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Wang L, Pattnaik A, Sahoo SS, Stone EG, Zhuang Y, Benton A, Tajmul M, Chakravorty S, Dhawan D, Nguyen MA, Sirit I, Mundy K, Ricketts CJ, Hadisurya M, Baral G, Tinsley SL, Anderson NL, Hoda S, Briggs SD, Kaimakliotis HZ, Allen-Petersen BL, Tao WA, Linehan WM, Knapp DW, Hanna JA, Olson MR, Afzali B, Kazemian M. Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark. Nat Commun 2024; 15:7288. [PMID: 39179644 PMCID: PMC11343859 DOI: 10.1038/s41467-024-51859-9] [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: 03/06/2023] [Accepted: 08/19/2024] [Indexed: 08/26/2024] Open
Abstract
Correctly identifying perturbed biological pathways is a critical step in uncovering basic disease mechanisms and developing much-needed therapeutic strategies. However, whether current tools are optimal for unbiased discovery of relevant pathways remains unclear. Here, we create "Benchmark" to critically evaluate existing tools and find that most function sub-optimally. We thus develop the "Pathway Ensemble Tool" (PET), which outperforms existing methods. Deploying PET, we identify prognostic pathways across 12 cancer types. PET-identified prognostic pathways offer additional insights, with genes within these pathways serving as reliable biomarkers for clinical outcomes. Additionally, normalizing these pathways using drug repurposing strategies represents therapeutic opportunities. For example, the top predicted repurposed drug for bladder cancer, a CDK2/9 inhibitor, represses cell growth in vitro and in vivo. We anticipate that using Benchmark and PET for unbiased pathway discovery will offer additional insights into disease mechanisms across a spectrum of diseases, enabling biomarker discovery and therapeutic strategies.
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Affiliation(s)
- Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Aryamav Pattnaik
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Subhransu Sekhar Sahoo
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Ella G Stone
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Yuxin Zhuang
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Annaleigh Benton
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Md Tajmul
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Immunoregulation Section, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Srishti Chakravorty
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - My An Nguyen
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Isabella Sirit
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Kyle Mundy
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch of Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Marco Hadisurya
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Garima Baral
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Samantha L Tinsley
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Nicole L Anderson
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Smriti Hoda
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Scott D Briggs
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Brittany L Allen-Petersen
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - W Andy Tao
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - W Marston Linehan
- Urologic Oncology Branch of Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Deborah W Knapp
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Jason A Hanna
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew R Olson
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
| | - Majid Kazemian
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA.
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
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2
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Zhou C, Zhao S, Zhang Y, Cheng J, Shi J, Du G. Mesoporous polydopamine Targeting CDK4/6 Inhibitor toward Brilliant Synergistic Immunotherapy of Breast Cancer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310565. [PMID: 38396273 DOI: 10.1002/smll.202310565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/11/2024] [Indexed: 02/25/2024]
Abstract
Immunotherapy utilizing anti-PD-L1 blockade has achieved dramatic success in clinical breast cancer management but is often hampered by the limited immune response. Increasing evidence shows that immunogenic cell death (ICD) recently arises as a promising strategy for enlarging tumor immunogenicity and eliciting systemic anti-tumor immunity effectively. However, developing simple but versatile, highly efficient but low-toxic, biosafe, and clinically available transformed ICD inducers remains a huge demand and is highly desirable. Herein, a multifunctional ICD inducer is purposefully developed A6-MPDA@PAL by integrating photothermal therapy (PTT) nanoplatforms mesoporous polydopamine (MPDA), CDK4/6 inhibitor palbociclib (PAL), and CD44-specific targeting A6 peptide in a simple way for augmenting the immune antitumor efficacy of anti-PD-L1 therapy. Remarkably, the light-inducible nanoplatforms exhibit multiple favorable therapeutic features ensuring a superior and biosafe PTT/chemotherapy efficacy. Together with stronger accumulative ICD induction, single administration of A6-MPDA@PAL can trigger robust systemic antitumor immunity and abscopal effect with the assistance of anti-PD-L1 blockade by fascinating the intratumoral infiltration of T lymphocytes and reversing the immunosuppressive tumor microenvironment simultaneously, therapy achieving brilliant synergistic immunotherapy with effective tumor ablation. This study presents a simple and smart ICD inducer opening up attractive clinical possibilities for reinforcing the anti-PD-L1 therapy against breast cancer.
