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Li J, Xiong S, He P, Liang P, Li C, Zhong R, Cai X, Xie Z, Liu J, Cheng B, Chen Z, Liang H, Lao S, Chen Z, Shi J, Li F, Feng Y, Huo Z, Deng H, Yu Z, Wang H, Zhan S, Xiang Y, Wang H, Zheng Y, Lin X, He J, Liang W. Spatial whole exome sequencing reveals the genetic features of highly-aggressive components in lung adenocarcinoma. Neoplasia 2024; 54:101013. [PMID: 38850835 DOI: 10.1016/j.neo.2024.101013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
In invasive lung adenocarcinoma (LUAD), patients with micropapillary (MIP) or solid (SOL) components had a significantly poorer prognosis than those with only lepidic (LEP), acinar (ACI) or papillary (PAP) components. It is interesting to explore the genetic features of different histologic subtypes, especially the highly aggressive components. Based on a cohort of 5,933 patients, this study observed that in different tumor size groups, LUAD with MIP/SOL components showed a different prevalence, and patients with ALK alteration or TP53 mutations had a higher probability of developing MIP/SOL components. To control individual differences, this research used spatial whole-exome sequencing (WES) via laser-capture microdissection of five patients harboring these five coexistent components and identified genetic features among different histologic components of the same tumor. In tracing the evolution of components, we found that titin (TTN) mutation might serve as a crucial intratumor potential driver for MIP/SOL components, which was validated by a cohort of 146 LUAD patients undergoing bulk WES. Functional analysis revealed that TTN mutations enriched the complement and coagulation cascades, which correlated with the pathway of cell adhesion, migration, and proliferation. Collectively, the histologic subtypes of invasive LUAD were genetically different, and certain trunk genotypes might synergize with branching TTN mutation to develop highly aggressive components.
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Affiliation(s)
- Jianfu Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Shan Xiong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Ping He
- Department of pathology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Peng Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Ran Zhong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangzhou, China
| | - Zhanhong Xie
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou 510120, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Bo Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Zhuxing Chen
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Hengrui Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Shen Lao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Zisheng Chen
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Jiang Shi
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Feng Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Yi Feng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Zhenyu Huo
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Hongsheng Deng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Ziwen Yu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Haixuan Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Shuting Zhan
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Yang Xiang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Huiting Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Yongmin Zheng
- Department of pathology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Xiaodong Lin
- Department of pathology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China; Southern Medical University, Guangzhou 510120, China.
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou 510120, China.
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Dong X, Shao C, Xu S, Tu J, Xu W, Chen D, Tang Y. Construction and validation of a prognostic signature based on anoikis-related lncRNAs in lung adenocarcinoma. Aging (Albany NY) 2024; 16:205905. [PMID: 38850527 DOI: 10.18632/aging.205905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/02/2024] [Indexed: 06/10/2024]
Abstract
Lung adenocarcinoma (LUAD) is the most common type of lung cancer and is characterized by a high death rate and a poor prospect for survival. Anoikis, which is a kind of programmed cell apoptosis, is an important factor in the advancement of tumors. Nonetheless, the function of anoikis-related lncRNAs (ARLRs) in LUAD is still not well understood. The TCGA database was queried for genomic and clinical information. A prognostic signature for ARLRs was established via the use of coexpression analysis and Cox regression. Validation of the model's accuracy was conducted utilizing K-M curves and receiver operating characteristic (ROC) curves, and the signature was utilized to develop a nomogram. LncRNAs were implicated in the progression of tumors, as determined by functional enrichment analysis. There was an improvement in prognosis, increased immune cell infiltration, and higher immune scores among the low-risk patients. Additionally, we found that the two groups had varied anticancer drug sensitivities, which could help guide treatment. The impact of one ARLR, AC026355.2, on migration and invasion was validated by in vitro experiments in LUAD cells. Herein, a new lncRNA signature associated with anoikis was identified and estimated, potentially serving as a prognostic indicator for LUAD patients.
