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Wei J, Zhang Y, Li H, Wang F, Yao S. Toll-like receptor 4: A potential therapeutic target for multiple human diseases. Biomed Pharmacother 2023; 166:115338. [PMID: 37595428 DOI: 10.1016/j.biopha.2023.115338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023] Open
Abstract
The immune response plays a pivotal role in the pathogenesis of diseases. Toll-like receptor 4 (TLR4), as an intrinsic immune receptor, exhibits widespread in vivo expression and its dysregulation significantly contributes to the onset of various diseases, encompassing cardiovascular disorders, neoplastic conditions, and inflammatory ailments. This comprehensive review centers on elucidating the architectural and distributive characteristics of TLR4, its conventional signaling pathways, and its mode of action in diverse disease contexts. Ultimately, this review aims to propose novel avenues and therapeutic targets for clinical intervention.
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Affiliation(s)
- Jinrui Wei
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
| | - Yan Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
| | - Haopeng Li
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
| | - Fuquan Wang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
| | - Shanglong Yao
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China.
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2
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Okuno Y, Hori M, Hattori-Kato M, Fukuhara H, Nomiya A, Mikami K, Takeuchi T. Structural Analysis of the Colony-Stimulating Factor 3 Gene of Granulocyte Colony-Stimulating Factor-Producing Urothelial Cancer. Cureus 2023; 15:e43981. [PMID: 37746465 PMCID: PMC10516146 DOI: 10.7759/cureus.43981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Granulocyte colony-stimulating factor (G-CSF) is a member of the CSF family of glycoproteins that regulate the proliferation, differentiation, and mobilization of neutrophils. G-CSF-producing malignant cancers have been reported to occur in various organs and are mostly associated with poor clinical prognosis. Here, we analyzed the structure of the CSF3 gene encoding the G-CSF protein to delineate the mechanism of G-CSF production by the cancer cells. Methodology Two cases of G-CSF-producing urothelial cancers and three cases of G-CSF-nonproducing bladder cancers were enrolled for genetic analysis. Results In one case of G-CSF-producing bladder cancer, six somatic mutations were detected in the 5'- upstream region of the CSF3 gene. No somatic mutations in the CSF3 gene were detected in another case of G-CSF-producing renal pelvic cancer and G-CSF-nonproducing bladder cancers. Copy numbers of the CSF3 gene were not increased in G-CSF-producing urothelial cancers. Conclusions Somatic mutations in the 5'- upstream region of the CSF3 gene may cause G-CSF protein overproduction.
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Affiliation(s)
- Yumiko Okuno
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, Kawasaki, JPN
| | - Mai Hori
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, Kawasaki, JPN
| | - Mami Hattori-Kato
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, Kawasaki, JPN
| | - Hiroshi Fukuhara
- Department of Urology, Kyorin University Faculty of Medicine, Tokyo, JPN
| | - Akira Nomiya
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, Kawasaki, JPN
| | - Koji Mikami
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, Kawasaki, JPN
| | - Takumi Takeuchi
- Department of Urology, Japan Organization of Occupational Health and Safety, Kanto Rosai Hospital, Kawasaki, JPN
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3
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Boström M, Larsson E. Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer. Nat Commun 2022; 13:7023. [PMID: 36396655 PMCID: PMC9671924 DOI: 10.1038/s41467-022-34746-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
Cancer gene discovery is reliant on distinguishing driver mutations from a multitude of passenger mutations in tumour genomes. While driver genes may be revealed based on excess mutation recurrence or clustering, there is a need for orthogonal principles. Here, we take advantage of the fact that non-cancer genes, containing only passenger mutations under neutral selection, exhibit a likelihood of mutagenesis in a given tumour determined by the tumour's mutational signature and burden. This relationship can be disrupted by positive selection, leading to a difference in the distribution of mutated cases across a cohort for driver and passenger genes. We apply this principle to detect cancer drivers independently of recurrence in large pan-cancer cohorts, and show that our method (SEISMIC) performs comparably to traditional approaches and can provide resistance to known confounding mutational phenomena. Being based on a different principle, the approach provides a much-needed complement to existing methods for detecting signals of selection.
