1
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Li S, Han T. Frequent loss of FAM126A expression in colorectal cancer results in selective FAM126B dependency. iScience 2024; 27:109646. [PMID: 38638566 PMCID: PMC11025007 DOI: 10.1016/j.isci.2024.109646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/01/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Most advanced colorectal cancer (CRC) patients cannot benefit from targeted therapy due to lack of actionable targets. By mining data from the DepMap, we identified FAM126B as a specific vulnerability in CRC cell lines exhibiting low FAM126A expression. Employing a combination of genetic perturbation and inducible protein degradation techniques, we demonstrate that FAM126A and FAM126B function in a redundant manner to facilitate the recruitment of PI4KIIIα to the plasma membrane for PI4P synthesis. Examination of data from TCGA and GTEx revealed that over 7% of CRC tumor samples exhibited loss of FAM126A expression, contrasting with uniform FAM126A expression in normal tissues. In both CRC cell lines and tumor samples, promoter hypermethylation correlated with the loss of FAM126A expression, which could be reversed by DNA methylation inhibitors. In conclusion, our study reveals that loss of FAM126A expression results in FAM126B dependency, thus proposing FAM126B as a therapeutic target for CRC treatment.
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Affiliation(s)
- Shuang Li
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ting Han
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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2
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Kim U, Debnath R, Maiz JE, Rico J, Sinha S, Blanco MA, Chakrabarti R. ΔNp63 regulates MDSC survival and metabolism in triple-negative breast cancer. iScience 2024; 27:109366. [PMID: 38510127 PMCID: PMC10951988 DOI: 10.1016/j.isci.2024.109366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Triple-negative breast cancer (TNBC) contributes greatly to mortality of breast cancer, demanding new targetable options. We have shown that TNBC patients have high ΔNp63 expression in tumors. However, the function of ΔNp63 in established TNBC is yet to be explored. In current studies, targeting ΔNp63 with inducible CRISPR knockout and Histone deacetylase inhibitor Quisinostat showed that ΔNp63 is important for tumor progression and metastasis in established tumors by promoting myeloid-derived suppressor cell (MDSC) survival through tumor necrosis factor alpha. Decreasing ΔNp63 levels are associated with decreased CD4+ and FOXP3+ T-cells but increased CD8+ T-cells. RNA sequencing analysis indicates that loss of ΔNp63 alters multiple MDSC properties such as lipid metabolism, chemotaxis, migration, and neutrophil degranulation besides survival. We further demonstrated that targeting ΔNp63 sensitizes chemotherapy. Overall, we showed that ΔNp63 reprograms the MDSC-mediated immunosuppressive functions in TNBC, highlighting the benefit of targeting ΔNp63 in chemotherapy-resistant TNBC.
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Affiliation(s)
- Ukjin Kim
- Department of Surgery, Sylvester Comprehensive Cancer, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Rahul Debnath
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Javier E. Maiz
- Department of Surgery, Sylvester Comprehensive Cancer, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joshua Rico
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Mario Andrés Blanco
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rumela Chakrabarti
- Department of Surgery, Sylvester Comprehensive Cancer, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Coleman JC, Tattersall L, Yianni V, Knight L, Yu H, Hallett SR, Johnson P, Caetano AJ, Cosstick C, Ridley AJ, Gartland A, Conte MR, Grigoriadis AE. The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis. iScience 2024; 27:109288. [PMID: 38532886 PMCID: PMC10963253 DOI: 10.1016/j.isci.2024.109288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important regulators of cancer pathogenesis. We reveal that the RBPs LARP4A and LARP4B are differentially overexpressed in osteosarcoma and osteosarcoma lung metastases, as well as in prostate cancer. Depletion of LARP4A and LARP4B reduced tumor growth and metastatic spread in xenografts, as well as inhibiting cell proliferation, motility, and migration. Transcriptomic profiling and high-content multiparametric analyses unveiled a central role for LARP4B, but not LARP4A, in regulating cell cycle progression in osteosarcoma and prostate cancer cells, potentially through modulating key cell cycle proteins such as Cyclins B1 and E2, Aurora B, and E2F1. This first systematic comparison between LARP4A and LARP4B assigns new pro-tumorigenic functions to LARP4A and LARP4B in bone and prostate cancer, highlighting their similarities while also indicating distinct functional differences. Uncovering clear biological roles for these paralogous proteins provides new avenues for identifying tissue-specific targets and potential druggable intervention.
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Affiliation(s)
- Jennifer C. Coleman
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Val Yianni
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Laura Knight
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Hongqiang Yu
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Sadie R. Hallett
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Philip Johnson
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Ana J. Caetano
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Charlie Cosstick
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Anne J. Ridley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD UK
| | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
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4
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Shireman JM, White Q, Ni Z, Mohanty C, Cai Y, Zhao L, Agrawal N, Gonugunta N, Wang X, Mccarthy L, Kasulabada V, Pattnaik A, Ahmed AU, Miller J, Kulwin C, Cohen-Gadol A, Payner T, Lin CT, Savage JJ, Lane B, Shiue K, Kamer A, Shah M, Iyer G, Watson G, Kendziorski C, Dey M. Genomic analysis of human brain metastases treated with stereotactic radiosurgery reveals unique signature based on treatment failure. iScience 2024; 27:109601. [PMID: 38623341 PMCID: PMC11016778 DOI: 10.1016/j.isci.2024.109601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Stereotactic radiosurgery (SRS) has been shown to be efficacious for the treatment of limited brain metastasis (BM); however, the effects of SRS on human brain metastases have yet to be studied. We performed genomic analysis on resected brain metastases from patients whose resected lesion was previously treated with SRS. Our analyses demonstrated for the first time that patients possess a distinct genomic signature based on type of treatment failure including local failure, leptomeningeal spread, and radio-necrosis. Examination of the center and peripheral edge of the tumors treated with SRS indicated differential DNA damage distribution and an enrichment for tumor suppressor mutations and DNA damage repair pathways along the peripheral edge. Furthermore, the two clinical modalities used to deliver SRS, LINAC and GK, demonstrated differential effects on the tumor landscape even between controlled primary sites. Our study provides, in human, biological evidence of differential effects of SRS across BM's.
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Affiliation(s)
- Jack M. Shireman
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Quinn White
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Zijian Ni
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Yujia Cai
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Lei Zhao
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Namita Agrawal
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nikita Gonugunta
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Xiaohu Wang
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Liam Mccarthy
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Varshitha Kasulabada
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Akshita Pattnaik
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Atique U. Ahmed
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - James Miller
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Charles Kulwin
- Goodman Campbell Brain and Spine Neurological Surgery, Indianapolis, IN, USA
| | - Aaron Cohen-Gadol
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Troy Payner
- Goodman Campbell Brain and Spine Neurological Surgery, Indianapolis, IN, USA
| | - Chih-Ta Lin
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jesse J. Savage
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Brandon Lane
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kevin Shiue
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aaron Kamer
- Department of Clinical Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mitesh Shah
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Gordon Watson
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
| | - Mahua Dey
- Department of Neurosurgery, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA
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5
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Niu R, Guo Y, Shang X. GLIMS: A two-stage gradual-learning method for cancer genes prediction using multi-omics data and co-splicing network. iScience 2024; 27:109387. [PMID: 38510118 PMCID: PMC10951990 DOI: 10.1016/j.isci.2024.109387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Identifying cancer genes is vital for cancer diagnosis and treatment. However, because of the complexity of cancer occurrence and limited cancer genes knowledge, it is hard to identify cancer genes accurately using only a few omics data, and the overall performance of existing methods is being called for further improvement. Here, we introduce a two-stage gradual-learning strategy GLIMS to predict cancer genes using integrative features from multi-omics data. Firstly, it uses a semi-supervised hierarchical graph neural network to predict the initial candidate cancer genes by integrating multi-omics data and protein-protein interaction (PPI) network. Then, it uses an unsupervised approach to further optimize the initial prediction by integrating the co-splicing network in post-transcriptional regulation, which plays an important role in cancer development. Systematic experiments on multi-omics cancer data demonstrated that GLIMS outperforms the state-of-the-art methods for the identification of cancer genes and it could be a useful tool to help advance cancer analysis.
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Affiliation(s)
- Rui Niu
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
| | - Yang Guo
- School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
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6
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Wu Y, Yang F, Luo S, Li X, Gu Z, Fan R, Cao Y, Wang L, Song X. Single-cell RNA sequencing reveals epithelial cells driving brain metastasis in lung adenocarcinoma. iScience 2024; 27:109258. [PMID: 38433899 PMCID: PMC10905006 DOI: 10.1016/j.isci.2024.109258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/16/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Brain metastases (BM) of lung adenocarcinoma (LUAD) are the most common intracranial malignancy leading to death. However, the cellular origins and drivers of BM from LUAD have not been clarified. Cellular composition was characterized by single-cell sequencing analysis of primary lung adenocarcinoma (pLUAD), BM and lymph node metastasis (LNM) samples in GSE131907. Our study briefly analyzed the tumor microenvironment (TME), focusing on the role of epithelial cells (ECs) in BM. We have discovered a population of brain metastasis-associated epithelial cells (BMAECs) expressing SPP1, SAA1, and CDKN2A, and it has been observed that this population is mainly composed of aneuploid cells from pLUAD, playing a crucial role in brain metastasis. Our study concluded that both LNM and BM in LUAD originated from pLUAD lesions, but there is currently insufficient evidence to prove a direct association between BM lesions and LNM lesions, which provides inspiration for further investigation of the TME in BM.
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Affiliation(s)
- Yonghui Wu
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Graduate School of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fujun Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shilan Luo
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiang Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhan Gu
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rui Fan
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yajuan Cao
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lixin Wang
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiao Song
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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7
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Han H, Sun Y, Wei W, Huang Z, Cheng M, Qiu H, Wang J, Zheng S, Liu L, Zhang Q, Zhang C, Ma J, Guo S, Wang Z, Li Z, Jiang X, Lin S, Liu Q, Zhang S. RNA modification-related genes illuminate prognostic signature and mechanism in esophageal squamous cell carcinoma. iScience 2024; 27:109327. [PMID: 38487015 PMCID: PMC10937836 DOI: 10.1016/j.isci.2024.109327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/06/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
Emerging studies have demonstrated the link between RNA modifications and various cancers, while the predictive value and functional mechanisms of RNA modification-related genes (RMGs) in esophageal squamous cell carcinoma (ESCC) remain unclear. Here we established a prognostic signature for ESCC based on five RMGs. The analysis of ESCC clinical samples further verified the prognostic power of the prognostic signature. Moreover, we found that the knockdown of NSUN6 promotes ESCC progression in vitro and in vivo, whereas the overexpression of NSUN6 inhibits the malignant phenotype of ESCC cells. Mechanically, NSUN6 mediated tRNA m5C modifications selectively enhance the translation efficiency of CDH1 mRNA in a codon dependent manner. Rescue assays revealed that E-cadherin is an essential downstream target that mediates NSUN6's function in the regulation of ESCC progression. These findings offer additional insights into the link between ESCC and RMGs, as well as provide potential strategies for ESCC management and therapy.