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Affiliation(s)
- Xiaoqi Dong
- Department of Pulmonary and Critical Care Medicine, Ningbo Medical Center Lihuili Hospital (Lihuili Hospital Affiliated to Ningbo University), Ningbo, China
| | - Chuan Shao
- Department of Pulmonary and Critical Care Medicine, Ningbo Medical Center Lihuili Hospital (Lihuili Hospital Affiliated to Ningbo University), Ningbo, China
| | - Shuguang Xu
- Department of Pulmonary and Critical Care Medicine, Ningbo Medical Center Lihuili Hospital (Lihuili Hospital Affiliated to Ningbo University), Ningbo, China
| | - Jinjing Tu
- Department of Pulmonary and Critical Care Medicine, Ningbo Medical Center Lihuili Hospital (Lihuili Hospital Affiliated to Ningbo University), Ningbo, China
| | - Wenjing Xu
- Ningbo University Health Science Center, Ningbo, China
| | - Dahua Chen
- Department of Gastroenterology, Ningbo Medical Center Lihuili Hospital (Lihuili Hospital Affiliated to Ningbo University), Ningbo, China
| | - Yaodong Tang
- Department of Pulmonary and Critical Care Medicine, Ningbo Medical Center Lihuili Hospital (Lihuili Hospital Affiliated to Ningbo University), Ningbo, China
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Boța M, Vlaia L, Jîjie AR, Marcovici I, Crişan F, Oancea C, Dehelean CA, Mateescu T, Moacă EA. Exploring Synergistic Interactions between Natural Compounds and Conventional Chemotherapeutic Drugs in Preclinical Models of Lung Cancer. Pharmaceuticals (Basel) 2024; 17:598. [PMID: 38794168 PMCID: PMC11123751 DOI: 10.3390/ph17050598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
In the current work, the synergy between natural compounds and conventional chemotherapeutic drugs is comprehensively reviewed in light of current preclinical research findings. The prognosis for lung cancer patients is poor, with a 5-year survival rate of 18.1%. The use of natural compounds in combination with conventional chemotherapeutic drugs has gained significant attention as a potential novel approach in the treatment of lung cancer. The present work highlights the importance of finding more effective therapies to increase survival rates. Chemotherapy is a primary treatment option for lung cancer but it has limitations such as reduced effectiveness because cancer cells become resistant. Natural compounds isolated from medicinal plants have shown promising anticancer or chemopreventive properties and their synergistic effect has been observed when combined with conventional therapies. The combined use of an anti-cancer drug and a natural compound exhibits synergistic effects, enhancing overall therapeutic actions against cancer cells. In conclusion, this work provides an overview of the latest preclinical research on medicinal plants and plant-derived compounds as alternative or complementary treatment options for lung cancer chemotherapy and discusses the potential of natural compounds in treating lung cancer with minimal side effects.
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Affiliation(s)
- Mihaela Boța
- Department II—Pharmaceutical Technology, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (M.B.); (L.V.)
| | - Lavinia Vlaia
- Department II—Pharmaceutical Technology, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (M.B.); (L.V.)
- Formulation and Technology of Drugs Research Center, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
| | - Alex-Robert Jîjie
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (I.M.); (F.C.); (C.A.D.); (E.-A.M.)
- Research Centre for Pharmaco-Toxicological Evaluation, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
| | - Iasmina Marcovici
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (I.M.); (F.C.); (C.A.D.); (E.-A.M.)
- Research Centre for Pharmaco-Toxicological Evaluation, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
| | - Flavia Crişan
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (I.M.); (F.C.); (C.A.D.); (E.-A.M.)
- Research Centre for Pharmaco-Toxicological Evaluation, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
| | - Cristian Oancea
- Discipline of Pneumology, Department of Infectious Diseases, “Victor Babeș” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania;
| | - Cristina Adriana Dehelean
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (I.M.); (F.C.); (C.A.D.); (E.-A.M.)