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Affiliation(s)
- Martin Boström
- grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Erik Larsson
- grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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4
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Bispo IMC, Granger HP, Almeida PP, Nishiyama PB, de Freitas LM. Systems biology and OMIC data integration to understand gastrointestinal cancers. World J Clin Oncol 2022; 13:762-778. [PMID: 36337313 PMCID: PMC9630993 DOI: 10.5306/wjco.v13.i10.762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/22/2021] [Accepted: 10/03/2022] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancers are a set of diverse diseases affecting many parts/ organs. The five most frequent GI cancer types are esophageal, gastric cancer (GC), liver cancer, pancreatic cancer, and colorectal cancer (CRC); together, they give rise to 5 million new cases and cause the death of 3.5 million people annually. We provide information about molecular changes crucial to tumorigenesis and the behavior and prognosis. During the formation of cancer cells, the genomic changes are microsatellite instability with multiple chromosomal arrangements in GC and CRC. The genomically stable subtype is observed in GC and pancreatic cancer. Besides these genomic subtypes, CRC has epigenetic modification (hypermethylation) associated with a poor prognosis. The pathway information highlights the functions shared by GI cancers such as apoptosis; focal adhesion; and the p21-activated kinase, phosphoinositide 3-kinase/Akt, transforming growth factor beta, and Toll-like receptor signaling pathways. These pathways show survival, cell proliferation, and cell motility. In addition, the immune response and inflammation are also essential elements in the shared functions. We also retrieved information on protein-protein interaction from the STRING database, and found that proteins Akt1, catenin beta 1 (CTNNB1), E1A binding protein P300, tumor protein p53 (TP53), and TP53 binding protein 1 (TP53BP1) are central nodes in the network. The protein expression of these genes is associated with overall survival in some GI cancers. The low TP53BP1 expression in CRC, high EP300 expression in esophageal cancer, and increased expression of Akt1/TP53 or low CTNNB1 expression in GC are associated with a poor prognosis. The Kaplan Meier plotter database also confirmed the association between expression of the five central genes and GC survival rates. In conclusion, GI cancers are very diverse at the molecular level. However, the shared mutations and protein pathways might be used to understand better and reveal diagnostic/prognostic or drug targets.
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Affiliation(s)
- Iasmin Moreira Costa Bispo
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45.029-094, Bahia, Brazil
| | - Henry Paul Granger
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45.029-094, Bahia, Brazil
| | - Palloma Porto Almeida
- Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro 20231-050, Brazil
| | - Patricia Belini Nishiyama
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45.029-094, Bahia, Brazil
| | - Leandro Martins de Freitas
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45.029-094, Bahia, Brazil
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5
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Man SM, Jenkins BJ. Context-dependent functions of pattern recognition receptors in cancer. Nat Rev Cancer 2022; 22:397-413. [PMID: 35355007 DOI: 10.1038/s41568-022-00462-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 02/07/2023]
Abstract
The immune system plays a critical role in shaping all facets of cancer, from the early initiation stage through to metastatic disease and resistance to therapy. Our understanding of the importance of the adaptive arm of the immune system in antitumour immunity has led to the implementation of immunotherapy with immune checkpoint inhibitors in numerous cancers, albeit with differing efficacy. By contrast, the clinical utility of innate immunity in cancer has not been exploited, despite dysregulated innate immunity being a feature of at least one-third of all cancers associated with tumour-promoting chronic inflammation. The past two decades have seen innate immune pattern recognition receptors (PRRs) emerge as critical regulators of the immune response to microbial infection and host tissue damage. More recently, it has become apparent that in many cancer types, PRRs play a central role in modulating a vast array of tumour-inhibiting and tumour-promoting cellular responses both in immune cells within the tumour microenvironment and directly in cancer cells. Herein, we provide a comprehensive overview of the fast-evolving field of PRRs in cancer, and discuss the potential to target PRRs for drug development and biomarker discovery in a wide range of oncology settings.
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Affiliation(s)
- Si Ming Man
- Division of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, School of Clinical Sciences, Monash University, Clayton, VIC, Australia.