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Affiliation(s)
- Hui Han
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yucong Sun
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei Wei
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Maosheng Cheng
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongshen Qiu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Juan Wang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Siyi Zheng
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Lianlian Liu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Qiang Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Canfeng Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Jieyi Ma
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Siyao Guo
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhaoyu Wang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhenpeng Li
- Department of Microsurgery, Orthopedic Trauma and Hand Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xu Jiang
- School of basic medical sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuibin Lin
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Qianwen Liu
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510080, China
- Guangdong Esophageal Cancer Institute, Guangzhou 510080, China
| | - Shuishen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
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8
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Zhang H, Ma S, Wang Y, Chen X, Li Y, Wang M, Xu Y. Development of an obesity-related multi-gene prognostic model incorporating clinical characteristics in luminal breast cancer. iScience 2024; 27:109133. [PMID: 38384850 PMCID: PMC10879711 DOI: 10.1016/j.isci.2024.109133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/13/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Despite adjuvant chemotherapy and endocrine therapy in luminal breast cancer (LBC), relapses are common. Addressing this, we aim to develop a prognostic model to refine adjuvant therapy strategies, particularly for patients at high recurrence risk. Notably, obesity profoundly affects the tumor microenvironment (TME) of LBC. However, it is unclear whether obesity-related biological features can effectively screen high-risk patients. Utilizing weighted gene coexpression network analysis (WGCNA) on RNA sequencing (RNAseq) data, we identified seven obese LBC genes (OLGs) closely associated with patient prognosis. Subsequently, we developed a luminal obesity-gene clinical prognostic index (LOG-CPI), combining a 7-gene signature, TNM staging, and age. Its predictive efficacy was confirmed across validation datasets and a clinical cohort (5-year accuracy = 0.828, 0.760, 0.751, and 0.792, respectively). LOG-CPI emerges as a promising predictor for clinical prognosis and treatment response, helping distinguish molecular and immunological features in LBC patients and guiding clinical practice by identifying varying prognoses.
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Affiliation(s)
- Hengjun Zhang
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Shuai Ma
- Department of Thyroid and Breast Surgery, People’s Hospital of China Medical University (Liaoning Provincial People's Hospital), Shenyang, China
| | - Yusong Wang
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Xiuyun Chen
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Yumeng Li
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Mozhi Wang
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Yingying Xu
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
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9
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Rodriguez E, Lindijer DV, van Vliet SJ, Garcia Vallejo JJ, van Kooyk Y. The transcriptional landscape of glycosylation-related genes in cancer. iScience 2024; 27:109037. [PMID: 38384845 PMCID: PMC10879703 DOI: 10.1016/j.isci.2024.109037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/12/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
Changes in glycosylation patterns have been associated with malignant transformation and clinical outcomes in several cancer types, prompting ongoing research into the mechanisms involved and potential clinical applications. In this study, we performed an extensive transcriptomic analysis of glycosylation-related genes and pathways, using publicly available bulk and single cell transcriptomic datasets from tumor samples and cancer cell lines. We identified genes and pathways strongly associated with different tumor types, which may represent novel diagnostic biomarkers. By using single cell RNA-seq data, we characterized the contribution of different cell types to the overall tumor glycosylation. Transcriptomic analysis of cancer cell lines revealed that they present a simplified landscape of genes compared to tissue. Lastly, we describe the association of different genes and pathways with the clinical outcome of patients. These results can serve as a resource for future research aimed to unravel the role of the glyco-code in cancer.
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Affiliation(s)
- Ernesto Rodriguez
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Dimitri V. Lindijer
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Sandra J. van Vliet
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Juan J. Garcia Vallejo
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Yvette van Kooyk
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
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10
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Xing M, Yao B, Xu J, Lu P, Li Q, Wu D, Chen B, Wei J, Su L, Zhao Q. NatD epigenetically activates FOXA2 expression to promote breast cancer progression by facilitating MMP14 expression. iScience 2024; 27:108840. [PMID: 38303717 PMCID: PMC10830889 DOI: 10.1016/j.isci.2024.108840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/09/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
N-α-acetyltransferase D (NatD) mediates N-α-terminal acetylation of histone H4 (Nt-Ac-H4), but its role in breast cancer metastasis remains unknown. Here, we show that depletion of NatD directly represses the expression of FOXA2, and is accompanied by a significant reduction in Nt-Ac-H4 enrichment at the FOXA2 promoter. We show that NatD is commonly upregulated in primary breast cancer tissues, where its expression level correlates with FOXA2 expression, enhanced invasiveness, and poor clinical outcomes. Furthermore, we show that FOXA2 promotes the migration and invasion of breast cancer cells by activating MMP14 expression. MMP14 is also upregulated in breast cancer tissues, where its expression level correlates with FOXA2 expression and poor clinical prognosis. Our study shows that the NatD-FOXA2-MMP14 axis functions as a key signaling pathway to promote the migratory and invasive capabilities of breast cancer cells, suggesting that NatD is a critical epigenetic modulator of cell invasion during breast cancer progression.
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Affiliation(s)
- Mengying Xing
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Bing Yao
- National Experimental Teaching Center of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Jiaxuan Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Peifen Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Qixiang Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Dongliang Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Bing Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Jiwu Wei
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Lei Su
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology and General Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, Nanjing 210046, China
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11
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Cai M, Luo J, Yang C, Yang X, Zhang C, Ma L, Cheng Y. ABHD12 contributes to tumorigenesis and sorafenib resistance by preventing ferroptosis in hepatocellular carcinoma. iScience 2023; 26:108340. [PMID: 38053637 PMCID: PMC10694648 DOI: 10.1016/j.isci.2023.108340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
Sorafenib induces ferroptosis, making it a useful treatment against advanced liver hepatocellular carcinoma (LIHC). However, sorafenib resistance is extremely common among LIHC patients. Here, we used a comprehensive approach to investigate the effects of ABHD12, which regulates tumorigenesis and sorafenib resistance in LIHC. We validated ABHD12 expression was upregulated in LIHC tissue, which correlated with worse overall survival and related to tumor size or stage. ABHD12 facilitated a pro-tumorigenic phenotype involving increased cell proliferation, migration, and clonogenicity as well as sorafenib resistance. Knockout of ABHD12 sensitized liver cancer cells to sorafenib-induced ferroptosis. Co-delivery of sorafenib and ABHD12 inhibitor into a nude mouse model enhanced therapeutic efficacy for LIHC. Our study demonstrates that ABHD12 contributes to tumor growth and sorafenib resistance in liver cancer, which indicate the promising potential of ABHD12 in diagnosis and prognosis as well as highlight the potential therapeutic applications for co-delivery of sorafenib and ABHD12 inhibitor.
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Affiliation(s)
- Mengxing Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jingwen Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chunxiu Yang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaopeng Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Cheng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yibin Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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12
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Triantafyllidis CP, Barberis A, Hartley F, Cuervo AM, Gjerga E, Charlton P, van Bijsterveldt L, Rodriguez JS, Buffa FM. A machine learning and directed network optimization approach to uncover TP53 regulatory patterns. iScience 2023; 26:108291. [PMID: 38047081 PMCID: PMC10692668 DOI: 10.1016/j.isci.2023.108291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/21/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
TP53, the Guardian of the Genome, is the most frequently mutated gene in human cancers and the functional characterization of its regulation is fundamental. To address this we employ two strategies: machine learning to predict the mutation status of TP53from transcriptomic data, and directed regulatory networks to reconstruct the effect of mutations on the transcipt levels of TP53 targets. Using data from established databases (Cancer Cell Line Encyclopedia, The Cancer Genome Atlas), machine learning could predict the mutation status, but not resolve different mutations. On the contrary, directed network optimization allowed to infer the TP53 regulatory profile across: (1) mutations, (2) irradiation in lung cancer, and (3) hypoxia in breast cancer, and we could observe differential regulatory profiles dictated by (1) mutation type, (2) deleterious consequences of the mutation, (3) known hotspots, (4) protein changes, (5) stress condition (irradiation/hypoxia). This is an important first step toward using regulatory networks for the characterization of the functional consequences of mutations, and could be extended to other perturbations, with implications for drug design and precision medicine.
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Affiliation(s)
- Charalampos P. Triantafyllidis
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Alessandro Barberis
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fiona Hartley
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Ana Miar Cuervo
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Enio Gjerga
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Philip Charlton
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | | | - Julio Saez Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Francesca M. Buffa
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
- Department of Computing Sciences, BIDSA, Bocconi University, Milan, Italy
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13
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Lee SM, Han Y, Cho KH. Deep learning untangles the resistance mechanism of p53 reactivator in lung cancer cells. iScience 2023; 26:108377. [PMID: 38034356 PMCID: PMC10682260 DOI: 10.1016/j.isci.2023.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/12/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Tumor suppressor p53 plays a pivotal role in suppressing cancer, so various drugs has been suggested to upregulate its function. However, drug resistance is still the biggest hurdle to be overcome. To address this, we developed a deep learning model called AnoDAN (anomalous gene detection using generative adversarial networks and graph neural networks for overcoming drug resistance) that unravels the hidden resistance mechanisms and identifies a combinatorial target to overcome the resistance. Our findings reveal that the TGF-β signaling pathway, alongside the p53 signaling pathway, mediates the resistance, with THBS1 serving as a core regulatory target in both pathways. Experimental validation in lung cancer cells confirms the effects of THBS1 on responsiveness to a p53 reactivator. We further discovered the positive feedback loop between THBS1 and the TGF-β pathway as the main source of resistance. This study enhances our understanding of p53 regulation and offers insights into overcoming drug resistance.
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Affiliation(s)
- Soo Min Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Younghyun Han
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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14
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Zhou BW, Wu QQ, Mauki DH, Wang X, Zhang SR, Yin TT, Chen FL, Li C, Liu YH, Wang GD, Zhang YP. Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility. iScience 2023; 26:108431. [PMID: 38205119 PMCID: PMC10777377 DOI: 10.1016/j.isci.2023.108431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/24/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024] Open
Abstract
The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using multi-omics data we identified 11 germline gene fusions (GGFs) in CTVT, which showed higher genetic susceptibility than others. Additionally, we illustrate a mechanism of a complex gene fusion of three gene segments (HSD17B4-DMXL1-TNFAIP8) that we refer to "greedy fusion". Our findings also provided evidence that expressions of GGFs are downregulated during the tumor regressive phase, which is associated with DNA methylation level. This study presents a comprehensive landscape of gene fusions (GFs) in CTVT, which offers a valuable genetic resource for exploring potential genetic mechanisms underlying the development of cancers in both dogs and humans.
