognostic signature in bladder cancer. This study aimed to establish a hypoxia-related signature with high accuracy for prognosis and immune microenvironment prediction in bladder cancer. We obtained expression profiles and clinical information from Gene Expression Omnibus and The Cancer Genome Atlas. Then the univariate Cox regression, random survival forest algorithm, and multivariate Cox regression analysis were conducted to identify the core genes and four hypoxia-related genes (ANXA2, GALK1, COL5A1, and HS3ST1) were selected to construct the signature. Kaplan-Meier survival analysis demonstrated that patients with a low-risk score had a higher disease-specific survival rate (p < 0.0001). The areas under the curve of the signature were 0.829 at 1 year, 0.869 at 3 years, and 0.848 at 5 years, respectively. Additionally, we found this hypoxia-related signature was highly correlated with tumor immune microenvironment and had the potential to predict the efficacy of immunotherapy. In summary, our study developed a hypoxia-related signature, which had high accuracy for prognosis prediction and the potential to guide the immunotherapy for bladder cancer patients.
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Affiliation(s)
- Minxiao Jiang
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liangliang Ren
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuanlei Chen
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huan Wang
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyang Wu
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sheng Cheng
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gonghui Li
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shicheng Yu
- Department of Urology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Zhao W, Hu X, Li W, Li R, Chen J, Zhou L, Qiang S, Wu W, Shi S, Dong C. M2-Like TAMs Function Reversal Contributes to Breast Cancer Eradication by Combination Dual Immune Checkpoint Blockade and Photothermal Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007051. [PMID: 33599061 DOI: 10.1002/smll.202007051] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Immune checkpoint inhibitor (ICI) therapy is considered to be a revolutionary anti-tumor strategy that may surpass other traditional therapies. Breast cancer is particularly suitable for it theoretically due to upregulation of programmed cell death 1 (PD-1) / programmed cell death ligand 1 (PD-L1) immune checkpoint pathway which exhausts the adaptive immune response mediated by T lymphocytes. However, its blockades exhibit very little effect in breast cancer, owing to the lack of T lymphocytes pre-infiltration and co-existing of intricate immune negative microenvironment including the macrophage-suppressed "Don't eat me" CD47 signal overexpression. Herein, a stimuli-responsive multifunctional nanoplatform (ZIF-PQ-PDA-AUN) is built. Its photothermal therapy can promote the infiltration of T lymphocytes in addition to ablating tumor cells and AUNP-12 and PQ912 further boost both the innate and adaptive immune reactions by cutting off PD-L1 and CD47 signals, respectively. In contrast to earlier single immunotherapy, the nanocomposites exhibit a stronger anti-tumor immune effect without obvious autoimmune side effects, promoting infiltration of T lymphocyte into the tumor site and strengthening phagocytosis of macrophages, even more exciting, significantly reversing pro-tumor M2-like tumor-associated macrophages (TAMs) to anti-tumor M1-like TAMs. The research may provide a promising strategy to develop high-efficient and low-toxic immunotherapy based on nanotechnology.