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6
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Ma T, Ru J, Xue J, Schulz S, Mirzaei MK, Janssen KP, Quante M, Deng L. Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma. Microorganisms 2021; 9:microorganisms9081701. [PMID: 34442780 PMCID: PMC8401523 DOI: 10.3390/microorganisms9081701] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022] Open
Abstract
The relationship between viruses (dominated by bacteriophages or phages) and lower gastrointestinal (GI) tract diseases has been investigated, whereas the relationship between gut bacteriophages and upper GI tract diseases, such as esophageal diseases, which mainly include Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC), remains poorly described. This study aimed to reveal the gut bacteriophage community and their behavior in the progression of esophageal diseases. In total, we analyzed the gut phage community of sixteen samples from patients with esophageal diseases (six BE patients and four EAC patients) as well as six healthy controls. Differences were found in the community composition of abundant and rare bacteriophages among three groups. In addition, the auxiliary metabolic genes (AMGs) related to bacterial exotoxin and virulence factors such as lipopolysaccharides (LPS) biosynthesis proteins were found to be more abundant in the genome of rare phages from BE and EAC samples compared to the controls. These results suggest that the community composition of gut phages and functional traits encoded by them were different in two stages of esophageal diseases. However, the findings from this study need to be validated with larger sample sizes in the future.
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Affiliation(s)
- Tianli Ma
- Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; (T.M.); (J.R.); (J.X.); (S.S.); (M.K.M.)
- Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Jinlong Ru
- Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; (T.M.); (J.R.); (J.X.); (S.S.); (M.K.M.)
- Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Jinling Xue
- Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; (T.M.); (J.R.); (J.X.); (S.S.); (M.K.M.)
- Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Sarah Schulz
- Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; (T.M.); (J.R.); (J.X.); (S.S.); (M.K.M.)
- Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Mohammadali Khan Mirzaei
- Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; (T.M.); (J.R.); (J.X.); (S.S.); (M.K.M.)
- Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany;
| | - Michael Quante
- II. Medizinische Klinik, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany
- Innere Medizin II, Universitätsklinik Freiburg, Universität Freiburg, 79106 Freiburg, Germany
- Correspondence: (M.Q.); (L.D.)
| | - Li Deng
- Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; (T.M.); (J.R.); (J.X.); (S.S.); (M.K.M.)
- Institute of Virology, Technical University of Munich, 81675 Munich, Germany
- Correspondence: (M.Q.); (L.D.)
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7
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Yan‐Fei H, Han Y, Yan‐Ting Z, Hui Y, Yu‐Qing Y, Ipsita P, Hui‐Ying H, Wei‐Gang F, Xin‐Xia T. Dysregulation in nucleic acid-sensing pathway genes is associated with cancer patients' prognosis. Cancer Sci 2020; 111:2212-2222. [PMID: 32391619 PMCID: PMC7385384 DOI: 10.1111/cas.14450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
The innate immune system, the first line of defense against pathogens, is activated by nucleic acids from microbial invaders that are recognized by nucleic acid-sensing receptors. Recent evidence affirms the ability of these receptors to respond to nucleic acids released by damaged cancer cells. The innate immune system is also involved in cancer immunosurveillance, and could be modulated for devising effective antitumor therapies by targeting nucleic acid-sensing pathways. A systematic, comprehensive analysis of dysregulation in nucleic acid-sensing pathways in cancer is required to fully understand its role. Based on multidimensional data of The Cancer Genome Atlas pan-cancer cohort, we revealed that upregulation of cytosolic DNA-sensing genes like AIM2 and CGAS was common in tumor tissues. We used 15 genes in the nucleic acid-sensing pathway to cluster all tumor patients into 2 subgroups and found that the subgroup with higher expression of nucleic acid-sensing pathway genes was associated with poorer prognosis across cancer types. However, in homologous recombination deficient patients, the nucleic acid recognition activated subgroup was associated with better prognosis, which confirms the therapeutic effect of nucleic acid recognition. This study contributes to a better understanding of the functions and mechanisms of nucleic acid recognition in cancer, lays the foundation for new therapeutic strategies, and enlarges the scope of development of new drugs.
