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Dong C, Zhang F, He E, Ren P, Verma N, Zhu X, Feng D, Zhao H, Chen S. Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601809. [PMID: 39005443 PMCID: PMC11245041 DOI: 10.1101/2024.07.02.601809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Emerging immunotherapies such as immune checkpoint blockade (ICB) and chimeric antigen receptor T-cell (CAR-T) therapy have revolutionized cancer treatment and have improved the survival of patients with multiple cancer types. Despite this success many patients are unresponsive to these treatments or relapse following treatment. CRISPR activation and knockout (KO) screens have been used to identify novel single gene targets that can enhance effector T cell function and promote immune cell targeting and eradication of tumors. However, cancer cells often employ multiple genes to promote an immunosuppressive pathway and thus modulating individual genes often has a limited effect. Paralogs are genes that originate from common ancestors and retain similar functions. They often have complex effects on a particular phenotype depending on factors like gene family similarity, each individual gene's expression and the physiological or pathological context. Some paralogs exhibit synthetic lethal interactions in cancer cell survival; however, a thorough investigation of paralog pairs that could enhance the efficacy of cancer immunotherapy is lacking. Here we introduce a sensitive computational approach that uses sgRNA sets enrichment analysis to identify cancer-intrinsic paralog pairs which have the potential to synergistically enhance T cell-mediated tumor destruction. We have further developed an ensemble learning model that uses an XGBoost classifier and incorporates features such as gene characteristics, sequence and structural similarities, protein-protein interaction (PPI) networks, and gene coevolution data to predict paralog pairs that are likely to enhance immunotherapy efficacy. We experimentally validated the functional significance of these predicted paralog pairs using double knockout (DKO) of identified paralog gene pairs as compared to single gene knockouts (SKOs). These data and analyses collectively provide a sensitive approach to identify previously undetected paralog pairs that can enhance cancer immunotherapy even when individual genes within the pair has a limited effect.
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Affiliation(s)
- Chuanpeng Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
- Yale-Boehringer Ingelheim Biomedical Data Science Fellowship Program
| | - Feifei Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Emily He
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Ping Ren
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Nipun Verma
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Xinxin Zhu
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
- Yale-Boehringer Ingelheim Biomedical Data Science Fellowship Program
| | - Di Feng
- Yale-Boehringer Ingelheim Biomedical Data Science Fellowship Program
- Computational Biology, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
- Yale-Boehringer Ingelheim Biomedical Data Science Fellowship Program
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
- Yale-Boehringer Ingelheim Biomedical Data Science Fellowship Program
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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Wang Q, Lin B, Wei H, Wang X, Nie X, Shi Y. AQP3 Promotes the Invasion and Metastasis in Cervical Cancer by Regulating NOX4-derived H 2O 2 Activation of Syk/PI3K/Akt Signaling Axis. J Cancer 2024; 15:1124-1137. [PMID: 38230207 PMCID: PMC10788729 DOI: 10.7150/jca.91360] [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: 10/20/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
Unrestrained chronic inflammation leads to the abnormal activity of NOX4 and the subsequent production of excessive hydrogen peroxide (H2O2). Excessive H2O2 signaling triggered by prolonged inflammation is thought to be one of the important reasons for the progression of some types of cancer including cervical cancer. Aquaporin 3 (AQP3) is a member of the water channel protein family, and it remains unknown whether AQP3 can regulate the transmembrane transport of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 4 (NOX4)-derived H2O2 induced by the stimulation of inflammatory factors to facilitate the malignant progression in cervical cancer. In this study, cervical cancer HeLa cell line was respectively treated with diphenyleneiodonium (DPI), N-Acetylcysteine (NAC) or lentivirus-shRNA- AQP3. Plate cloning, cell migration or transwell invasion assays, etc. were performed to detect the invasive and migration ability of the cells. Western blot and CO-IP were used to analyze the mechanism of AQP3 regulating H2O2 conduction. Finally, in vivo assays were performed for validation in nude mice. AQP3 Knockdown, DPI or NAC treatments all reduced intracellular H2O2 influx, and the activation of Syk/PI3K/Akt signal axis was inhibited, the migration and invasive ability of the cells was attenuated. In vivo assays confirmed that the excessive H2O2 transport through AQP3 enhanced the infiltration and metastasis of cervical cancer. These results suggest that AQP3 activates H2O2/Syk/PI3K/Akt signaling axis through regulating NOX4-derived H2O2 transport to contribute to the progression of cervical cancer, and AQP3 may be a potential target for the clinical treatment of advanced cervical cancer.