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Affiliation(s)
- Bo-Wen Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing-Qin Wu
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - David H. Mauki
- Institute of Neurological Disease, National-Local Joint Engineering Research Center of Translational Medicine, State Key Lab of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Shu-Run Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang-Liang Chen
- Kunming Police Dog Base of the Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Chao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, Yunnan 650500, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
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15
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Li Q, Fan J, Zhou Z, Ma Z, Che Z, Wu Y, Yang X, Liang P, Li H. AID-induced CXCL12 upregulation enhances castration-resistant prostate cancer cell metastasis by stabilizing β-catenin expression. iScience 2023; 26:108523. [PMID: 38162032 PMCID: PMC10755053 DOI: 10.1016/j.isci.2023.108523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Prostate cancer (PCa) is one of the most common malignant diseases of urinary system and has poor prognosis after progression to castration-resistant prostate cancer (CRPC), and increased cytosine methylation heterogeneity is associated with the more aggressive phenotype of PCa cell line. Activation-induced cytidine deaminase (AID) is a multifunctional enzyme and contributes to antibody diversification. However, the dysregulation of AID participates in the progression of multiple diseases and related with certain oncogenes through demethylation. Nevertheless, the role of AID in PCa remains elusive. We observed a significant upregulation of AID expression in PCa samples, which exhibited a negative correlation with E-cadherin expression. Furthermore, AID expression is remarkably higher in CRPC cells than that in HSPC cells, and AID induced the demethylation of CXCL12, which is required to stabilize the Wnt signaling pathway executor β-catenin and EMT procedure. Our study suggests that AID drives CRPC metastasis by demethylation and can be a potential therapeutic target for CRPC.
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Affiliation(s)
- Qi Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
- Department of Urology, TianYou Hospital affiliated to Wuhan University of Science & Technology, Wuhan, Hubei Province, China
| | - Jinfeng Fan
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Zhiyan Zhou
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Zhe Ma
- The First Hospital of Tsinghua University, Beijing, China
| | - Zhifei Che
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Yaoxi Wu
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Xiangli Yang
- Department of Urology, TianYou Hospital affiliated to Wuhan University of Science & Technology, Wuhan, Hubei Province, China
| | - Peiyu Liang
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Haoyong Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
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16
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Plattner C, Lamberti G, Blattmann P, Kirchmair A, Rieder D, Loncova Z, Sturm G, Scheidl S, Ijsselsteijn M, Fotakis G, Noureen A, Lisandrelli R, Böck N, Nemati N, Krogsdam A, Daum S, Finotello F, Somarakis A, Schäfer A, Wilflingseder D, Gonzalez Acera M, Öfner D, Huber LA, Clevers H, Becker C, Farin HF, Greten FR, Aebersold R, de Miranda NF, Trajanoski Z. Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer. iScience 2023; 26:108399. [PMID: 38047086 PMCID: PMC10692669 DOI: 10.1016/j.isci.2023.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/21/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.
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Affiliation(s)
- Christina Plattner
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Giorgia Lamberti
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Scheidl
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Asma Noureen
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rebecca Lisandrelli
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Böck
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Niloofar Nemati
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sophia Daum
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander Schäfer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Miguel Gonzalez Acera
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Dietmar Öfner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas A. Huber
- Biocenter, Institute of Cell Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hans Clevers
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Christoph Becker
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Noel F.C.C. de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
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17
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Fu Z, Gao C, Wu T, Wang L, Li S, Zhang Y, Shi C. Peripheral neuropathy associated with monomethyl auristatin E-based antibody-drug conjugates. iScience 2023; 26:107778. [PMID: 37727735 PMCID: PMC10505985 DOI: 10.1016/j.isci.2023.107778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Since the successful approval of gemtuzumab ozogamicin, antibody-drug conjugates (ADCs) have emerged as a pivotal category of targeted therapies for cancer. Among these ADCs, the use of monomethyl auristatin E (MMAE) as a payload is prevalent in the development of ADC drugs, which has significantly improved overall therapeutic efficacy against various malignancies. However, increasing clinical observations have raised concerns regarding the potential nervous system toxicity associated with MMAE-based ADCs. Specifically, a higher incidence of peripheral neuropathy has been reported in ADCs incorporating MMAE as payloads. Considering the increasing global use of MMAE-based ADCs, it is imperative to provide an inclusive overview of diagnostic and management strategies for this adverse event. In this review, we examine current information and what future research directions are required to better understand and manage this type of clinical challenge.
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Affiliation(s)
- Zhiwen Fu
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
| | - Chen Gao
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
| | - Tingting Wu
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
| | - Lulu Wang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
| | - Shijun Li
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
| | - Yu Zhang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
| | - Chen Shi
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430000, China
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18
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He Z, Zhang K, Zhao N, Wang Y, Hou W, Meng Q, Li C, Chen J, Li J. Deep learning for real-time detection of nasopharyngeal carcinoma during nasopharyngeal endoscopy. iScience 2023; 26:107463. [PMID: 37720094 PMCID: PMC10502364 DOI: 10.1016/j.isci.2023.107463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 09/19/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is known for high curability during early stage of the disease, and early diagnosis relies on nasopharyngeal endoscopy and subsequent pathological biopsy. To enhance the early diagnosis rate by aiding physicians in the real-time identification of NPC and directing biopsy site selection during endoscopy, we assembled a dataset comprising 2,429 nasopharyngeal endoscopy video frames from 690 patients across three medical centers. With these data, we developed a deep learning-based NPC detection model using the you only look once (YOLO) network. Our model demonstrated high performance, with precision, recall, mean average precision, and F1-score values of 0.977, 0.943, 0.977, and 0.960, respectively, for internal test set and 0.825, 0.743, 0.814, and 0.780 for external test set at 0.5 intersection over union. Remarkably, our model demonstrated a high inference speed (52.9 FPS), surpassing the average frame rate (25.0 FPS) of endoscopy videos, thus making real-time detection in endoscopy feasible.
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Affiliation(s)
- Zicheng He
- Department of Otolaryngology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou Key Laboratory of Otorhinolaryngology, Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou 510080, P.R.China
- Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning 530000, P.R.China
| | - Kai Zhang
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R.China
| | - Nan Zhao
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R.China
| | - Yongquan Wang
- Department of Otolaryngology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou Key Laboratory of Otorhinolaryngology, Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou 510080, P.R.China
| | | | - Qinxiang Meng
- Guangzhou First People’s Hospital, Guangzhou 510180, P.R.China
| | - Chunwei Li
- Department of Otolaryngology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou Key Laboratory of Otorhinolaryngology, Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou 510080, P.R.China
| | - Junzhou Chen
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R.China
| | - Jian Li
- Department of Otolaryngology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou Key Laboratory of Otorhinolaryngology, Otorhinolaryngology Institute of Sun Yat-sen University, Guangzhou 510080, P.R.China
- Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning 530000, P.R.China
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19
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Purwin TJ, Caksa S, Sacan A, Capparelli C, Aplin AE. Gene signature reveals decreased SOX10-dependent transcripts in malignant cells from immune checkpoint inhibitor-resistant cutaneous melanomas. iScience 2023; 26:107472. [PMID: 37636077 PMCID: PMC10450419 DOI: 10.1016/j.isci.2023.107472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/18/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Evidence is mounting for cross-resistance between immune checkpoint and targeted kinase inhibitor therapies in cutaneous melanoma patients. Since the loss of the transcription factor, SOX10, causes tolerance to MAPK pathway inhibitors, we used bioinformatic techniques to determine if reduced SOX10 expression/activity is associated with immune checkpoint inhibitor resistance. We integrated SOX10 ChIP-seq, knockout RNA-seq, and knockdown ATAC-seq data from melanoma cell models to develop a robust SOX10 gene signature. We used computational methods to validate this signature as a measure of SOX10-dependent activity in independent single-cell and bulk RNA-seq SOX10 knockdown, cell line panel, and MAPK inhibitor drug-resistant datasets. Evaluation of patient single-cell RNA-seq data revealed lower levels of SOX10-dependent transcripts in immune checkpoint inhibitor-resistant tumors. Our results suggest that SOX10-deficient melanoma cells are associated with cross-resistance between targeted and immune checkpoint inhibitors and highlight the need to identify therapeutic strategies that target this subpopulation.
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Affiliation(s)
- Timothy J. Purwin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
| | - Signe Caksa
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ahmet Sacan
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
| | - Claudia Capparelli
- Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew E. Aplin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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20
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Liang Y, Cui J, Ding F, Zou Y, Guo H, Man Q, Chang S, Gao S, Hao J. A new staging system for postoperative prognostication in pancreatic ductal adenocarcinoma. iScience 2023; 26:107589. [PMID: 37664604 PMCID: PMC10469961 DOI: 10.1016/j.isci.2023.107589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/09/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
The current TNM staging system for pancreatic ductal adenocarcinoma (PDAC) has revised the definitions of T and N categories as well as stage groups. However, studies validating these modifications have yielded inconsistent results. The existing TNM staging system in prognostic prediction remains unsatisfactory. The prognosis of PDAC is closely associated with pathological and biological factors. Herein, we propose a new staging system incorporating distant metastasis, postoperative serum levels of CA19-9 and CEA, tumor size, lymph node metastasis, lymphovascular involvement, and perineural invasion to enhance the accuracy of prognosis assessment. The proposed staging system exhibited a strong correlation with both overall survival and recurrence-free survival, effectively stratifying survival into five distinct tiers. Additionally, it had favorable discrimination and calibration. Thus, the proposed staging system demonstrates superior prognostic performance compared to the TNM staging system, and can serve as a valuable complementary tool to address the limitations of TNM staging in prognostication.