- Research Centre for Pharmaco-Toxicological Evaluation, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
| | - Tudor Mateescu
- Department of Thoracic Surgery, Clinical Hospital for Infectious Diseases and Pneumophthiology Dr. Victor Babes, 13 Gheorghe Adam Street, RO-300310 Timisoara, Romania;
| | - Elena-Alina Moacă
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (I.M.); (F.C.); (C.A.D.); (E.-A.M.)
- Research Centre for Pharmaco-Toxicological Evaluation, “Victor Babeş” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
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Chang F, Xi B, Chai X, Wang X, Ma M, Fan Y. Molecular mechanism of radiation tolerance in lung adenocarcinoma cells using single-cell RNA sequencing. J Cell Mol Med 2024; 28:e18378. [PMID: 38760895 PMCID: PMC11101670 DOI: 10.1111/jcmm.18378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/20/2024] Open
Abstract
The efficacy of radiotherapy, a cornerstone in the treatment of lung adenocarcinoma (LUAD), is profoundly undermined by radiotolerance. This resistance not only poses a significant clinical challenge but also compromises patient survival rates. Therefore, it is important to explore this mechanism for the treatment of LUAD. Multiple public databases were used for single-cell RNA sequencing (scRNA-seq) data. We filtered, normalized and downscaled scRNA-seq data based on the Seurat package to obtain different cell subpopulations. Subsequently, the ssGSEA algorithm was used to assess the enrichment scores of the different cell subpopulations, and thus screen the cell subpopulations that are most relevant to radiotherapy tolerance based on the Pearson method. Finally, pseudotime analysis was performed, and a preliminary exploration of gene mutations in different cell subpopulations was performed. We identified HIST1H1D+ A549 and PIF1+ A549 as the cell subpopulations related to radiotolerance. The expression levels of cell cycle-related genes and pathway enrichment scores of these two cell subpopulations increased gradually with the extension of radiation treatment time. Finally, we found that the proportion of TP53 mutations in patients who had received radiotherapy was significantly higher than that in patients who had not received radiotherapy. We identified two cellular subpopulations associated with radiotherapy tolerance, which may shed light on the molecular mechanisms of radiotherapy tolerance in LUAD and provide new clinical perspectives.
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Affiliation(s)
- Feiyun Chang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Bozhou Xi
- The Second Clinical Medical SchoolShanxi Medical UniversityTaiyuanChina
| | - Xinchun Chai
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Xiuyan Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen YuceBioTechnology Co., LtdShenzhenChina
| | - Manyuan Ma
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen YuceBioTechnology Co., LtdShenzhenChina
| | - Yafeng Fan
- Department of Respiration, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
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Wei J, Ji K, Zhang Y, Zhang J, Wu X, Ji X, Zhou K, Yang X, Lu H, Wang A, Bu Z. Exploration of molecular markers related to chemotherapy efficacy of hepatoid adenocarcinoma of the stomach. Cell Oncol (Dordr) 2024; 47:677-693. [PMID: 37943484 DOI: 10.1007/s13402-023-00892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2023] [Indexed: 11/10/2023] Open
Abstract
PURPOSE Preoperative neoadjuvant chemotherapy may not improve the prognosis of patients with hepatoid adenocarcinoma of the stomach (HAS), a rare pathological type of gastric cancer. Thus, the study aimed at the genomic and transcriptomic impacts of preoperative chemotherapy on HAS. METHODS Patients with HAS who underwent surgical resection at Peking University Cancer Hospital were retrospectively included in this study. Whole exome sequencing and transcriptome sequencing were performed on pre-chemotherapy, non-chemotherapy and post-chemotherapy samples. We then compared the alterations in molecular markers between the post-chemotherapy and non-chemotherapy groups, and between the chemotherapy-effective and chemotherapy-ineffective groups, respectively. RESULTS A total of 79 tumor samples from 72 patients were collected. Compared to the non-chemotherapy group, the mutation frequencies of several genes were changed after chemotherapy, including TP53. In addition, there was a significant increase in the frequency of frameshift mutations and cytosine transversion to adenine (C > A), appearance of COSMIC signature 6 and 14, and a reduced gene copy number amplification. Interestingly, the same phenomenon was observed in chemotherapy-ineffective patients. In addition, many HAS patients had ERBB2, FGFR2, MET and HGF gene amplification. Moreover, the expression of immune-related genes, especially those related to lymphocyte activation, was down-regulated after chemotherapy. CONCLUSION Chemotherapy is closely associated with changes in the molecular characteristics of HAS. After chemotherapy, at genomic and transcriptome level, many features were altered. These changes may be molecular markers of poor chemotherapeutic efficacy and play an important role in chemoresistance in HAS. In addition, ERBB2, FGFR2, MET and HGF gene amplification may be potential therapeutic targets for HAS.