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Affiliation(s)
- Conglei Zhou
- Key Laboratory of Natural Medicine and Immune Engineering, Henan University, Kaifeng, Henan, 475004, China
| | - Shuang Zhao
- Key Laboratory of Natural Medicine and Immune Engineering, Henan University, Kaifeng, Henan, 475004, China
| | - Yongbo Zhang
- Key Laboratory of Natural Medicine and Immune Engineering, Henan University, Kaifeng, Henan, 475004, China
| | - Jianjun Cheng
- Key Laboratory of Natural Medicine and Immune Engineering, Henan University, Kaifeng, Henan, 475004, China
- State Key Laboratory of Antiviral Drugs, Henan University, China
| | - Jiahua Shi
- Key Laboratory of Natural Medicine and Immune Engineering, Henan University, Kaifeng, Henan, 475004, China
- State Key Laboratory of Antiviral Drugs, Henan University, China
| | - Guanhua Du
- Key Laboratory of Natural Medicine and Immune Engineering, Henan University, Kaifeng, Henan, 475004, China
- State Key Laboratory of Antiviral Drugs, Henan University, China
- Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100050, China
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3
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Liang Y, Hu L, Wu H, Yin T, Zhang J. Treatment with palbociclib and tislelizumab for CDKN2A-mutated and PD-L1-positive advanced intrahepatic cholangiocarcinoma: a case report and literature review. Front Oncol 2024; 14:1292319. [PMID: 38327739 PMCID: PMC10848247 DOI: 10.3389/fonc.2024.1292319] [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: 09/11/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Background Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver malignancy with a steadily increasing incidence worldwide. ICC has insidious onset, rapid progression, and poor prognosis. More multidisciplinary clinical studies are needed to continuously explore safer and more efficient diagnosis and treatment modes for ICC. Methods and results A 66-year-old female patient with ICC rapidly developed systemic multiple metastases after surgery, and the first-line two-drug combination chemotherapy was not effective. Due to cyclin-dependent kinase inhibitor 2A mutation and programmed cell death-ligand 1-positive, a partial response and progression-free survival of 9.5 months were achieved after a second-line treatment with cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) combined with immunotherapy. The patient developed thromboembolism 7 months after treatment and died due to disseminated intravascular coagulation. Conclusion The combination of targeted and immune therapy has revealed a potentially effective regimen for the effective treatment of patients with ICC, which needs to be observed in larger clinical studies. The thromboembolism rates in real-world patients treated with CDK4/6 inhibitors are higher than those reported in clinical trials, and the application of prophylactic anticoagulation in this patient population may be questionable.
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Affiliation(s)
- Yajun Liang
- IV Ward of Pulmonary and Critial Care Medicine, Wuhan Pulmonary Hospotal, Wuhan, Hubei, China
| | - Liya Hu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huanlei Wu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tiejun Yin
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Internal Medicine, The Fifth People’s Hospital of Jingzhou, Jingzhou, Hubei, China
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4
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Arndt C, Tunger A, Wehner R, Rothe R, Kourtellari E, Luttosch S, Hannemann K, Koristka S, Loureiro LR, Feldmann A, Tonn T, Link T, Kuhlmann JD, Wimberger P, Bachmann MP, Schmitz M. Palbociclib impairs the proliferative capacity of activated T cells while retaining their cytotoxic efficacy. Front Pharmacol 2023; 14:970457. [PMID: 36817127 PMCID: PMC9935825 DOI: 10.3389/fphar.2023.970457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
The cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitor palbociclib is an emerging cancer therapeutic that just recently gained Food and Drug Administration approval for treatment of estrogen receptor (ER)-positive, human epidermal growth factor receptor (Her)2-negative breast cancer in combination with the ER degrader fulvestrant. However, CDK4/6 inhibitors are not cancer-specific and may affect also other proliferating cells. Given the importance of T cells in antitumor defense, we studied the influence of palbociclib/fulvestrant on human CD3+ T cells and novel emerging T cell-based cancer immunotherapies. Palbociclib considerably inhibited the proliferation of activated T cells by mediating G0/G1 cell cycle arrest. However, after stopping the drug supply this suppression was fully reversible. In light of combination approaches, we further investigated the effect of palbociclib/fulvestrant on T cell-based immunotherapies by using a CD3-PSCA bispecific antibody or universal chimeric antigen receptor (UniCAR) T cells. Thereby, we observed that palbociclib clearly impaired T cell expansion. This effect resulted in a lower total concentration of interferon-γ and tumor necrosis factor, while palbociclib did not inhibit the average cytokine release per cell. In addition, the cytotoxic potential of the redirected T cells was unaffected by palbociclib and fulvestrant. Overall, these novel findings may have implications for the design of treatment modalities combining CDK4/6 inhibition and T cell-based cancer immunotherapeutic strategies.