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Affiliation(s)
- Yuexiang Liang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
- Department of Gastrointestinal Oncology Surgery, Center of Cancer Prevention and Therapy, the First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Jingli Cui
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
- Department of General Surgery, Weifang People’s Hospital, Weifang 261044, China
| | - Fanghui Ding
- Department of General Surgery, the First Hospital of Lanzhou University, Lanzhou 730013, China
| | - Yiping Zou
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
| | - Hanhan Guo
- Department of Gastrointestinal Oncology Surgery, Center of Cancer Prevention and Therapy, the First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Quan Man
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
| | - Shaofei Chang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
- Department of Gastrointestinal Pancreatic Surgery, Shanxi Provincial People’s Hospital, Taiyuan 030012, China
| | - Song Gao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center For Cancer, Tianjin 30060, China
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21
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Moysiadis T, Koparanis D, Liapis K, Ganopoulou M, Vrachiolias G, Katakis I, Moyssiadis C, Vizirianakis IS, Angelis L, Fokianos K, Kotsianidis I. A personalized stepwise dynamic predictive algorithm of the time to first treatment in chronic lymphocytic leukemia. iScience 2023; 26:107591. [PMID: 37664638 PMCID: PMC10470317 DOI: 10.1016/j.isci.2023.107591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/27/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Personalized prediction is ideal in chronic lymphocytic leukemia (CLL). Although refined models have been developed, stratifying patients in risk groups, it is required to accommodate time-dependent information of patients, to address the clinical heterogeneity observed within these groups. In this direction, this study proposes a personalized stepwise dynamic predictive algorithm (PSDPA) for the time-to-first-treatment of the individual patient. The PSDPA introduces a personalized Score, reflecting the evolution in the patient's follow-up, employed to develop a reference pool of patients. Score evolution's similarity is used to predict, at a selected time point, the time-to-first-treatment for a new patient. Additional patient's biological information may be utilized. The algorithm was applied to 20 CLL patients, indicating that stricter assessment criteria for the Score evolution's similarity, and biological similarity exploitation, may improve prediction. The PSDPA capitalizes on both the follow-up and the biological background of the individual patient, dynamically promoting personalized prediction in CLL.
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Affiliation(s)
- Theodoros Moysiadis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace Medical School, 68100 Alexandroupolis, Greece
| | - Dimitris Koparanis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace Medical School, 68100 Alexandroupolis, Greece
| | - Konstantinos Liapis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace Medical School, 68100 Alexandroupolis, Greece
| | - Maria Ganopoulou
- School of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - George Vrachiolias
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace Medical School, 68100 Alexandroupolis, Greece
| | - Ioannis Katakis
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, 2417 Nicosia, Cyprus
| | - Chronis Moyssiadis
- School of Mathematics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis S. Vizirianakis
- School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Department of Health Sciences, School of Life and Health Sciences, University of Nicosia, 2417 Nicosia, Cyprus
| | - Lefteris Angelis
- School of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | | | - Ioannis Kotsianidis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace Medical School, 68100 Alexandroupolis, Greece
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22
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Wang H, Liu B, Long J, Yu J, Ji X, Li J, Zhu N, Zhuang X, Li L, Chen Y, Liu Z, Wang S, Zhao S. Integrative analysis identifies two molecular and clinical subsets in Luminal B breast cancer. iScience 2023; 26:107466. [PMID: 37636034 PMCID: PMC10448479 DOI: 10.1016/j.isci.2023.107466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/30/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Comprehensive multiplatform analysis of Luminal B breast cancer (LBBC) specimens identifies two molecularly distinct, clinically relevant subtypes: Cluster A associated with cell cycle and metabolic signaling and Cluster B with predominant epithelial mesenchymal transition (EMT) and immune response pathways. Whole-exome sequencing identified significantly mutated genes including TP53, PIK3CA, ERBB2, and GATA3 with recurrent somatic mutations. Alterations in DNA methylation or transcriptomic regulation in genes (FN1, ESR1, CCND1, and YAP1) result in tumor microenvironment reprogramming. Integrated analysis revealed enriched biological pathways and unexplored druggable targets (cancer-testis antigens, metabolic enzymes, kinases, and transcription regulators). A systematic comparison between mRNA and protein displayed emerging expression patterns of key therapeutic targets (CD274, YAP1, AKT1, and CDH1). A potential ceRNA network was developed with a significantly different prognosis between the two subtypes. This integrated analysis reveals a complex molecular landscape of LBBC and provides the utility of targets and signaling pathways for precision medicine.
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Affiliation(s)
- Huina Wang
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Bo Liu
- School of Mathematical and Computational Sciences, Massey University, Palmerston North 4472, New Zealand
| | - Junqi Long
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Jiangyong Yu
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xinchan Ji
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Jinmeng Li
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Nian Zhu
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Xujie Zhuang
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Lujia Li
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Yuhaoran Chen
- School of Software Engineering, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Zhidong Liu
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Shu Wang
- Breast Disease Center, Peking University People’s Hospital, Peking University, Beijing 100044, China
| | - Shuangtao Zhao
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
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23
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Liu G, Bu C, Guo G, Zhang Z, Sheng Z, Deng K, Wu S, Xu S, Bu Y, Gao Y, Wang M, Liu G, Kong L, Li T, Li M, Bu X. Molecular and clonal evolution in vivo reveal a common pathway of distant relapse gliomas. iScience 2023; 26:107528. [PMID: 37649695 PMCID: PMC10462858 DOI: 10.1016/j.isci.2023.107528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 06/18/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023] Open
Abstract
The evolutionary trajectories of genomic alterations underlying distant recurrence in glioma remain largely unknown. To elucidate glioma evolution, we analyzed the evolutionary trajectories of matched pairs of primary tumors and relapse tumors or tumor in situ fluid (TISF) based on deep whole-genome sequencing data (ctDNA). We found that MMR gene mutations occurred in the late stage in IDH-mutant glioma during gene evolution, which activates multiple signaling pathways and significantly increases distant recurrence potential. The proneural subtype characterized by PDGFRA amplification was likely prone to hypermutation and distant recurrence following treatment. The classical and mesenchymal subtypes tended to progress locally through subclonal reconstruction, trunk genes transformation, and convergence evolution. EGFR and NOTCH signaling pathways and CDNK2A mutation play an important role in promoting tumor local progression. Glioma subtypes displayed distinct preferred evolutionary patterns. ClinicalTrials.gov, NCT05512325.
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Affiliation(s)
- Guanzheng Liu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Chaojie Bu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Guangzhong Guo
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Zhiyue Zhang
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Zhiyuan Sheng
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Kaiyuan Deng
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Shuang Wu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Sensen Xu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Yage Bu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Yushuai Gao
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Meiyun Wang
- Department of Radiology, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Gang Liu
- Department of Center for Clinical Single Cell Biomedicine, Clinical Research Center, Department of Oncology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou 450003, China
| | - Lingfei Kong
- Department of Pathology, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Tianxiao Li
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Ming Li
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Xingyao Bu
- Department of Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People’s Hospital, Zhengzhou 450003, China
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24
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Abdel-Hafiz HA, Kailasam Mani SK, Huang W, Gouin KH, Chang Y, Xiao T, Ma Q, Li Z, Knott SR, Theodorescu D. Single-cell profiling of murine bladder cancer identifies sex-specific transcriptional signatures with prognostic relevance. iScience 2023; 26:107703. [PMID: 37701814 PMCID: PMC10494466 DOI: 10.1016/j.isci.2023.107703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/18/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Bladder cancer (BLCA) is more common in men but more aggressive in women. Sex-based differences in cancer biology are commonly studied using a murine model with BLCA generated by N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN). While tumors in the BBN model have been profiled, these profiles provide limited information on the tumor microenvironment. Here, we applied single-cell RNA sequencing to characterize cell-type specific transcriptional differences between male and female BBN-induced tumors. We found proportional and gene expression differences in epithelial and non-epithelial subpopulations between male and female tumors. Expression of several genes predicted sex-specific survival in several human BLCA datasets. We identified novel and clinically relevant sex-specific transcriptional signatures including immune cells in the tumor microenvironment and it validated the relevance of the BBN model for studying sex differences in human BLCA. This work highlights the importance of considering sex as a biological variable in the development of new and accurate cancer markers.
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Affiliation(s)
- Hany A. Abdel-Hafiz
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | | | - Wesley Huang
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kenneth H. Gouin
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yuzhou Chang
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center – The James, Columbus, OH 43210, USA
| | - Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center – The James, Columbus, OH 43210, USA
| | - Qin Ma
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center – The James, Columbus, OH 43210, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center – The James, Columbus, OH 43210, USA
| | - Simon R.V. Knott
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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25
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Riley-Gillis B, Tsaih SW, King E, Wollenhaupt S, Reeb J, Peck AR, Wackman K, Lemke A, Rui H, Dezso Z, Flister MJ. Machine learning reveals genetic modifiers of the immune microenvironment of cancer. iScience 2023; 26:107576. [PMID: 37664640 PMCID: PMC10470213 DOI: 10.1016/j.isci.2023.107576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Heritability in the immune tumor microenvironment (iTME) has been widely observed yet remains largely uncharacterized. Here, we developed a machine learning approach to map iTME modifiers within loci from genome-wide association studies (GWASs) for breast cancer (BrCa) incidence. A random forest model was trained on a positive set of immune-oncology (I-O) targets, and then used to assign I-O target probability scores to 1,362 candidate genes in linkage disequilibrium with 155 BrCa GWAS loci. Cluster analysis of the most probable candidates revealed two subfamilies of genes related to effector functions and adaptive immune responses, suggesting that iTME modifiers impact multiple aspects of anticancer immunity. Two of the top ranking BrCa candidates, LSP1 and TLR1, were orthogonally validated as iTME modifiers using BrCa patient biopsies and comparative mapping studies, respectively. Collectively, these data demonstrate a robust and flexible framework for functionally fine-mapping GWAS risk loci to identify translatable therapeutic targets.
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Affiliation(s)
- Bridget Riley-Gillis
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Shirng-Wern Tsaih
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Emily King
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Amy R. Peck
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kelsey Wackman
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela Lemke
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Zoltan Dezso
- Genomics Research Center, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA 94080, USA
| | - Michael J. Flister
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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26
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Jethalia M, Jani SP, Ceccarelli M, Mall R. Pancancer network analysis reveals key master regulators for cancer invasiveness. J Transl Med 2023; 21:558. [PMID: 37599366 PMCID: PMC10440887 DOI: 10.1186/s12967-023-04435-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Tumor invasiveness reflects numerous biological changes, including tumorigenesis, progression, and metastasis. To decipher the role of transcriptional regulators (TR) involved in tumor invasiveness, we performed a systematic network-based pan-cancer assessment of master regulators of cancer invasiveness. MATERIALS AND METHODS We stratified patients in The Cancer Genome Atlas (TCGA) into invasiveness high (INV-H) and low (INV-L) groups using consensus clustering based on an established robust 24-gene signature to determine the prognostic association of invasiveness with overall survival (OS) across 32 different cancers. We devise a network-based protocol to identify TRs as master regulators (MRs) unique to INV-H and INV-L phenotypes. We validated the activity of MRs coherently associated with INV-H phenotype and worse OS across cancers in TCGA on a series of additional datasets in the Prediction of Clinical Outcomes from the Genomic Profiles (PRECOG) repository. RESULTS Based on the 24-gene signature, we defined the invasiveness score for each patient sample and stratified patients into INV-H and INV-L clusters. We observed that invasiveness was associated with worse survival outcomes in almost all cancers and had a significant association with OS in ten out of 32 cancers. Our network-based framework identified common invasiveness-associated MRs specific to INV-H and INV-L groups across the ten prognostic cancers, including COL1A1, which is also part of the 24-gene signature, thus acting as a positive control. Downstream pathway analysis of MRs specific to INV-H phenotype resulted in the identification of several enriched pathways, including Epithelial into Mesenchymal Transition, TGF-β signaling pathway, regulation of Toll-like receptors, cytokines, and inflammatory response, and selective expression of chemokine receptors during T-cell polarization. Most of these pathways have connotations of inflammatory immune response and feasibility for metastasis. CONCLUSION Our pan-cancer study provides a comprehensive master regulator analysis of tumor invasiveness and can suggest more precise therapeutic strategies by targeting the identified MRs and downstream enriched pathways for patients across multiple cancers.