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Affiliation(s)
- Wenrong Zhao
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Xiaochun Hu
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Wenhui Li
- Shanghai Institute of Quality Inspection and Technical Research, Shanghai, 201100, P. R. China
| | - Ruihao Li
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Jinjin Chen
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Lulu Zhou
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Sufeng Qiang
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Wenjing Wu
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Shuo Shi
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
| | - Chunyan Dong
- Breast Cancer Center, Shanghai East Hospital, Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200120, P. R. China
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Zhang T, Zheng S, Liu Y, Li X, Wu J, Sun Y, Liu G. DNA damage response and PD-1/PD-L1 pathway in ovarian cancer. DNA Repair (Amst) 2021; 102:103112. [PMID: 33838550 DOI: 10.1016/j.dnarep.2021.103112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 03/17/2021] [Accepted: 03/27/2021] [Indexed: 12/15/2022]
Abstract
Ovarian cancer has a poor prognosis due to drug resistance, relapse and metastasis. In recent years, immunotherapy has been applied in numerous cancers clinically. However, the effect of immunotherapy monotherapy in ovarian cancer is limited. DNA damage response (DDR) is an essential factor affecting the efficacy of tumor immunotherapy. Defective DNA repair may lead to carcinogenesis and tumor genomic instability, but on the other hand, it may also portend particular vulnerability of tumors and can be used as biomarkers for immunotherapy patient selection. Programmed cell death 1 (PD-1)/programmed death-ligand 1 (PD-L1) pathway mediates tumor immune escape, which may be a promising target for immunotherapy. Therefore, further understanding of the mechanism of PD-L1 expression after DDR may help guide the development of immunotherapy in ovarian cancer. In this review, we present the DNA damage repair pathway and summarize how DNA damage repair affects the PD-1/PD-L1 pathway in cancer cells. And then we look for biomarkers that affect efficacy or prognosis. Finally, we review the progress of PD-1/PD-L1-based immunotherapy in combination with other therapies that may affect the DDR pathway in ovarian cancer.
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Affiliation(s)
- Tianyu Zhang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
| | - Shuangshuang Zheng
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
| | - Yang Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
| | - Xiao Li
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
| | - Jing Wu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
| | - Yue Sun
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
| | - Guoyan Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, No. 154 Anshan Road, Tianjin, 300052, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin, 300052, China.
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Huang H, Tan M, Zheng L, Yan G, Li K, Lu D, Cui X, He S, Lei D, Zhu B, Zhao J. Prognostic Implications of the Complement Protein C1Q and Its Correlation with Immune Infiltrates in Osteosarcoma. Onco Targets Ther 2021; 14:1737-1751. [PMID: 33707956 PMCID: PMC7943548 DOI: 10.2147/ott.s295063] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Osteosarcoma (OS) is the most widespread bone tumour among childhood cancers, and distant metastasis is the dominant factor in poor prognosis for patients with OS. Therefore, it is necessary to identify new prognostic biomarkers for identifying patients with aggressive disease. METHODS Two OS datasets (GSE21257 and GSE33383) were downloaded from the Gene Expression Omnibus (GEO) and subsequently subjected to weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis (DGE) to screen candidate genes. A prognostic model was constructed using OS data derived from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program to further screen key genes and perform gene ontology (GO) analysis. The prognostic values of key genes were assessed using the Kaplan-Meier (KM) plotter. The GEO dataset was used for immune infiltration analysis and association analysis of key genes. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) was employed to validate the expression levels of potentially crucial genes in OS cell lines. RESULTS In the present study, we found 114 genes with a highly significant correlation in the module and 44 downregulated genes; 25 candidate genes overlapped in the two parts of the genes. Among these, three key genes, C1QA, C1QB, and C1QC, were the most significant hub genes, which had the highest node degrees, were clustered into one group, and implicated in most significant biological processes (regulation of immune effector process). Moreover, these three key genes were negatively associated with the prognosis of OS and positively associated with three immune cells (follicular helper T cells, memory B cells, and CD8 T cells). Additionally, compared to non-metastatic OS cell lines, the expression of three key genes was significantly downregulated in metastatic OS cell lines. CONCLUSION Our results revealed that three key genes (C1QA, C1QB, and C1QC) were implicated in tumour immune infiltration and may be promising biomarkers for predicting metastasis and prognosis of patients with OS.