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Affiliation(s)
- Claudia Arndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany,Mildred Scheel Early Career Center, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany,*Correspondence: Claudia Arndt, ; Marc Schmitz,
| | - Antje Tunger
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Rebekka Wehner
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany,German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebecca Rothe
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Eleni Kourtellari
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Stephanie Luttosch
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Katharina Hannemann
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Stefanie Koristka
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Liliana R. Loureiro
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Anja Feldmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Torsten Tonn
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Red Cross Blood Donation Service North-East, Institute for Transfusion Medicine, Dresden, Germany,Experimental Transfusion Medicine, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Theresa Link
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Jan Dominik Kuhlmann
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Pauline Wimberger
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Michael Philipp Bachmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany,Tumor Immunology, University Cancer Center (UCC), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Marc Schmitz
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany,Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany,German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany,*Correspondence: Claudia Arndt, ; Marc Schmitz,
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5
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The Roles of miRNAs in Predicting Bladder Cancer Recurrence and Resistance to Treatment. Int J Mol Sci 2023; 24:ijms24020964. [PMID: 36674480 PMCID: PMC9864802 DOI: 10.3390/ijms24020964] [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: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Bladder cancer (BCa) is associated with significant morbidity, with development linked to environmental, lifestyle, and genetic causes. Recurrence presents a significant issue and is managed in the clinical setting with intravesical chemotherapy or immunotherapy. In order to address challenges such as a limited supply of BCG and identifying cases likely to recur, it would be advantageous to use molecular biomarkers to determine likelihood of recurrence and treatment response. Here, we review microRNAs (miRNAs) that have shown promise as predictors of BCa recurrence. MiRNAs are also discussed in the context of predicting resistance or susceptibility to BCa treatment.
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Applications and mechanisms of the cyclin-dependent kinase 4/6 inhibitor, PD-0332991, in solid tumors. Cell Oncol (Dordr) 2022; 45:1053-1071. [PMID: 36087253 DOI: 10.1007/s13402-022-00714-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2022] [Indexed: 01/10/2023] Open
Abstract
Abnormal CDK4/6-Rb-E2F signal transduction is a common finding in tumors and is a driving factor for the excessive proliferation of various tumor cells. PD-0332991, a highly specific, small molecule inhibitor for CDK4 and 6, has been shown to inhibit tumor growth by abrogating the phosphorylating capacity of CDK4/6 and suppressing Rb phosphorylation. It has been promoted for the treatment of breast cancer and potentially for other tumor types such as liver cancers, lung cancers and sarcomas. Due to the risk of monotherapy resistance, PD-0332991 is commonly used in combination with other drugs. Such combination treatments have proved able to inhibit tumor proliferation more effectively, induce stronger senescence and apoptosis, and enhance the efficiency of immunotherapy. Therefore, tumor cells with senescence induced by PD-0332991 are now used as ideal screening tools of cytolytic drugs with more efficient and thorough anti-tumor properties. With more extensive understandings about the branching points between senescence and apoptosis, it is possible to refine the dosage of PD-0332991. Better characterization of resistant cells, of inhibitors and of adverse effects such as leukopenia are needed to overcome obstacles in the use of PD-0332991. In this review of PD-0332991 research, we hope to provide guidance of transitions from laboratory findings to clinical applications of PD-0332991 and to facilitate PD-0332991-based multi-inhibitor combination therapies for various tumors.
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7
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İnce O, Yıldız H, Kisbet T, Ertürk ŞM, Önder H. Classification of retinoblastoma-1 gene mutation with machine learning-based models in bladder cancer. Heliyon 2022; 8:e09311. [PMID: 35520623 PMCID: PMC9061624 DOI: 10.1016/j.heliyon.2022.e09311] [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: 11/26/2021] [Revised: 01/19/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Purpose This study aims to evaluate the potential of machine learning algorithms built with radiomics features from computed tomography urography (CTU) images that classify RB1 gene mutation status in bladder cancer. Method The study enrolled CTU images of 18 patients with and 54 without RB1 mutation from a public database. Image and data preprocessing were performed after data augmentation. Feature selection steps were consisted of filter and wrapper methods. Pearson’s correlation analysis was the filter, and a wrapper-based sequential feature selection algorithm was the wrapper. Models with XGBoost, Random Forest (RF), and k-Nearest Neighbors (kNN) algorithms were developed. Performance metrics of the models were calculated. Models’ performances were compared by using Friedman’s test. Results 8 features were selected from 851 total extracted features. Accuracy, sensitivity, specificity, precision, recall, F1 measure and AUC were 84%, 80%, 88%, 86%, 80%, 0.83 and 0.84, for XGBoost; 72%, 80%, 65%, 67%, 80%, 0.73 and 0.72 for RF; 66%, 53%, 76%, 67%, 53%, 0.60 and 0.65 for kNN, respectively. XGBoost model had outperformed kNN model in Friedman’s test (p = 0.006). Conclusions Machine learning algorithms with radiomics features from CTU images show promising results in classifying bladder cancer by RB1 mutation status non-invasively.