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Affiliation(s)
- Mahesh Jethalia
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Siddhi P Jani
- Centre of Brain Research, Indian Institute of Sciences, Bangalore, Karnataka, India
- Institute of Science, Nirma University, Ahmedabad, India
| | - Michele Ceccarelli
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Raghvendra Mall
- St. Jude Children's Hospital, Memphis, TN, USA.
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates.
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27
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Zhang G, Liu B, Yang Y, Xie S, Chen L, Luo H, Zhong J, Wei Y, Guo F, Gan J, Zhu F, Xu L, Li Q, Shen Y, Zhang H, Liu Y, Li R, Deng H, Yang H. Mitochondrial UQCC3 controls embryonic and tumor angiogenesis by regulating VEGF expression. iScience 2023; 26:107370. [PMID: 37539028 PMCID: PMC10393800 DOI: 10.1016/j.isci.2023.107370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/05/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
Mitochondria play important roles in angiogenesis. However, the mechanisms remain elusive. In this study, we found that mitochondrial ubiquinol-cytochrome c reductase complex assembly factor 3 (UQCC3) is a key regulator of angiogenesis. TALEN-mediated knockout of Uqcc3 in mice caused embryonic lethality at 9.5-10.5 days postcoitum, and vessel density was dramatically reduced. Similarly, knockout of uqcc3 in zebrafish induced lethality post-fertilization and impaired vascular development. Knockout of UQCC3 resulted in slower tumor growth and angiogenesis. Mechanistically, UQCC3 was upregulated under hypoxia, promoted reactive oxygen species (ROS) generation, enhanced HIF-1α stability and increased VEGF expression. Finally, higher expression of UQCC3 was associated with poor prognosis in multiple types tumors, implying a role for UQCC3 in tumor progression. In conclusion, our findings highlight the important contribution of UQCC3 to angiogenesis under both physiological and pathological conditions, indicating the potential of UQCC3 as a therapeutic target for cancer.
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Affiliation(s)
- Guimin Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Binrui Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yun Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shuo Xie
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lingcheng Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hui Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jian Zhong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yinhao Wei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fengzhu Guo
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jia Gan
- Department of Pathology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R.China
| | - Fan Zhu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lin Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiqi Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuge Shen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huajin Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rong Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hanshuo Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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28
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Koch J, Neuberger M, Schmidt-Dengler M, Xu J, Carneiro VC, Ellinger J, Kriegmair MC, Nuhn P, Erben P, Michel MS, Helm M, Rodríguez-Paredes M, Nientiedt M, Lyko F. Reinvestigating the clinical relevance of the m 6A writer METTL3 in urothelial carcinoma of the bladder. iScience 2023; 26:107300. [PMID: 37554463 PMCID: PMC10405067 DOI: 10.1016/j.isci.2023.107300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/13/2023] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
METTL3 is the major writer of N6-Methyladenosine (m6A) and has been associated with controversial roles in cancer. This is best illustrated in urothelial carcinoma of the bladder (UCB), where METTL3 was described to have both oncogenic and tumor-suppressive functions. Here, we reinvestigated the role of METTL3 in UCB. METTL3 knockout reduced the oncogenic phenotype and m6A levels of UCB cell lines. However, complete depletion of METTL3/m6A was not achieved due to selection of cells expressing alternative METTL3 isoforms. Systematic vulnerability and inhibitor response analyses suggested that uroepithelial cells depend on METTL3 for viability. Furthermore, expression and survival analyses of clinical data revealed a complex role for METTL3 in UCB, with decreased m6A mRNA levels in UCB tumors. Our results suggest that METTL3 expression may be a suitable diagnostic UCB biomarker, as the enzyme promotes UCB formation. However, the suitability of the enzyme as a therapeutic target should be evaluated carefully.
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Affiliation(s)
- Jonas Koch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Manuel Neuberger
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Martina Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Jinyun Xu
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Vitor Coutinho Carneiro
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, 53127 Bonn, Germany
| | - Maximilian C. Kriegmair
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Philipp Nuhn
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Philipp Erben
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Maurice Stephan Michel
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Malin Nientiedt
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
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29
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Chen Y, Wen Y, Xie C, Chen X, He S, Bo X, Zhang Z. MOCSS: Multi-omics data clustering and cancer subtyping via shared and specific representation learning. iScience 2023; 26:107378. [PMID: 37559907 PMCID: PMC10407241 DOI: 10.1016/j.isci.2023.107378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/23/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023] Open
Abstract
Cancer is an extremely complex disease and each type of cancer usually has several different subtypes. Multi-omics data can provide more comprehensive biological information for identifying and discovering cancer subtypes. However, existing unsupervised cancer subtyping methods cannot effectively learn comprehensive shared and specific information of multi-omics data. Therefore, a novel method is proposed based on shared and specific representation learning. For each omics data, two autoencoders are applied to extract shared and specific information, respectively. To reduce redundancy and mutual interference, orthogonality constraint is introduced to separate shared and specific information. In addition, contrastive learning is applied to align the shared information and strengthen their consistency. Finally, the obtained shared and specific information for all samples are used for clustering tasks to achieve cancer subtyping. Experimental results demonstrate that the proposed method can effectively capture shared and specific information of multi-omics data and outperform other state-of-the-art methods on cancer subtyping.
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Affiliation(s)
- Yuxin Chen
- School of Informatics, Xiamen University, Xiamen 361005, China
| | - Yuqi Wen
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Chenyang Xie
- School of Informatics, Xiamen University, Xiamen 361005, China
| | - Xinjian Chen
- School of Informatics, Xiamen University, Xiamen 361005, China
| | - Song He
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Zhongnan Zhang
- School of Informatics, Xiamen University, Xiamen 361005, China
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30
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Liu C, Ding X, Li G, Zhang Y, Shao Y, Liu L, Zhang W, Ma Y, Guan W, Wang L, Xu Z, Chang Y, Zhang Y, Jiang B, Yin Q, Tao R. Targeting Bcl-xL is a potential therapeutic strategy for extranodal NK/T cell lymphoma. iScience 2023; 26:107369. [PMID: 37539026 PMCID: PMC10393801 DOI: 10.1016/j.isci.2023.107369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
Extranodal natural killer/T cell lymphoma, nasal type (ENKTL) is an aggressive lymphoid malignancy with a poor prognosis and lacks standard treatment. Targeted therapies are urgently needed. Here we systematically investigated the druggable mechanisms through chemogenomic screening and identified that Bcl-xL-specific BH3 mimetics effectively induced ENKTL cell apoptosis. Notably, the specific accumulation of Bcl-xL, but not other Bcl-2 family members, was verified in ENKTL cell lines and patient tissues. Furthermore, Bcl-xL high expression was shown to be closely associated with worse patient survival. The critical role of Bcl-xL in ENKTL cell survival was demonstrated utilizing selective inhibitors, genetic silencing, and a specific degrader. Additionally, the IL2-JAK1/3-STAT5 signaling was implicated in Bcl-xL dysregulation. In vivo, Bcl-xL inhibition reduced tumor burden, increased apoptosis, and prolonged survival in ENKTL cell line xenograft and patient-derived xenograft models. Our study indicates Bcl-xL as a promising therapeutic target for ENKTL, warranting monitoring in ongoing clinical trials by targeting Bcl-xL.
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Affiliation(s)
- Chuanxu Liu
- Department of Lymphoma, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xinyu Ding
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gaoyang Li
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Youping Zhang
- Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Yubao Shao
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Linyi Liu
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenhao Zhang
- Department of Lymphoma, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Yujie Ma
- Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Wenbin Guan
- Department of Pathology, Xinhua Hospital of Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Lifeng Wang
- Department of Pathology, Xinhua Hospital of Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Zhongli Xu
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - YungTing Chang
- Department of Pharmacy, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yongqiang Zhang
- State Key Laboratory of Bioengineering Reactor, Shanghai Key Laboratory of New Drug Design and School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qianqian Yin
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Rong Tao
- Department of Lymphoma, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Hematology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
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31
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Wu HW, Wu JD, Yeh YP, Wu TH, Chao CH, Wang W, Chen TW. DoSurvive: A webtool for investigating the prognostic power of a single or combined cancer biomarker. iScience 2023; 26:107269. [PMID: 37609633 PMCID: PMC10440714 DOI: 10.1016/j.isci.2023.107269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/26/2023] [Accepted: 06/28/2023] [Indexed: 08/24/2023] Open
Abstract
We present DoSurvive, a user-friendly survival analysis web tool and a cancer prognostic biomarker centered database. DoSurvive is the first database that allows users to perform multivariant survival analysis for cancers with customized gene/patient list. DoSurvive offers three survival analysis methods, Log rank test, Cox regression and accelerated failure time model (AFT), for users to analyze five types of quantitative features (mRNA, miRNA, lncRNA, protein and methylation of CpG islands) with four survival types, i.e. overall survival, disease-specific survival, disease-free interval, and progression-free interval, in 33 cancer types. Notably, the implemented AFT model provides an alternative method for genes/features which failed the proportional hazard assumption in Cox regression. With the unprecedented number of survival models implemented and high flexibility in analysis, DoSurvive is a unique platform for the identification of clinically relevant targets for cancer researcher and practitioners. DoSurvive is freely available at http://dosurvive.lab.nycu.edu.tw/.