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Affiliation(s)
- Jingtao Wei
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Ke Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Yue Zhang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- The Cardiomyopathy Research Group at Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Beijing, 100037, China
| | - Ji Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xiaojiang Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xin Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Kai Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Xuesong Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China
| | - Hongfeng Lu
- Berry Genomics Corporation, Beijing, 102206, China
| | - Anqiang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.
| | - Zhaode Bu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian District, Beijing, 100142, China.
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Prasad R, Sharma K, Bhutani K, Prasad S, Manhas S, Kishan J. Identification of Genetic Variants in Exon 4 of TP53 in Lung Carcinoma and in Silico Prediction of Their Significance. Indian J Clin Biochem 2024; 39:276-282. [PMID: 38577139 PMCID: PMC10987423 DOI: 10.1007/s12291-022-01099-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
Abstract
Lung cancer is a severe and the leading cause of cancer related deaths in men and women all over the world. Tumor suppressor protein (TP53) encoded by the TP53 gene which plays a pivotal role in various cellular tumor suppression processes viz cell cycle arrest and apoptosis. Henceforth, the present study was aimed to TP53 exon4 variants from lung carcinoma. Histopathologic and clinically proven 20 patients of lung cancer were enrolled in this study the average age of patients was 45 ± 8 years which categorized as early onset of lung cancer. Genomic DNA was isolated from the blood specimen of patients. Extracted DNA was subjected to PCR amplification for exon 4 of TP53 using appropriate primers and subsequently amplified products were applied to nucleotide alterations via using the DNA sanger sequencing. The genetic analysis documented five variants in exon4 of TP53 which include viz. 4 substitutions [c.215 > C at codon 72, C. 358-359AA > GG at codon 120] were highly prevalent, occurring in 63% and 25% frequency in patients. Other two variants viz. C. 358 A > C at codon 120, C. 365T > G at codon 122 were present at frequency of 15% whilst one deletion variant [152 del C] was found with 5% frequency. Furthermore, alterations on codon 72, 120,122 and 51 were characterized as possibly damaging by Poly Phen-2 and decreased stability using stability bioinformatic tool. Taken together all these findings infer that TP53 gene involved in modulation and susceptibility to lung cancer.