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Affiliation(s)
- Hanji Huang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Manli Tan
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Li Zheng
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- International Joint Laboratory of Ministry of Education for Regeneration of Bone and Soft Tissues, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Guohua Yan
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Kanglu Li
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Dejie Lu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Xiaofei Cui
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Si He
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Danqing Lei
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, People’s Republic of China
- The Medical and Scientific Research Center, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Bo Zhu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
| | - Jinmin Zhao
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, People’s Republic of China
- International Joint Laboratory of Ministry of Education for Regeneration of Bone and Soft Tissues, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People’s Republic of China
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Guo E, Wu C, Ming J, Zhang W, Zhang L, Hu G. The Clinical Significance of DNA Damage Repair Signatures in Clear Cell Renal Cell Carcinoma. Front Genet 2021; 11:593039. [PMID: 33488669 PMCID: PMC7820869 DOI: 10.3389/fgene.2020.593039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
DNA damage repair plays an important role in cancer’s initiation and progression, and in therapeutic resistance. The prognostic potential of damage repair indicators was studied in the case of clear cell renal cell carcinoma (ccRCC). Gene expression profiles of the disease were downloaded from cancer genome databases and gene ontology was applied to the DNA repair-related genes. Twenty-six differentially expressed DNA repair genes were identified, and regression analysis was used to identify those with prognostic potential and to construct a risk model. The model accurately predicted patient outcomes and distinguished among patients with different expression levels of immune evasion genes. The data indicate that DNA repair genes can be valuable for predicting the progression of clear cell renal cell carcinoma and the clinical benefits of immunotherapy.
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Affiliation(s)
- Ergang Guo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Cheng Wu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Jun Ming
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Wei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Linli Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
| | - Guoqing Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan
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Lopez-Beltran A, Cimadamore A, Blanca A, Massari F, Vau N, Scarpelli M, Cheng L, Montironi R. Immune Checkpoint Inhibitors for the Treatment of Bladder Cancer. Cancers (Basel) 2021; 13:E131. [PMID: 33401585 PMCID: PMC7795541 DOI: 10.3390/cancers13010131] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
A number of immune checkpoint inhibitors (ICIs) have been approved as first-line therapy in case of cisplatin-ineligible patients or as second-line therapy for patients with metastatic urothelial carcinoma (mUC) of the bladder. About 30% of patients with mUC will respond to ICIs immunotherapy. Programmed death-ligand 1 (PD-L1) expression detected by immunohistochemistry seems to predict response to immune checkpoint inhibitors in patients with mUC as supported by the objective response rate (ORR) and overall survival (OS) associated with the response observed in most clinical trials. Pembrolizumab, an anti-PD-1 antibody, demonstrated better OS respective to chemotherapy in a randomized phase 3 study for second-line treatment of mUC. Nivolumab, a PD-1 antibody, also demonstrated an OS benefit when compared to controls. Atezolizumab, Durvalumab, and Avelumab antibodies targeting PD-L1 have also received approval as second-line treatments for mUC with durable response for more than 1 year in selected patients. Atezolizumab and Pembrolizumab also received approval for first-line treatment of patients that are ineligible for cisplatin. A focus on the utility of ICIs in the adjuvant or neoadjuvant setting, or as combination with chemotherapy, is the basis of some ongoing trials. The identification of a clinically useful biomarker, single or in association, to determine the optimal ICIs treatment for patients with mUC is very much needed as emphasized by the current literature. In this review, we examined relevant clinical trial results with ICIs in patients with mUC alone or as part of drug combinations; emphasis is also placed on the adjuvant and neoadjuvant setting. The current landscape of selected biomarkers of response to ICIs including anti-PD-L1 immunohistochemistry is also briefly reviewed.
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Affiliation(s)
- Antonio Lopez-Beltran
- Unit of Anatomic Pathology, Department of Morphological Sciences, Cordoba University Medical School, 14004 Cordoba, Spain
| | - Alessia Cimadamore
- Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (M.S.)
| | - Ana Blanca
- Maimonides Biomedical Research Institute of Cordoba, Department of Urology, University Hospital of Reina Sofia, 14004 Cordoba, Spain;
| | - Francesco Massari
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Nuno Vau
- Medical Oncology, Champalimaud Clinical Center, 1400-038 Lisbon, Portugal;
| | - Marina Scarpelli
- Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (M.S.)