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Affiliation(s)
- Hao-Wei Wu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jian-De Wu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yen-Ping Yeh
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Timothy H. Wu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Hong Chao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Weijing Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
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32
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Li Y, Huang H, Zhu Z, Chen S, Liang Y, Shu L. TSC22D3 as an immune-related prognostic biomarker for acute myeloid leukemia. iScience 2023; 26:107451. [PMID: 37575189 PMCID: PMC10415931 DOI: 10.1016/j.isci.2023.107451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Acute myeloid leukemia (AML) is the type of hematologic neoplasm most common in adults. Glucocorticoid-induced gene TSC22D3 regulates cell proliferation through its function as a transcription factor. However, there is no consensus on the prognostic and immunoregulatory significance of TSC22D3 in AML. In the present study, we evaluated the correlation between TSC22D3 expression, immunoinfiltration, and prognostic significance in AML. Knockdown of TSC22D3 significantly attenuated the proliferation of Hel cells and increased sensitivity to cytarabine (Ara-c) drugs. Furthermore, TSC22D3 reduced the release of interleukin-1β (IL-1β) by inhibiting the NF-κB/NLRP3 signaling pathway, thereby inhibiting macrophage polarization to M1 subtype, and attenuating the pro-inflammatory tumor microenvironment. In conclusion, this study identified TSC22D3 as an immune-related prognostic biomarker for AML patients and suggested that therapeutic targeting of TSC22D3 may be a potential treatment option for AML through tumor immune escape.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Hematological Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Hanying Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Hematological Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Ziang Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Hematological Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Shuzhao Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Hematological Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Yang Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Hematological Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Lingling Shu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Hematological Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong 999077, P.R. China
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Zhang P, Tao C, Shimura T, Huang AC, Kong N, Dai Y, Yao S, Xi Y, Wang X, Fang J, Moses MA, Guo P. ICAM1 antibody drug conjugates exert potent antitumor activity in papillary and anaplastic thyroid carcinoma. iScience 2023; 26:107272. [PMID: 37520726 PMCID: PMC10371847 DOI: 10.1016/j.isci.2023.107272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Treatment options for anaplastic thyroid cancer (ATC) and refractory papillary thyroid carcinoma (PTC) are limited and outcomes remain poor. In this study, we determined via bioinformatic expression analyses and immunohistochemistry staining that intercellular adhesion molecule-1(ICAM1) is an attractive target for ATC and PTC. We designed and engineered two ICAM1-directed antibody-drug conjugate (I1-MMAE and I1-DXd), both of which potently and selectively ablate multiple human ATC and PTC cell lines without affecting non-plastic cells in vitro. Furthermore, I1-MMAE and I1-DXd mediated a potent tumor regression in ATC and PTC xenograft models. To develop a precision medicine, we also explored magnetic resonance imaging (MRI) as a non-invasive biomarker detection method to quantitatively map ICAM1 antigen expression in heterogeneous thyroid tumors. Taken together, this study provides a strong rationale for the further development of I1-MMAE and I1-DXd as promising therapeutic candidates to treat advanced PTC and ATC.
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Affiliation(s)
- Peng Zhang
- Department of Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Changjuan Tao
- Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Radiation Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | | | - Nana Kong
- MabPlex International, Yantai, Shandong 264006, China
| | - Yujie Dai
- MabPlex International, Yantai, Shandong 264006, China
| | - Shili Yao
- School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yun Xi
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Xing Wang
- Department of Head and Neck Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Jianmin Fang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Marsha A. Moses
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peng Guo
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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34
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Guccini I, Tang G, To TT, Di Rito L, Le Blanc S, Strobel O, D’Ambrosio M, Pasquini E, Bolis M, Silva P, Kabakci HA, Godbersen S, Alimonti A, Schwank G, Stoffel M. Genetic ablation of ketohexokinase C isoform impairs pancreatic cancer development. iScience 2023; 26:107368. [PMID: 37559908 PMCID: PMC10407955 DOI: 10.1016/j.isci.2023.107368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
Although dietary fructose is associated with an elevated risk for pancreatic cancer, the underlying mechanisms remain elusive. Here, we report that ketohexokinase (KHK), the rate-limiting enzyme of fructose metabolism, is a driver of PDAC development. We demonstrate that fructose triggers KHK and induces fructolytic gene expression in mouse and human PDAC. Genetic inactivation of KhkC enhances the survival of KPC-driven PDAC even in the absence of high fructose diet. Furthermore, it decreases the viability, migratory capability, and growth of KPC cells in a cell autonomous manner. Mechanistically, we demonstrate that genetic ablation of KHKC strongly impairs the activation of KRAS-MAPK pathway and of rpS6, a downstream target of mTORC signaling. Moreover, overexpression of KHKC in KPC cells enhances the downstream KRAS pathway and cell viability. Our data provide new insights into the role of KHK in PDAC progression and imply that inhibiting KHK could have profound implications for pancreatic cancer therapy.
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Affiliation(s)
- Ilaria Guccini
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Guanghui Tang
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Trang Thuy To
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Laura Di Rito
- Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, 20156 Milano, Italy
| | - Solange Le Blanc
- European Pancreas Center, Department of General Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Oliver Strobel
- European Pancreas Center, Department of General Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Mariantonietta D’Ambrosio
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), 6500 Bellinzona, Switzerland
- Universita’ della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), 6500 Bellinzona, Switzerland
- Universita’ della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Marco Bolis
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), 6500 Bellinzona, Switzerland
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, TI, 6500 Bellinzona, Switzerland
| | - Pamuditha Silva
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Hasan Ali Kabakci
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Svenja Godbersen
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Andrea Alimonti
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), 6500 Bellinzona, Switzerland
- Universita’ della Svizzera Italiana, 6900 Lugano, Switzerland
- Department of Medicine, University of Padua, 35128 Padua, Italy
- Department of Health Sciences and Technology (D-HEST) ETH Zurich, 8093 Zurich, Switzerland
| | - Gerald Schwank
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
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Zhang S, Deshpande A, Verma BK, Wang H, Mi H, Yuan L, Ho WJ, Jaffee EM, Zhu Q, Anders RA, Yarchoan M, Kagohara LT, Fertig EJ, Popel AS. Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial. bioRxiv 2023:2023.08.11.553000. [PMID: 37645761 PMCID: PMC10462044 DOI: 10.1101/2023.08.11.553000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Human clinical trials are important tools to advance novel systemic therapies improve treatment outcomes for cancer patients. The few durable treatment options have led to a critical need to advance new therapeutics in hepatocellular carcinoma (HCC). Recent human clinical trials have shown that new combination immunotherapeutic regimens provide unprecedented clinical response in a subset of patients. Computational methods that can simulate tumors from mathematical equations describing cellular and molecular interactions are emerging as promising tools to simulate the impact of therapy entirely in silico. To facilitate designing dosing regimen and identifying potential biomarkers, we developed a new computational model to track tumor progression at organ scale while reflecting the spatial heterogeneity in the tumor at tissue scale in HCC. This computational model is called a spatial quantitative systems pharmacology (spQSP) platform and it is also designed to simulate the effects of combination immunotherapy. We then validate the results from the spQSP system by leveraging real-world spatial multi-omics data from a neoadjuvant HCC clinical trial combining anti-PD-1 immunotherapy and a multitargeted tyrosine kinase inhibitor (TKI) cabozantinib. The model output is compared with spatial data from Imaging Mass Cytometry (IMC). Both IMC data and simulation results suggest closer proximity between CD8 T cell and macrophages among non-responders while the reverse trend was observed for responders. The analyses also imply wider dispersion of immune cells and less scattered cancer cells in responders' samples. We also compared the model output with Visium spatial transcriptomics analyses of samples from post-treatment tumor resections in the original clinical trial. Both spatial transcriptomic data and simulation results identify the role of spatial patterns of tumor vasculature and TGFβ in tumor and immune cell interactions. To our knowledge, this is the first spatial tumor model for virtual clinical trials at a molecular scale that is grounded in high-throughput spatial multi-omics data from a human clinical trial.
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Affiliation(s)
- Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Atul Deshpande
- Bloomberg-Kimmel Immunotherapy Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Babita K. Verma
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Long Yuan
- Bloomberg-Kimmel Immunotherapy Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Won Jin Ho
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth M. Jaffee
- Bloomberg-Kimmel Immunotherapy Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Qingfeng Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert A. Anders
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark Yarchoan
- Bloomberg-Kimmel Immunotherapy Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Luciane T. Kagohara
- Bloomberg-Kimmel Immunotherapy Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J. Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Immunotherapy Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Convergence Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Jointly supervised research
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Jointly supervised research
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36
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Dardis GJ, Wang J, Simon JM, Wang GG, Baldwin AS. An EZH2-NF-κB regulatory axis drives expression of pro-oncogenic gene signatures in triple negative breast cancer. iScience 2023; 26:107115. [PMID: 37416481 PMCID: PMC10319845 DOI: 10.1016/j.isci.2023.107115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/10/2023] [Accepted: 06/09/2023] [Indexed: 07/08/2023] Open
Abstract
The histone methyltransferase EZH2 has been studied most extensively in the context of PRC2-dependent gene repression. Accumulating evidence indicates non-canonical functions for EZH2 in cancer contexts including promoting paradoxical gene expression through interactions with transcription factors, including NF-κB in triple negative breast cancer (TNBC). We profile EZH2 and NF-κB factor co-localization and positive gene regulation genome-wide, and define a subset of NF-κB targets and genes associated with oncogenic functions in TNBC that is enriched in patient datasets. We demonstrate interaction between EZH2 and RelA requiring the recently identified transactivation domain (TAD) which mediates EZH2 recruitment to, and activation of certain NF-κB-dependent genes, and supports downstream migration and stemness phenotypes in TNBC cells. Interestingly, EZH2-NF-κB positive regulation of genes and stemness does not require PRC2. This study provides new insight into pro-oncogenic regulatory functions for EZH2 in breast cancer through PRC2-independent, and NF-κB-dependent regulatory mechanisms.
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Affiliation(s)
- Gabrielle J. Dardis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jeremy M. Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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37
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Ornos ED, Cando LF, Catral CD, Quebral EP, Tantengco OA, Arevalo MVP, Dee EC. Molecular basis of sex differences in cancer: Perspective from Asia. iScience 2023; 26:107101. [PMID: 37404373 PMCID: PMC10316661 DOI: 10.1016/j.isci.2023.107101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023] Open
Abstract
Cancer is a leading cause of mortality and morbidity globally. Sex differences in cancer are evident in death rates and treatment responses in several cancers. Asian patients have unique cancer epidemiology influenced by their genetic ancestry and sociocultural factors in the region. In this review, we show molecular associations that potentially mediate sex disparities observed in cancer in Asian populations. Differences in sex characteristics are evident at the cytogenetic, genetic, and epigenetic levels mediating processes that include cell cycle, oncogenesis, and metastasis. Larger clinical and in vitro studies that explore mechanisms can confirm the associations of these molecular markers. In-depth studies of these markers can reveal their importance as diagnostics, prognostics, and therapeutic efficacy markers. Sex differences should be considered in designing novel cancer therapeutics in this era of precision medicine.