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Affiliation(s)
- Rajendra Prasad
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Kirti Sharma
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Karanpreet Bhutani
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Suvarna Prasad
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
- Department of Biochemistry, AIIMS, Deoghar, India
| | - Sunita Manhas
- Department of Biochemistry, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
| | - Jai Kishan
- Department of Respiratory Medicine, M.M. Institute of Medical Sciences and Research (MMIMSR), Maharishi Markandeshwar University (MMU), Mullana, Ambala India
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Lee JY, Bhandare RR, Boddu SHS, Shaik AB, Saktivel LP, Gupta G, Negi P, Barakat M, Singh SK, Dua K, Chellappan DK. Molecular mechanisms underlying the regulation of tumour suppressor genes in lung cancer. Biomed Pharmacother 2024; 173:116275. [PMID: 38394846 DOI: 10.1016/j.biopha.2024.116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Tumour suppressor genes play a cardinal role in the development of a large array of human cancers, including lung cancer, which is one of the most frequently diagnosed cancers worldwide. Therefore, extensive studies have been committed to deciphering the underlying mechanisms of alterations of tumour suppressor genes in governing tumourigenesis, as well as resistance to cancer therapies. In spite of the encouraging clinical outcomes demonstrated by lung cancer patients on initial treatment, the subsequent unresponsiveness to first-line treatments manifested by virtually all the patients is inherently a contentious issue. In light of the aforementioned concerns, this review compiles the current knowledge on the molecular mechanisms of some of the tumour suppressor genes implicated in lung cancer that are either frequently mutated and/or are located on the chromosomal arms having high LOH rates (1p, 3p, 9p, 10q, 13q, and 17p). Our study identifies specific genomic loci prone to LOH, revealing a recurrent pattern in lung cancer cases. These loci, including 3p14.2 (FHIT), 9p21.3 (p16INK4a), 10q23 (PTEN), 17p13 (TP53), exhibit a higher susceptibility to LOH due to environmental factors such as exposure to DNA-damaging agents (carcinogens in cigarette smoke) and genetic factors such as chromosomal instability, genetic mutations, DNA replication errors, and genetic predisposition. Furthermore, this review summarizes the current treatment landscape and advancements for lung cancers, including the challenges and endeavours to overcome it. This review envisages inspired researchers to embark on a journey of discovery to add to the list of what was known in hopes of prompting the development of effective therapeutic strategies for lung cancer.
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Affiliation(s)
- Jia Yee Lee
- School of Health Sciences, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Richie R Bhandare
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates.
| | - Sai H S Boddu
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada, Chebrolu, Guntur, Andhra Pradesh 522212, India; Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India
| | - Lakshmana Prabu Saktivel
- Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University, Tiruchirappalli 620024, India
| | - Gaurav Gupta
- Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; School of Pharmacy, Suresh Gyan Vihar University, Jaipur, Rajasthan 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University, PO Box 9, Solan, Himachal Pradesh 173229, India
| | - Muna Barakat
- Department of Clinical Pharmacy & Therapeutics, Applied Science Private University, Amman-11937, Jordan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara 144411, India; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Kamal Dua
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
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8
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Najafiyan B, Bokaii Hosseini Z, Esmaelian S, Firuzpour F, Rahimipour Anaraki S, Kalantari L, Hheidari A, Mesgari H, Nabi-Afjadi M. Unveiling the potential effects of resveratrol in lung cancer treatment: Mechanisms and nanoparticle-based drug delivery strategies. Biomed Pharmacother 2024; 172:116207. [PMID: 38295754 DOI: 10.1016/j.biopha.2024.116207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 03/03/2024] Open
Abstract
Lung cancer ranks among the most prevalent forms of cancer and remains a significant factor in cancer-related mortality across the world. It poses significant challenges to healthcare systems and society as a whole due to its high incidence, mortality rates, and late-stage diagnosis. Resveratrol (RV), a natural compound found in various plants, has shown potential as a nanomedicine for lung cancer treatment. RV has varied effects on cancer cells, including promoting apoptosis by increasing pro-apoptotic proteins (Bax and Bak) and decreasing anti-apoptotic proteins (Bcl-2). It also hinders cell proliferation by influencing important signaling pathways (MAPK, mTOR, PI3K/Akt, and Wnt/β-catenin) that govern cancer progression. In addition, RV acts as a potent antioxidant, diminishing oxidative stress and safeguarding cells against DNA damage. However, using RV alone in cancer treatment has drawbacks, such as low bioavailability, lack of targeting ability, and susceptibility to degradation. In contrast, nanoparticle-based delivery systems address these limitations and hold promise for improving treatment outcomes in lung cancer; nanoparticle formulations of RV offer advantages such as improved drug delivery, increased stability, controlled release, and targeted delivery to lung cancer cells. This article will provide an overview of lung cancer, explore the potential of RV as a therapeutic agent, discuss the benefits and challenges of nanoparticle-based drug delivery, and highlight the promise of RV nanoparticles for cancer treatment, including lung cancer. By optimizing these systems for clinical application, future studies aim to enhance overall treatment outcomes and improve the prognosis for lung cancer patients.