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
| | - Rodolfo Montironi
- Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy; (A.C.); (M.S.)
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Huang H, Li H. Tumor heterogeneity and the potential role of liquid biopsy in bladder cancer. Cancer Commun (Lond) 2020; 41:91-108. [PMID: 33377623 PMCID: PMC7896752 DOI: 10.1002/cac2.12129] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/28/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is a heterogeneous disease that characterized by genomic instability and a high mutation rate. Heterogeneity in tumor may partially explain the diversity of responses to targeted therapies and the various clinical outcomes. A combination of cytology and cystoscopy is the standard methodology for BC diagnosis, prognosis, and disease surveillance. However, genomics analyses of single tumor‐biopsy specimens may underestimate the mutational burden of heterogeneous tumors. Liquid biopsy, as a promising technology, enables analysis of tumor components in the bodily fluids, such as blood and urine, at multiple time points and provides a minimally invasive approach that can track the evolutionary dynamics and monitor tumor heterogeneity. In this review, we describe the multiple faces of BC heterogeneity at the genomic and transcriptional levels and how they affect clinical care and outcomes. We also summarize the outcomes of liquid biopsy in BC, which plays a potential role in revealing tumor heterogeneity. Finally, we discuss the challenges that must be addressed before liquid biopsy can be widely used in clinical treatment.
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Affiliation(s)
- Hai‐Ming Huang
- Department of Clinical LaboratoryPeking University First HospitalBeijing100034P. R. China
| | - Hai‐Xia Li
- Department of Clinical LaboratoryPeking University First HospitalBeijing100034P. R. China
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Zheng Z, Mao S, Zhang W, Liu J, Li C, Wang R, Yao X. Dysregulation of the Immune Microenvironment Contributes to Malignant Progression and Has Prognostic Value in Bladder Cancer. Front Oncol 2020; 10:542492. [PMID: 33392066 PMCID: PMC7773013 DOI: 10.3389/fonc.2020.542492] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 11/16/2020] [Indexed: 02/05/2023] Open
Abstract
Objective The malignant progression from non-muscle-invasive bladder cancer (NMIBC) to muscle-invasive bladder cancer (MIBC) is common and has detrimental effect on patients. We aimed to elucidate the underlying mechanisms of the malignant progression from an immunological perspective and establish a reliable signature for prognostic prediction and immunotherapeutic strategies. Methods The Cell Type Identification by Estimating Relative Subsets of RNA Transcripts algorithm was applied to the GSE32894 data set to identify the different tumor-infiltrating immune cells involved in NMIBC and MIBC. Using weighted gene correlation network analysis, survival analysis and least absolute shrinkage and selection operator Cox analysis, we established an immune prognostic signature (IPS) based on 14 overall survival-associated immune genes in The Cancer Genome Atlas (TCGA). Functional enrichment analyses and nomogram were performed to explore the potential effects and prognostic performance of the IPS. Furthermore, the RNA-sequence data from our center were used to validate the expression levels of the selected immune genes in BLCA samples. Results Diverse proportions of macrophage subtypes were observed between NMIBC and MIBC. Patients with high risk scores had a worse prognosis than patients with low risk scores in training (TCGA) and validation data sets (GSE32894, GSE13507, and GSE48277). The IPS was a useful prognostic factor for patients treated with immunotherapy in the IMvigor210 trial. Hallmarks of multiple oncogenic pathways were significantly enriched in the high risk group. A novel nomogram model was established for prognostic predictions. The dysregulated expression of the selected immune genes between NMIBC and MIBC was also validated in BLCA samples. Conclusion Dysregulation of the immune microenvironment promoted the malignant progression from NMIBC to MIBC. The IPS can stratify patients into different risk groups with distinct prognoses and immunotherapeutic susceptibility, thus facilitating personalized immunotherapy.
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Affiliation(s)
- Zongtai Zheng
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shiyu Mao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wentao Zhang
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ji Liu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Cheng Li
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruiliang Wang
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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