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Affiliation(s)
- Huo Yan‐Fei
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Yang Han
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Zhou Yan‐Ting
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Yang Hui
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Yu Yu‐Qing
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Panda Ipsita
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - He Hui‐Ying
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Fang Wei‐Gang
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
| | - Tian Xin‐Xia
- Department of PathologySchool of Basic Medical SciencesThird HospitalPeking University Health Science CenterBeijingChina
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8
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Fu XQ, Liu B, Wang YP, Li JK, Zhu PL, Li T, Tse KW, Chou JY, Yin CL, Bai JX, Liu YX, Chen YJ, Yu ZL. Activation of STAT3 is a key event in TLR4 signaling-mediated melanoma progression. Cell Death Dis 2020; 11:246. [PMID: 32312954 PMCID: PMC7171093 DOI: 10.1038/s41419-020-2440-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/22/2022]
Abstract
Malignant melanoma is aggressive and has a high mortality rate. Toll-like receptor 4 (TLR4) has been linked to melanoma growth, angiogenesis and metastasis. However, signal transduction mediated by TLR4 for driving melanoma progression is not fully understood. Signal transducer and activator of transcription 3 (STAT3) has been identified as a major oncogene in melanoma progression. We found: that TLR4 expression positively correlates with activation/phosphorylation of STAT3 in human melanoma samples; that TLR4 ligands activate STAT3 through MYD88 and TRIF in melanoma cells; and that intratumoral activation of TLR4 increases STAT3 activation in the tumor and promotes tumor growth, angiogenesis, epithelial-mesenchymal transition (EMT) and the formation of an immunosuppressive tumor microenvironment in mice. Further, we found that the effects mediated by activating TLR4 are weakened by suppressing STAT3 function with a dominant negative STAT3 variant in melanoma. Collectively, our work identifies STAT3 activation as a key event in TLR4 signaling-mediated melanoma progression, shedding new light on the pathophysiology of melanoma.
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Affiliation(s)
- Xiu-Qiong Fu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
- Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Bin Liu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ya-Ping Wang
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Jun-Kui Li
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Li Zhu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
- Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Ting Li
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Kai-Wing Tse
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ji-Yao Chou
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Cheng-Le Yin
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Jing-Xuan Bai
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Yu-Xi Liu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Ying-Jie Chen
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China
| | - Zhi-Ling Yu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China.
- Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China.
- JaneClare Transdermal TCM Therapy Laboratory, Hong Kong Baptist University, Hong Kong, China.
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9
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Jiang L, Zheng J, Kwan JSH, Dai S, Li C, Li MJ, Yu B, To KF, Sham PC, Zhu Y, Li M. WITER: a powerful method for estimation of cancer-driver genes using a weighted iterative regression modelling background mutation counts. Nucleic Acids Res 2019; 47:e96. [PMID: 31287869 PMCID: PMC6895256 DOI: 10.1093/nar/gkz566] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/30/2019] [Accepted: 06/26/2019] [Indexed: 12/31/2022] Open
Abstract
Genomic identification of driver mutations and genes in cancer cells are critical for precision medicine. Due to difficulty in modelling distribution of background mutation counts, existing statistical methods are often underpowered to discriminate cancer-driver genes from passenger genes. Here we propose a novel statistical approach, weighted iterative zero-truncated negative-binomial regression (WITER, http://grass.cgs.hku.hk/limx/witer or KGGSeq,http://grass.cgs.hku.hk/limx/kggseq/), to detect cancer-driver genes showing an excess of somatic mutations. By fitting the distribution of background mutation counts properly, this approach works well even in small or moderate samples. Compared to alternative methods, it detected more significant and cancer-consensus genes in most tested cancers. Applying this approach, we estimated 229 driver genes in 26 different types of cancers. In silico validation confirmed 78% of predicted genes as likely known drivers and many other genes as very likely new drivers for corresponding cancers. The technical advances of WITER enable the detection of driver genes in TCGA datasets as small as 30 subjects and rescue of more genes missed by alternative tools in moderate or small samples.