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Affiliation(s)
- Behnam Najafiyan
- Faculty of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
| | | | - Samar Esmaelian
- Faculty of Dentistry, Islamic Azad University, Tehran Branch, Tehran, Iran
| | - Faezeh Firuzpour
- Student of Research Committee, Babol University of Medical Sciences, Babol, Iran
| | | | - Leila Kalantari
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Ali Hheidari
- Department of Mechanical Engineering, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Hassan Mesgari
- Oral and Maxillofacial Surgery Department, Faculty of Dentistry, Islamic Azad University, Tehran Branch, Tehran, Iran.
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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9
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Siwachat S, Tantraworasin A, Lertprasertsuke N, Saeteng S. Frequency and predictive factors of nodal micro-metastasis (NMM) in resectable non-small cell lung cancer. J Thorac Dis 2024; 16:1270-1278. [PMID: 38505058 PMCID: PMC10944788 DOI: 10.21037/jtd-23-1240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024]
Abstract
Background The frequency of lymph nodal micrometastasis (NMM) in resectable non-small cell lung cancer (NSCLC) is frequently underestimated when relying solely on standard hematoxylin and eosin staining during pathological examination. Methods This is a retrospective cross-sectional diagnostic research. Medical records of resectable pN0 NSCLC patients who underwent curative resection in Maharaj Nakorn Chiang Mai Hospital between January 2006 to December 2017 were retrospectively reviewed. Immunohistochemistry (IHC) staining using cytokeratin AE1/AE3, p53 and BerEP4 markers was employed to detect NMM. Primary objective of this study was to determine frequency of NMM in pN0 resectable NSCLC. Results This study included 98 patients with pN0 NSCLC, of which 47 were male and 51 were female. NMM was detected in 21 of 98 patients (21.43%). Lymph node station 10 and 7 were the most common site of micrometastasis among patients with N1 and N2 micrometastasis, respectively. Cytokeratin AE1/AE3 was the most sensitive antibody in detecting micrometastasis in lymph nodes, identifying 25 out of 27 positive lymph nodes. Tumor size greater than 4 cm was a statistically significant predictive factor for NMM with risk ratio 6.69 [95% confidence interval (CI): 2.38-18.85, P<0.001]. Conclusions NMM was identified in 21.43% of pN0 resectable NSCLC patients and tumor size greater than 4 cm is predictive factor for NMM.
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Affiliation(s)
- Sophon Siwachat
- General Thoracic Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Clinical Surgical Research Center, Chiang Mai University, Chiang Mai, Thailand
- Clinical Epidemiology and Clinical Statistic Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Apichat Tantraworasin
- General Thoracic Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Clinical Surgical Research Center, Chiang Mai University, Chiang Mai, Thailand
- Clinical Epidemiology and Clinical Statistic Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nirush Lertprasertsuke
- Department of Pathology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Somcharoen Saeteng
- General Thoracic Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Clinical Surgical Research Center, Chiang Mai University, Chiang Mai, Thailand
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10
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Ye Z, Huang T, Hu K, Zhou H, Huang L, Wang L. Genomic Profiling Reveals Immune-Related Gene Differences in Lung Cancer Patients Stratified by PD1/PDL1 Expression: Implications for Immunotherapy Efficacy. J Appl Genet 2024:10.1007/s13353-024-00841-8. [PMID: 38363451 DOI: 10.1007/s13353-024-00841-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Lung cancer remains a leading cause of global cancer-related mortality, and the exploration of innovative therapeutic approaches, such as PD1/PDL1 immunotherapy, is critical. This study leverages comprehensive data from the Cancer Genome Atlas (TCGA) to investigate the differential expression of PD1/PDL1 in lung cancer patients and explores its implications. Clinical data, RNA expression, somatic mutations, and copy number variations of 1017 lung cancer patients were obtained from TCGA. Patients were categorized into high (HE) and low (LE) PD1/PDL1 expression groups based on mRNA levels. Analyses included differential gene expression, functional enrichment, protein-protein interaction networks, and mutational landscape exploration. The study identified 391 differentially expressed genes, with CD4 and PTPRC among the upregulated genes in the HE group. Although overall survival did not significantly differ between HE and LE groups, enrichment analysis revealed a strong association with immunoregulatory signaling pathways, emphasizing the relevance of PD1/PDL1 in immune response modulation. Notably, TP53 mutations were significantly correlated with high PD1/PDL1 expression. This study provides a comprehensive analysis of PD1/PDL1 expression in lung cancer, uncovering potential biomarkers and highlighting the intricate interplay between PD1/PDL1 and the immune response. The identified upregulated genes, including CD4 and PTPRC, warrant further investigation for their roles in the context of lung cancer and immunotherapy. The study underscores the importance of considering molecular heterogeneity in shaping personalized treatment strategies for lung cancer patients. Limitations, such as the retrospective nature of TCGA data, should be acknowledged.