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Affiliation(s)
- Okan İnce
- Health Sciences University Prof. Dr. Cemil Tascioglu City Hospital, Department of Radiology, Turkey
- Corresponding author.
| | - Hülya Yıldız
- Health Sciences University Prof. Dr. Cemil Tascioglu City Hospital, Department of Radiology, Turkey
| | - Tanju Kisbet
- Health Sciences University Prof. Dr. Cemil Tascioglu City Hospital, Department of Radiology, Turkey
| | - Şükrü Mehmet Ertürk
- Istanbul University Istanbul Medical Faculty, Department of Radiology, Turkey
| | - Hakan Önder
- Health Sciences University Prof. Dr. Cemil Tascioglu City Hospital, Department of Radiology, Turkey
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8
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Green JL, Osterhout RE, Klova AL, Merkwirth C, McDonnell SRP, Zavareh RB, Fuchs BC, Kamal A, Jakobsen JS. Molecular characterization of type I IFN-induced cytotoxicity in bladder cancer cells reveals biomarkers of resistance. Mol Ther Oncolytics 2021; 23:547-559. [PMID: 34938855 PMCID: PMC8645427 DOI: 10.1016/j.omto.2021.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/05/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022] Open
Abstract
Although anti-tumor activities of type I interferons (IFNs) have been recognized for decades, the molecular mechanisms contributing to clinical response remain poorly understood. The complex functions of these pleiotropic cytokines include stimulation of innate and adaptive immune responses against tumors as well as direct inhibition of tumor cells. In high-grade, Bacillus Calmette-Guérin (BCG)-unresponsive non-muscle-invasive bladder cancer, nadofaragene firadenovec, a non-replicating adenovirus administered locally to express the IFNα2b transgene, embodies a novel approach to deploy the therapeutic activity of type I IFNs while minimizing systemic toxicities. Deciphering which functions of type I IFN are required for clinical activity will bolster efforts to maximize the efficacy of nadofaragene firadenovec and other type I IFN-based therapies, and inform strategies to address resistance. As such, we characterized the phenotypic and molecular response of human bladder cancer cell lines to IFNα delivered in multiple contexts, including adenoviral delivery. We found that constitutive activation of the type I IFN signaling pathway is a biomarker for resistance to both transcriptional response and direct cytotoxic effects of IFNα. We present several genes that discriminate between sensitive and resistant tumor cells, suggesting they should be explored for utility as biomarkers in future clinical trials of type I IFN-based anti-tumor therapies.
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Affiliation(s)
| | | | - Amy L Klova
- Ferring Research Institute, San Diego, CA, USA
| | | | | | | | | | | | - Jørn S Jakobsen
- Ferring Pharmaceuticals, International PharmaScience Center, Copenhagen, Denmark
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9
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Zhu S, Zhang T, Zheng L, Liu H, Song W, Liu D, Li Z, Pan CX. Combination strategies to maximize the benefits of cancer immunotherapy. J Hematol Oncol 2021; 14:156. [PMID: 34579759 PMCID: PMC8475356 DOI: 10.1186/s13045-021-01164-5] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
Immunotherapies such as immune checkpoint blockade (ICB) and adoptive cell therapy (ACT) have revolutionized cancer treatment, especially in patients whose disease was otherwise considered incurable. However, primary and secondary resistance to single agent immunotherapy often results in treatment failure, and only a minority of patients experience long-term benefits. This review article will discuss the relationship between cancer immune response and mechanisms of resistance to immunotherapy. It will also provide a comprehensive review on the latest clinical status of combination therapies (e.g., immunotherapy with chemotherapy, radiation therapy and targeted therapy), and discuss combination therapies approved by the US Food and Drug Administration. It will provide an overview of therapies targeting cytokines and other soluble immunoregulatory factors, ACT, virotherapy, innate immune modifiers and cancer vaccines, as well as combination therapies that exploit alternative immune targets and other therapeutic modalities. Finally, this review will include the stimulating insights from the 2020 China Immuno-Oncology Workshop co-organized by the Chinese American Hematologist and Oncologist Network (CAHON), the China National Medical Product Administration (NMPA) and Tsinghua University School of Medicine.