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Affiliation(s)
- Eric David Ornos
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
| | - Leslie Faye Cando
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
| | | | - Elgin Paul Quebral
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
- Virology Laboratory, Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ourlad Alzeus Tantengco
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
- Department of Physiology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines
- Department of Biology, College of Science, De La Salle University, Manila 0922, Philippines
| | | | - Edward Christopher Dee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10028, USA
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38
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Islam R, Jenkins CE, Cao Q, Wong J, Bilenky M, Carles A, Moksa M, Weng AP, Hirst M. RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia. iScience 2023; 26:106795. [PMID: 37213235 PMCID: PMC10199266 DOI: 10.1016/j.isci.2023.106795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 02/10/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.
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Affiliation(s)
- Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | | | - Qi Cao
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jasper Wong
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Misha Bilenky
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Annaïck Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Martin Hirst
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Corresponding author
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Xie X, Li L, Xie L, Liu Z, Zhang G, Gao X, Peng W, Deng H, Yang Y, Yang M, Chang L, Yi X, Xia X, He Z, Zhou C. Stratification of non-small cell lung adenocarcinoma patients with EGFR actionable mutations based on drug-resistant stem cell genes. iScience 2023; 26:106584. [PMID: 37288343 PMCID: PMC10241979 DOI: 10.1016/j.isci.2023.106584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/02/2023] [Accepted: 03/30/2023] [Indexed: 06/09/2023] Open
Abstract
EGFR-TKIs were used in NSCLC patients with actionable EGFR mutations and prolong prognosis. However, most patients treated with EGFR-TKIs developed resistance within around one year. This suggests that residual EGFR-TKIs resistant cells may eventually lead to relapse. Predicting resistance risk in patients will facilitate individualized management. Herein, we built an EGFR-TKIs resistance prediction (R-index) model and validate in cell line, mice, and cohort. We found significantly higher R-index value in resistant cell lines, mice models and relapsed patients. Patients with an elevated R-index had significantly shorter relapse time. We also found that the glycolysis pathway and the KRAS upregulation pathway were related to EGFR-TKIs resistance. MDSC is a significant immunosuppression factor in the resistant microenvironment. Our model provides an executable method for assessing patient resistance status based on transcriptional reprogramming and may contribute to the clinical translation of patient individual management and the study of unclear resistance mechanisms.
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Affiliation(s)
- Xiaohong Xie
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Lifeng Li
- Geneplus-Beijing, Beijing 102206, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | | | | | - Xuan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Shenzhen Clinical Laboratory, Shenzhen, Guangdong 518122, China
| | - Wenying Peng
- The Second Department of Oncology, Yunnan Cancer Hospital & The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming 650000, China
| | - Haiyi Deng
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Yilin Yang
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Meiling Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | | | - Xin Yi
- Geneplus-Beijing, Beijing 102206, China
| | | | - Zhiyi He
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Chengzhi Zhou
- Pulmonary and Critical Care Medicine, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
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40
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Wang J, Nakato R. Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells. iScience 2023; 26:106908. [PMID: 37283809 PMCID: PMC10239702 DOI: 10.1016/j.isci.2023.106908] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
Chromatin organization, whose malfunction causes various diseases including cancer, is fundamentally controlled by cohesin. While cancer cells have been found with mutated or misexpressed cohesin genes, there is no comprehensive survey about the presence and role of abnormal cohesin binding in cancer cells. Here, we systematically identified ∼1% of cohesin-binding sites (701-2,633) as cancer-aberrant binding sites of cohesin (CASs). We integrated CASs with large-scale transcriptomics, epigenomics, 3D genomics, and clinical information. CASs represent tissue-specific epigenomic signatures enriched for cancer-dysregulated genes with functional and clinical significance. CASs exhibited alterations in chromatin compartments, loops within topologically associated domains, and cis-regulatory elements, indicating that CASs induce dysregulated genes through misguided chromatin structure. Cohesin depletion data suggested that cohesin binding at CASs actively regulates cancer-dysregulated genes. Overall, our comprehensive investigation suggests that aberrant cohesin binding is an essential epigenomic signature responsible for dysregulated chromatin structure and transcription in cancer cells.
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Affiliation(s)
- Jiankang Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Reyes-Castellanos G, Abdel Hadi N, Gallardo-Arriaga S, Masoud R, Garcia J, Lac S, El Kaoutari A, Gicquel T, Planque M, Fendt SM, Linares LK, Gayet O, Guillaumond F, Dusetti N, Iovanna J, Carrier A. Combining the antianginal drug perhexiline with chemotherapy induces complete pancreatic cancer regression in vivo. iScience 2023; 26:106899. [PMID: 37305702 PMCID: PMC10250830 DOI: 10.1016/j.isci.2023.106899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/06/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the human cancers with the poorest prognosis. Interestingly, we found that mitochondrial respiration in primary human PDAC cells depends mainly on the fatty acid oxidation (FAO) to meet basic energy requirements. Therefore, we treated PDAC cells with perhexiline, a well-recognized FAO inhibitor used in cardiac diseases. Some PDAC cells respond efficiently to perhexiline, which acts synergistically with chemotherapy (gemcitabine) in vitro and in two xenografts in vivo. Importantly, perhexiline in combination with gemcitabine induces complete tumor regression in one PDAC xenograft. Mechanistically, this co-treatment causes energy and oxidative stress promoting apoptosis but does not exert inhibition of FAO. Yet, our molecular analysis indicates that the carnitine palmitoyltransferase 1C (CPT1C) isoform is a key player in the response to perhexiline and that patients with high CPT1C expression have better prognosis. Our study reveals that repurposing perhexiline in combination with chemotherapy is a promising approach to treat PDAC.
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Affiliation(s)
| | - Nadine Abdel Hadi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | | | - Rawand Masoud
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Julie Garcia
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Sophie Lac
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | | | - Tristan Gicquel
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Mélanie Planque
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Laetitia Karine Linares
- INSERM, Université de Montpellier, IRCM, Institut Régional Du Cancer de Montpellier, Montpellier, France
| | - Odile Gayet
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Fabienne Guillaumond
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nelson Dusetti
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Juan Iovanna
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Alice Carrier
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
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42
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Wu H, Wu Z, Qiu Y, Zhao F, Liao M, Zhong Z, Chen J, Zeng Y, Liu R. Supplementing a specific synbiotic suppressed the incidence of AOM/DSS-induced colorectal cancer in mice. iScience 2023; 26:106979. [PMID: 37378327 PMCID: PMC10291512 DOI: 10.1016/j.isci.2023.106979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 04/11/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
In this study, we evaluated the effect of a specific synbiotic on CAC (AOM/DSS-induced colitis-associated cancer). We confirmed that the synbiotic intervention was able to protect the intestinal barrier and inhibit CAC occurrence via upregulating tight junction proteins and anti-inflammatory cytokines, and downregulating pro-inflammatory cytokines. Moreover, the synbiotic significantly improved the disorder of the colonic microbiota of CAC mice, promoted the formation of SCFAs and the production of secondary bile acids, and alleviated the accumulation of primary bile acids in the CAC mice. Meanwhile, the synbiotic could significantly inhibit the abnormal activation of the intestinal Wnt/β-catenin signaling pathway significantly related to IL-23. In a word, the synbiotic can inhibit the occurrence and development of colorectal tumors and it may be a functional food to prevent inflammation-related colon tumors, and the research also provided a theoretical basis for improving the intestinal microecological environment through diet therapy.
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Affiliation(s)
- Huixia Wu
- Department of Medical Laboratory, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Zhengchun Wu
- Department of Hepatobiliary and Intestinal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Yilan Qiu
- School of Life Science, Hunan Normal University, Changsha 410018, China
- Changsha Tianan Biotechnology Co., Ltd., Changsha 410018, China
| | - Fangjian Zhao
- Medical Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha 410018, China
| | - Minjing Liao
- Department of Medical Laboratory, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Zhihong Zhong
- Department of Medical Laboratory, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Jian Chen
- Medical Laboratory, The First Affiliated Hospital of Hunan Normal University, Changsha 410018, China
| | - Yiliang Zeng
- Shaoshan Changbaitong Biological Technology Co., Ltd., Shaoshan 411100, China
| | - Rushi Liu
- Department of Medical Laboratory, School of Medicine, Hunan Normal University, Changsha 410013, China
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Liao J, Wang J, Xu Y, Wu Y, Wang M, Zhao Q, Tan X, Meng Y, Wei L, Huang A. LAPTM4B-YAP loop feedback amplification enhances the stemness of hepatocellular carcinoma. iScience 2023; 26:106754. [PMID: 37213231 PMCID: PMC10197148 DOI: 10.1016/j.isci.2023.106754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/10/2023] [Accepted: 04/23/2023] [Indexed: 05/23/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is highly heterogeneous, and stemness signatures are frequently elevated in HCC tumor cells to generate heterogeneous subtypes via multidirectional differentiation. However, the mechanisms affecting the regulation of stemness in HCC remain unclear. In this study, we identified that lysosome-associated protein transmembrane-4β (LAPTM4B) was significantly overexpressed in stem-like tumor cell populations with multidirectional differentiation potential at the single cell level, and verified that LAPTM4B was closely related to stemness of HCC using in vitro and in vivo experiments. Mechanistically, elevated LAPTM4B suppresses Yes-associated protein (YAP) phosphorylation and ubiquitination degradation. In turn, stabilized YAP localizes to the nucleus and binds to cAMP responsive element binding protein-1 (CREB1), which promotes transcription of LAPTM4B. Overall, our findings suggest that LAPTM4B forms a positive feedback loop with YAP, which maintains the stemness of HCC tumor cells and leads to an unfavorable prognosis for HCC patients.
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Affiliation(s)
- Jianping Liao
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
| | - Jiahong Wang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yu Xu
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yong Wu
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Meifeng Wang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Qiudong Zhao
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
| | - Xiaodan Tan
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yan Meng
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
- Department of Medical Ultrasound, Shanghai Tenth People’s Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai 200072, China
- Corresponding author
| | - Lixin Wei
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
- Corresponding author
| | - Aimin Huang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
- Corresponding author
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44
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Cai L, DeBerardinis RJ, Xiao G, Minna JD, Xie Y. Dissecting molecular, pathological, and clinical features associated with tumor neural/neuroendocrine heterogeneity. iScience 2023; 26:106983. [PMID: 37378310 PMCID: PMC10291506 DOI: 10.1016/j.isci.2023.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/21/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Lineage plasticity, especially transdifferentiation between neural/neuroendocrine (NE) and non-NE lineage, has been observed in multiple cancer types and linked to increased tumor aggressiveness. However, existing NE/non-NE subtype classifications in various cancer types were established through ad hoc approaches in different studies, making it difficult to align findings across cancer types and extend investigations to new datasets. To address this issue, we developed a generalized strategy to generate quantitative NE scores and a web application to facilitate its implementation. We applied this method to nine datasets covering seven cancer types, including two neural cancers, two neuroendocrine cancers, and three non-NE cancers. Our analysis revealed significant NE inter-tumoral heterogeneity and identified strong associations between NE scores and molecular, histological, and clinical features, including prognosis in different cancer types. These results support the translational utility of NE scores. Overall, our work demonstrated a broadly applicable strategy for determining the NE properties of tumors.