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Affiliation(s)
- Zhifeng Ye
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Zhejiang, Hangzhou, China
| | - Ting Huang
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Zhejiang, Hangzhou, China
| | - Keke Hu
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Zhejiang, Hangzhou, China
| | - HeRan Zhou
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Zhejiang, Hangzhou, China
| | - Ling Huang
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Zhejiang, Hangzhou, China
| | - Lu Wang
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Zhejiang, Hangzhou, China.
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11
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Kanagasabai T, Dunbar Z, Ochoa SG, Farris T, Dhandayuthapani S, Wijeratne EMK, Gunatilaka AAL, Shanker A. Bortezomib in Combination with Physachenolide C Reduces the Tumorigenic Properties of KRAS mut/P53 mut Lung Cancer Cells by Inhibiting c-FLIP. Cancers (Basel) 2024; 16:670. [PMID: 38339421 PMCID: PMC10854725 DOI: 10.3390/cancers16030670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Defects in apoptosis regulation are one of the classical features of cancer cells, often associated with more aggressiveness and failure to therapeutic options. We investigated the combinatorial antitumor effects of a natural product, physachenolide C (PCC) and bortezomib, in KRASmut/P53mut lung cancer cells and xenograft mice models. METHODS The in vitro anticancer effects of the bortezomib and PCC combination were investigated using cell viability, migration, and invasion assays in 344SQ, H23, and H358 cell lines. Furthermore, the effects of combination treatment on the critical parameters of cellular metabolism, including extracellular acidification rate (ECAR) and mitochondrial oxidative phosphorylation based on the oxygen consumption rate of cancer cells were assessed using Seahorse assay. Finally, the antitumor effect of the bortezomib (1 mg/kg) and PCC (10 mg/kg) combination was evaluated using xenograft mice models. RESULTS Our data showed that the bortezomib-PCC combination was more effective in reducing the viability of lung cancer cells in comparison with the individual treatments. Similarly, the combination treatment showed a significant inhibition of cell migration and invasion of cancer cells. Additionally, the key anti-apoptotic protein c-FLIP was significantly inhibited along with a substantial reduction in the key parameters of cellular metabolism in cancer cells. Notably, the bortezomib or PCC inhibited the tumor growth compared to the control group, the tumor growth inhibition was much more effective when bortezomib was combined with PCC in tumor xenograft mice models. CONCLUSION These findings demonstrate that PCC sensitizes cancer cells to bortezomib, potentially improving the antitumor effects against KRASmut/P53mut lung cancer cells, with an enhanced efficacy of combination treatments without causing significant side effects.
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Affiliation(s)
- Thanigaivelan Kanagasabai
- Department of Biomedical Sciences, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208, USA; (T.K.); (T.F.)
| | - Zerick Dunbar
- Department of Microbiology, Immunology & Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Salvador González Ochoa
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Tonie Farris
- Department of Biomedical Sciences, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208, USA; (T.K.); (T.F.)
| | | | - E. M. Kithsiri Wijeratne
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture, Life and Environmental Sciences, The University of Arizona, Tucson, AZ 85719, USA; (E.M.K.W.)