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Affiliation(s)
- Lin Jiang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Genome Research, Sun Yat-sen University, Guangzhou 510080, China.,First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingjing Zheng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Johnny S H Kwan
- Departmelnt of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, New Territories, Hong Kong.,State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, New Territories, Hong Kong.,Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Sheng Dai
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Cong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Mulin Jun Li
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Key Laboratory of Inflammation Biology, Tianjin Medical University, Tianjin 300070, China
| | - Bolan Yu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Ka F To
- Departmelnt of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, New Territories, Hong Kong.,State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, New Territories, Hong Kong.,Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Pak C Sham
- The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong.,Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Cognitive and Brain Sciences, the University of Hong Kong, Pokfulam, Hong Kong
| | - Yonghong Zhu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Center for Genome Research, Sun Yat-sen University, Guangzhou 510080, China.,The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou 510080, China
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10
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Li T, Li B, Sara A, Ay C, Leung WY, Zhang Y, Dong Y, Liang Q, Zhang X, Weidner P, Gutting T, Behrens HM, Röcken C, Sung JJ, Ebert MP, Yu J, Burgermeister E. Docking protein-1 promotes inflammatory macrophage signaling in gastric cancer. Oncoimmunology 2019; 8:e1649961. [PMID: 31646096 DOI: 10.1080/2162402x.2019.1649961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023] Open
Abstract
Docking protein-1 (DOK1) is a tumor suppressor frequently lost in malignant cells, however, it retains the ability to control activities of immune receptors in adjacent stroma cells of the tumor microenvironment. We therefore hypothesized that addressing DOK1 may be useful for cancer immunotherapy. DOK1 mRNA and DOK1 protein expression were downregulated in tumor cells of gastric cancer patients (n = 249). Conversely, its expression was up-regulated in cases positive for Epstein Barr Virus (EBV+) together with genes related to macrophage biology and targets of clinical immunotherapy such as programmed-cell-death-ligand-1 (PD-L1). Notably, high DOK1 positivity in stroma cells conferred poor prognosis in patients and correlated with high levels of inducible nitric oxide synthase in CD68+ tumor-associated macrophages. In macrophages derived from human monocytic leukemia cell lines, DOK1 (i) was inducible by agonists of the anti-diabetic transcription factor peroxisome proliferator-activated receptor-gamma (PPARγ), (ii) increased polarization towards an inflammatory phenotype, (iii) augmented nuclear factor-κB-dependent transcription of pro-inflammatory cytokines and (iv) reduced PD-L1 expression. These properties empowered DOK1+ macrophages to decrease the viability of human gastric cancer cells in contact-dependent co-cultures. DOK1 also reduced PD-L1 expression in human primary blood monocytes. Our data propose that the drugability of DOK1 may be exploited to reprogram myeloid cells and enforce the innate immune response against EBV+ human gastric cancer.
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Affiliation(s)
- Tong Li
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Beifang Li
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Asgharpour Sara
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christine Ay
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Wing Yan Leung
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yanquan Zhang
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yujuan Dong
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiaoyi Liang
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiang Zhang
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Philip Weidner
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tobias Gutting
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Christoph Röcken
- Dept. of Pathology, Christian-Albrechts University, Kiel, Germany
| | - Joseph Jy Sung
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthias P Ebert
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jun Yu
- Institute of Digestive Disease and The Dept. of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Elke Burgermeister
- Dept. of Medicine II, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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11
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Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nat Commun 2019; 10:3101. [PMID: 31308377 PMCID: PMC6629660 DOI: 10.1038/s41467-019-10898-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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Affiliation(s)
- Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Elizabeth Foxall
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Juliane Perner
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, 10126, Italy
| | - Jesper Lagergren
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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12
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Ma AG, Yu LM, Zhao H, Qin CW, Tian XY, Wang Q. PSMD4 regulates the malignancy of esophageal cancer cells by suppressing endoplasmic reticulum stress. Kaohsiung J Med Sci 2019; 35:591-597. [PMID: 31162820 DOI: 10.1002/kjm2.12093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/09/2019] [Indexed: 12/28/2022] Open
Abstract
Proteasome 26S subunit non-ATPase 4 (PSMD4) is an important proteasome ubiquitin receptor and plays a key role in endoplasmic reticulum stress (ERS). However, the study of PSMD4 in esophageal cancer (EC) is relatively rare. Here, we found that the expression of PSMD4 was markedly enhanced in EC tissues and cell lines. The cell counting kit-8 (CCK-8) assay showed that overexpression of PSMD4 significantly enhanced Eca109 cell viability, while inhibition of PSMD4 reduced Eca109 cell viability. Knockdown of PSMD4 induced Eca109 cell apoptosis and cell cycle arrest. More importantly, knockdown of PSMD4 significantly enhanced the expression of glucose regulated protein 78, activating transcription factor 6, and p-protein kinase R-like ER kinase, indicating an enhanced ERS response in esophageal cancer cells. Compared with the control cells, brefeldin A significantly inhibited the expression of PSMD4 and increased the expression of p53-upregulated modulator of apoptosis. However, such effects were largely reversed after overexpressing PSMD4 in Eca109 cells, suggesting that silencing PSMD4 could enhance ERS-induced cell apoptosis. In summary, upregulation of PSMD4 promoted the progression of esophageal cancer mainly by reducing ERS-induced cell apoptosis.
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Affiliation(s)
- Ai-Guo Ma
- Department of Thoracic Surgery, Tengzhou Central People's Hospital, Tengzhou City, Shandong Province, PR China
| | - Li-Mei Yu
- Department of Critical Care Medicine, Tengzhou Central People's Hospital, Tengzhou City, Shandong Province, PR China
| | - Hong Zhao
- Department of Thoracic Surgery, Tengzhou Central People's Hospital, Tengzhou City, Shandong Province, PR China
| | - Cun-Wei Qin
- Department of Thoracic Surgery, Tengzhou Central People's Hospital, Tengzhou City, Shandong Province, PR China
| | - Xiang-Yu Tian
- Imaging Center, Tengzhou Central People's Hospital, Tengzhou City, Shandong Province, PR China
| | - Qing Wang
- Department of Thoracic Surgery, Tengzhou Central People's Hospital, Tengzhou City, Shandong Province, PR China
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13
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Nesteruk K, Spaander MCW, Leeuwenburgh I, Peppelenbosch MP, Fuhler GM. Achalasia and associated esophageal cancer risk: What lessons can we learn from the molecular analysis of Barrett's-associated adenocarcinoma? Biochim Biophys Acta Rev Cancer 2019; 1872:188291. [PMID: 31059738 DOI: 10.1016/j.bbcan.2019.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/29/2019] [Indexed: 02/08/2023]
Abstract
Idiopathic achalasia and Barrett's esophagus (BE) are preneoplastic conditions of the esophagus. BE increases the risk of esophageal adenocarcinoma (EAC), while achalasia is associated with both EAC and esophageal squamous cell carcinoma (ESCC). However, while the molecular mechanisms underlying the transformation of esophageal epithelial cells in BE are relatively well characterized, less is known regarding these processes in achalasia. Nevertheless, both conditions are associated with chronic inflammation and BE can occur in achalasia patients, and it is likely that similar processes underlie cancer risk in both diseases. The present review will discuss possible lessons that we can learn from the molecular analysis of BE for the study of achalasia-associated cancer and contrast findings in BE with those in achalasia. First, we will describe cellular fate during development of BE, EAC, and ESCC, and consider the inflammatory status of the epithelial barrier in BE and achalasia in terms of its contribution to carcinogenesis. Next, we will summarize current data on genetic alterations and molecular pathways involved in these processes. Lastly, the plausible role of the microbiota in achalasia-associated carcinogenesis and its contribution to abnormal lower esophageal sphincter (LES) functioning, the maintenance of chronic inflammatory status and influence on the esophageal mucosa through carcinogenic by-products, will be discussed.
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Affiliation(s)
- K Nesteruk
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - I Leeuwenburgh
- Department of Gastroenterology and Hepatology, Franciscus Gasthuis, Rotterdam, the Netherlands
| | - M P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - G M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands..
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