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Affiliation(s)
- Ling Cai
- Quantitative Biomedical Research Center, Peter O’Donnell School of Public Health, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Children’s Research Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J. DeBerardinis
- Children’s Research Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell School of Public Health, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Minna
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Peter O’Donnell School of Public Health, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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45
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He W, Demas DM, Shajahan-Haq AN, Baumann WT. Modeling breast cancer proliferation, drug synergies, and alternating therapies. iScience 2023; 26:106714. [PMID: 37234088 PMCID: PMC10206440 DOI: 10.1016/j.isci.2023.106714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/12/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
Estrogen receptor positive (ER+) breast cancer is responsive to a number of targeted therapies used clinically. Unfortunately, the continuous application of targeted therapy often results in resistance, driving the consideration of combination and alternating therapies. Toward this end, we developed a mathematical model that can simulate various mono, combination, and alternating therapies for ER + breast cancer cells at different doses over long time scales. The model is used to look for optimal drug combinations and predicts a significant synergism between Cdk4/6 inhibitors in combination with the anti-estrogen fulvestrant, which may help explain the clinical success of adding Cdk4/6 inhibitors to anti-estrogen therapy. Furthermore, the model is used to optimize an alternating treatment protocol so it works as well as monotherapy while using less total drug dose.
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Affiliation(s)
- Wei He
- Program in Genetics, Bioinformatics, and Computational Biology, VT BIOTRANS, Virginia Tech, Blacksburg, VA 24061, USA
| | - Diane M. Demas
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Ayesha N. Shajahan-Haq
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - William T. Baumann
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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46
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Grody EI, Abraham A, Shukla V, Goyal Y. Toward a systems-level probing of tumor clonality. iScience 2023; 26:106574. [PMID: 37192968 PMCID: PMC10182304 DOI: 10.1016/j.isci.2023.106574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Cancer has been described as a genetic disease that clonally evolves in the face of selective pressures imposed by cell-intrinsic and extrinsic factors. Although classical models based on genetic data predominantly propose Darwinian mechanisms of cancer evolution, recent single-cell profiling of cancers has described unprecedented heterogeneity in tumors providing support for alternative models of branched and neutral evolution through both genetic and non-genetic mechanisms. Emerging evidence points to a complex interplay between genetic, non-genetic, and extrinsic environmental factors in shaping the evolution of tumors. In this perspective, we briefly discuss the role of cell-intrinsic and extrinsic factors that shape clonal behaviors during tumor progression, metastasis, and drug resistance. Taking examples of pre-malignant states associated with hematological malignancies and esophageal cancer, we discuss recent paradigms of tumor evolution and prospective approaches to further enhance our understanding of this spatiotemporally regulated process.
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Affiliation(s)
- Emanuelle I. Grody
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Corresponding author
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Corresponding author
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Dong S, Wang H, Ji H, Hu Y, Zhao S, Yan B, Wang G, Lin Z, Zhu W, Lu J, Cheng J, Wu Z, Zhu Q, Zhuo S, Chen G, Yan J. Development and validation of a collagen signature to predict the prognosis of patients with stage II/III colorectal cancer. iScience 2023; 26:106746. [PMID: 37216096 PMCID: PMC10192940 DOI: 10.1016/j.isci.2023.106746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/04/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
The tumor, nodes and metastasis (TNM) classification system provides useful but incomplete prognostic information and lacks the assessment of the tumor microenvironment (TME). Collagen, the main component of the TME extracellular matrix, plays a nonnegligible role in tumor invasion and metastasis. In this cohort study, we aimed to develop and validate a TME collagen signature (CSTME) for prognostic prediction of stage II/III colorectal cancer (CRC) and to compare the prognostic values of "TNM stage + CSTME" with that of TNM stage alone. Results indicated that the CSTME was an independent prognostic risk factor for stage II/III CRC (hazard ratio: 2.939, 95% CI: 2.180-3.962, p < 0.0001), and the integration of the TNM stage and CSTME had a better prognostic value than that of the TNM stage alone (AUC(TNM+CSTME) = 0.772, AUC TNM = 0.687, p < 0.0001). This study provided an application of "seed and soil" strategy for prognosis prediction and individualized therapy.
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Affiliation(s)
- Shumin Dong
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- School of Science, Jimei University, Xiamen 361021, China
| | - Huaiming Wang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases Supported by National Key Clinical Discipline, Guangzhou 510630, China
| | - Hongli Ji
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yaowen Hu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Shuhan Zhao
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Botao Yan
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Guangxing Wang
- School of Science, Jimei University, Xiamen 361021, China
- Center for Molecular Imaging and Translational Medicine, Xiamen University, Xiamen 361021, China
| | - Zexi Lin
- Fujian University, Fuzhou 350000, China
| | - Weifeng Zhu
- Department of Pathology & Precision Medicine Center, The Affiliated Cancer Hospital of Fujian Medical University, Fujian Provincial Cancer Hospital, Fuzhou 350011, China
| | - Jianping Lu
- Department of Pathology & Precision Medicine Center, The Affiliated Cancer Hospital of Fujian Medical University, Fujian Provincial Cancer Hospital, Fuzhou 350011, China
| | - Jiaxin Cheng
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhida Wu
- Department of Pathology & Precision Medicine Center, The Affiliated Cancer Hospital of Fujian Medical University, Fujian Provincial Cancer Hospital, Fuzhou 350011, China
| | - Qiong Zhu
- Department of Pathology & Precision Medicine Center, The Affiliated Cancer Hospital of Fujian Medical University, Fujian Provincial Cancer Hospital, Fuzhou 350011, China
| | - Shuangmu Zhuo
- School of Science, Jimei University, Xiamen 361021, China
| | - Gang Chen
- Department of Pathology & Precision Medicine Center, The Affiliated Cancer Hospital of Fujian Medical University, Fujian Provincial Cancer Hospital, Fuzhou 350011, China
| | - Jun Yan
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
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48
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Fathi M, Martinez-Paniagua M, Rezvan A, Montalvo MJ, Mohanty V, Chen K, Mani SA, Varadarajan N. Identifying signatures of EV secretion in metastatic breast cancer through functional single-cell profiling. iScience 2023; 26:106482. [PMID: 37091228 PMCID: PMC10119611 DOI: 10.1016/j.isci.2023.106482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/02/2023] [Accepted: 03/10/2023] [Indexed: 04/25/2023] Open
Abstract
Extracellular vesicles (EVs) regulate the tumor microenvironment by facilitating transport of biomolecules. Despite extensive investigation, heterogeneity in EV secretion among cancer cells and the mechanisms that support EV secretion are not well characterized. We developed an integrated method to identify individual cells with differences in EV secretion and performed linked single-cell RNA-sequencing on cloned single cells from the metastatic breast cancer cells. Differential gene expression analyses identified a four-gene signature of breast cancer EV secretion: HSP90AA1, HSPH1, EIF5, and DIAPH3. We functionally validated this gene signature by testing it across cell lines with different metastatic potential in vitro. Analysis of the TCGA and METABRIC datasets showed that this signature is associated with poor survival, invasive breast cancer types, and poor CD8+ T cell infiltration in human tumors. We anticipate that our method for directly identifying the molecular determinants of EV secretion will have broad applications across cell types and diseases.
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Affiliation(s)
- Mohsen Fathi
- Chemical and Biomolecular Engineering Department, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
| | - Melisa Martinez-Paniagua
- Chemical and Biomolecular Engineering Department, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
| | - Ali Rezvan
- Chemical and Biomolecular Engineering Department, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
| | - Melisa J. Montalvo
- Chemical and Biomolecular Engineering Department, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, 1400 Pressler Street, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, 1400 Pressler Street, Houston, TX, USA
| | - Sendurai A. Mani
- Department of Translational Molecular Pathology, University of Texas M.D. Anderson Cancer Center, 2130 W Holcombe Boulevard, Houston, TX 77030, USA
- Department of Pathology and Lab Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
- Legoretta Cancer Center, Brown University, Providence, RI 021912, USA
| | - Navin Varadarajan
- Chemical and Biomolecular Engineering Department, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
- Corresponding author
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Grazioso TP, Djouder N. A mechanistic view of the use of cold temperature in the treatment of cancer. iScience 2023; 26:106511. [PMID: 37091251 PMCID: PMC10119757 DOI: 10.1016/j.isci.2023.106511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
In their latest article, Seki and colleagues investigate the potential role of cold as a therapeutical option to treat various cancer types, including even clinically untreatable cancers such as pancreatic cancers. The authors suggest that cold exposure may have a tumor-suppressive effect mediated by the activation of brown adipose tissue (BAT), in charge of dissipating heat through non-shivering thermogenesis. In this regard, circulating blood glucose is decreased, restricting the tumor glucose uptake, which is redistributed, favoring BAT uptake to fuel thermogenesis.1.
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Affiliation(s)
- Tatiana P. Grazioso
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid, 28029, Spain
| | - Nabil Djouder
- Molecular Oncology Programme, Growth Factors, Nutrients and Cancer Group, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid, 28029, Spain
- Corresponding author
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50
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Li J, Li B, Zhao R, Li G. Systematic analysis of the aberrances and functional implications of cuproptosis in cancer. iScience 2023; 26:106319. [PMID: 36950125 PMCID: PMC10025971 DOI: 10.1016/j.isci.2023.106319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Cuproptosis is a novel form of cell death driven by a copper-dependent proteotoxic stress response whose comprehensive landscape in tumors remains unclear. Here, we comprehensively characterized cuproptosis-related genes (CRGs) across 33 cancers using multi-omic data from The Cancer Genome Atlas (TCGA), showing complicated and diverse results in different cancers. We also explored the relationships between CRGs and cancer metabolic patterns, pathway activity, and tumor microenvironment (TME), suggesting that they played critical roles in tumor progression and TME cell infiltration. We further established the cuproptosis potential index (CPI) to reveal the functional roles of cuproptosis, and characterized multi-omic molecular features associated with cuproptosis. In clinical applications, we performed a combined analysis of the sensitivity of CRGs and CPI to drug response and immunotherapy. This study provides a rich resource for understanding cuproptosis, offering a broad molecular perspective for future functional and therapeutic studies of multiple cancer pathways mediated by cuproptosis.
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Affiliation(s)
- Jiangbing Li
- Department of Cardiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021 Shandong, China
| | - Boyan Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, 250012 Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012 Shandong, China
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, 250012 Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012 Shandong, China
- Corresponding author
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, 250012 Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, 250012 Shandong, China
- Corresponding author
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