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Affiliation(s)
- Shaoming Zhu
- Chinese American Hematologist and Oncologist Network, New York, NY, USA.,Department of Urology, Beijing Chao-Yang Hospital, Beijing, China
| | - Tian Zhang
- Chinese American Hematologist and Oncologist Network, New York, NY, USA.,Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, DUMC 103861, Durham, NC, 27710, USA
| | - Lei Zheng
- Chinese American Hematologist and Oncologist Network, New York, NY, USA.,The Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hongtao Liu
- Chinese American Hematologist and Oncologist Network, New York, NY, USA.,University of Chicago, Chicago, IL, USA
| | - Wenru Song
- Chinese American Hematologist and Oncologist Network, New York, NY, USA.,Kira Pharmaceuticals, Cambridge, MA, USA
| | - Delong Liu
- Chinese American Hematologist and Oncologist Network, New York, NY, USA.,New York Medical College, Valhalla, NY, USA
| | - Zihai Li
- Chinese American Hematologist and Oncologist Network, New York, NY, USA. .,Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA.
| | - Chong-Xian Pan
- Chinese American Hematologist and Oncologist Network, New York, NY, USA. .,Harvard Medical School, West Roxbury, MA, 02132, USA.
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Zhu S, Zhu Z, Ma AH, Sonpavde GP, Cheng F, Pan CX. Preclinical Models for Bladder Cancer Research. Hematol Oncol Clin North Am 2021; 35:613-632. [PMID: 33958154 DOI: 10.1016/j.hoc.2021.02.007] [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] [Indexed: 12/09/2022]
Abstract
At diagnosis, more than 70% of bladder cancers (BCs) are at the non-muscle-invasive bladder cancer (NMIBC) stages, which are usually treated with transurethral resection followed by intravesical instillation. For the remaining advanced cancers, systemic therapy is the standard of care, with addition of radical cystectomy in cases of locally advanced cancer. Because of the difference in treatment modalities, different models are needed to advance the care of NMIBC and advanced BC. This article gives a comprehensive review of both in vitro and in vivo BC models and compares the advantages and drawbacks of these preclinical systems in BC research.
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Affiliation(s)
- Shaoming Zhu
- Department of Urology, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuchang District, Hubei Province, 430060, China; Division of Hematology and Oncology, Department of Internal Medicine, School of Medicine, University of California Davis, Sacramento, USA
| | - Zheng Zhu
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Ai-Hong Ma
- Department of Biochemistry and Molecular Medicine, University of California Davis, 2700 Stockton BLVD, Sacramento, CA 95817, USA
| | - Guru P Sonpavde
- Dana-Farber Cancer Institute, Harvard University, 450 Brookline Ave, Boston, MA 02215, USA
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuchang District, Hubei Province, 430060, China.
| | - Chong-Xian Pan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA; VA Boston Healthcare System, West Roxbury, MA, USA.
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Petroni G, Buqué A, Zitvogel L, Kroemer G, Galluzzi L. Immunomodulation by targeted anticancer agents. Cancer Cell 2021; 39:310-345. [PMID: 33338426 DOI: 10.1016/j.ccell.2020.11.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
Abstract
At odds with conventional chemotherapeutics, targeted anticancer agents are designed to inhibit precise molecular alterations that support oncogenesis or tumor progression. Despite such an elevated degree of molecular specificity, many clinically employed and experimental targeted anticancer agents also mediate immunostimulatory or immunosuppressive effects that (at least in some settings) influence therapeutic efficacy. Here, we discuss the main immunomodulatory effects of targeted anticancer agents and explore potential avenues to harness them in support of superior clinical efficacy.
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Affiliation(s)
- Giulia Petroni
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Aitziber Buqué
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Laurence Zitvogel
- Gustave Roussy Cancer Center, Villejuif, France; INSERM U1015, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France; Faculty of Medicine, Paris-Saclay University, Le Kremlin-Bicêtre, France
| | - Guido Kroemer
- Equipe Labellisée Par La Ligue Contre le Cancer, Centre de Recherche des Cordeliers, INSERM U1138, Université de Paris, Sorbonne Université, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China; Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA; Department of Dermatology, Yale School of Medicine, New Haven, CT, USA; Université de Paris, Paris, France.
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