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Affiliation(s)
- Qixin Wang
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
| | - Bingjie Lin
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
| | - Hongjian Wei
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
| | - Xin Wang
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
| | - Xiaojing Nie
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
| | - Yonghua Shi
- Department of Pathology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Diseases, Xinjiang Medical University, Urumqi, Xinjiang 830017, China
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Moreira RS, da Silva MM, de Melo Vasconcelos CF, da Silva TD, Cordeiro GG, Mattos-Jr LAR, da Rocha Pitta MG, de Melo Rêgo MJB, Pereira MC. Siglec 15 as a biomarker or a druggable molecule for non-small cell lung cancer. J Cancer Res Clin Oncol 2023; 149:17651-17661. [PMID: 37843557 DOI: 10.1007/s00432-023-05437-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023]
Abstract
Lung cancer has been the main cause of cancer mortality worldwide. Furthermore, lung cancer rates of new cases per year evidenced a large incidence of this neoplasm in both men and women. Because there is no biomarker for early detection, it is frequently detected late, at an advanced state. The introduction of multiple lines of tyrosine kinase inhibitors in patients with EGFR, ALK, ROS1, and NTRK mutations has modified the therapy of lung cancer. Immunotherapy advances have resulted in substantial improvements in overall survival and disease-free survival, making immune checkpoint inhibitors (ICIs) a potential option for lung cancer treatment. Current PD-1/PD-L1/CTLA-4 immunotherapies have resulted in important response and survival rates. However, existing medicines only function in around 20% of unselected, advanced NSCLC patients, and primary and acquired resistance remain unsolved obstacles. Therefore, precise predictive indicators must be identified to choose the best patients for ICI treatment. Thus, Sialic acid-binding immunoglobulin-like lectin 15 (Siglec-15) stands out as a potential tumor biomarker, with distinctive expression in normal tissues, in tumor immune involvement, and a high structural similarity to PD-L1. Understanding the tumor immune response and the search for new therapeutic targets leads to the improvement of therapeutic pathways directed at the tumor microenvironment. The present review aims to analyze Siglec-15 potential as a diagnostic, prognostic, and response biomarker in lung cancer, considering its results evidenced in the current literature.
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Affiliation(s)
- Rodrigo Santiago Moreira
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Marillya Morais da Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Thiago Douberin da Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Luiz Alberto Reis Mattos-Jr
- Department of Clinic Medicine, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife, PE, Brazil
| | - Maira Galdino da Rocha Pitta
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Michelly Cristiny Pereira
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco, Recife, Pernambuco, Brazil.
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Linos K, Dermawan JK, Bale T, Rosenblum MK, Singer S, Tap W, Dickson MA, Hornick JL, Antonescu CR. Expanding the Molecular Diversity of CIC-Rearranged Sarcomas With Novel and Very Rare Partners. Mod Pathol 2023; 36:100103. [PMID: 36788092 PMCID: PMC10324473 DOI: 10.1016/j.modpat.2023.100103] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Capicua transcriptional repressor (CIC)-rearranged sarcoma represents a distinct pathologic entity and constitutes the second most prevalent category of undifferentiated round cell sarcomas (URCSs) after Ewing sarcoma. The 2 most common translocations are t(4;19) and t(10;19), resulting in CIC fusions with either DUX4 and DUX4L paralog, respectively; however, other rare variant fusions have also been reported. In this study, we expand the molecular spectrum of CIC-gene partners, reporting on 5 cases of URCSs showing CIC fusions with AXL, CITED1, SYK, and LEUTX by targeted RNA or DNA sequencing. There were 4 female patients and 1 male patient with a wide age range (12-70 years; median, 36 years). Four cases occurred in the deep soft tissues (lower extremity, 3; neck, 1) and 1 case in the central nervous system (midbrain/thalamus). All cases showed similar histologic findings within the spectrum of URCSs. Immunohistochemistry, showed variable positivity for ETV4 in 4 of the 4 cases and positive results for ERG in 3 of the 4 cases and for WT1 in 1 of the 4 cases. CD31 showed positivity in 2 of the 3 cases, including one coexpressing ERG. Unsupervised clustering of methylation profiles by T-distributed stochastic neighborhood embedding performed in 4 cases showed that all clustered tightly together and along the CIC sarcoma methylation class. RNA-sequencing data showed consistent upregulation of ETV1 and ETV4 mRNA in all cases examined, at similar levels to CIC::DUX4 URCSs. Our study expands the molecular diversity of CIC-rearranged URCSs to include novel and rare partners, providing morphologic, immunohistochemical, gene expression, and methylation evidence supporting their classification within the family of tumors harboring the more common DUX4/DUX4L partner genes.
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Affiliation(s)
- Konstantinos Linos
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tejus Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc K Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William Tap
- Department of Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark A Dickson
- Department of Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason L Hornick
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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