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture, Life and Environmental Sciences, The University of Arizona, Tucson, AZ 85719, USA; (E.M.K.W.)
| | - Anil Shanker
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
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12
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Dwivedi K, Rajpal A, Rajpal S, Kumar V, Agarwal M, Kumar N. XL 1R-Net: Explainable AI-driven improved L 1-regularized deep neural architecture for NSCLC biomarker identification. Comput Biol Chem 2024; 108:107990. [PMID: 38000327 DOI: 10.1016/j.compbiolchem.2023.107990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/29/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND AND OBJECTIVE Non-small cell lung cancer (NSCLC) exhibits intrinsic molecular heterogeneity, primarily driven by the mutation of specific biomarkers. Identification of these biomarkers would assist not only in distinguishing NSCLC into its major subtypes - Adenocarcinoma and Squamous Cell Carcinoma, but also in developing targeted therapy. Medical practitioners use one or more types of omic data to identify these biomarkers, copy number variation (CNV) being one such type. CNV provides a measure of genomic instability, which is considered a hallmark of carcinoma. However, the CNV data has not received much attention for biomarker identification. This paper aims to identify biomarkers for NSCLC using CNV data. METHODS An eXplainable AI (XAI)-driven L1-regularized deep learning architecture, XL1R-Net, is proposed that introduces a novel modification of the standard L1-regularized gradient descent algorithm to arrive at an improved deep neural classifier for NSCLC subtyping. Further, XAI-based feature identification has been used to leverage the trained classifier to uncover a set of twenty NCSLC-relevant biomarkers. RESULTS The identified biomarkers are evaluated based on their classification performance and clinical relevance. Using Multilayer Perceptron (MLP)-based model, a classification accuracy of 84.95% using 10-fold cross-validation is achieved. Moreover, the statistical significance test on the classification performance also revealed the superiority of the MLP model over the competitive machine learning models. Further, the publicly available Drug-Gene Interaction Database reveals twelve of the identified biomarkers as potentially druggable. The K-M Plotter tool was used to verify eighteen of the identified biomarkers with a high probability of predicting NSCLC patients' likelihood of survival. While nine of the identified biomarkers confirm the recent literature, five find mention in the OncoKB Gene List. CONCLUSION A set of seven novel biomarkers that have not been reported in the literature could be investigated for their potential contribution towards NSCLC therapy. Given NSCLC's genetic diversity, using only one omics data type may not adequately capture the tumor's complexity. Multiomics data and its integration with other sources will be examined in the future to better understand NSCLC heterogeneity.
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Affiliation(s)
- Kountay Dwivedi
- Department of Computer Science, University of Delhi, Delhi, India.
| | - Ankit Rajpal
- Department of Computer Science, University of Delhi, Delhi, India.
| | - Sheetal Rajpal
- Department of Computer Science, Dyal Singh College, Delhi, India.
| | - Virendra Kumar
- Department of Nuclear Magnetic Resonance, All India Institute of Medical Sciences, New Delhi, India.
| | - Manoj Agarwal
- Department of Computer Science, Hans Raj College, University of Delhi, Delhi, India.
| | - Naveen Kumar
- Department of Computer Science, University of Delhi, Delhi, India.
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13
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Vescio M, Bulloni M, Pelosi G, Pattini L. Lack of imbalance between the master regulators TTF1/NKX2-1 and ΔNp63/p40 implies adverse prognosis in non-small cell lung cancer. Sci Rep 2024; 14:2467. [PMID: 38291083 PMCID: PMC10827720 DOI: 10.1038/s41598-024-52776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
The transcription factors TTF1/NKX2-1 and ΔNp63/p40 are the counterposed molecular markers associated with the main Non-Small Cell Lung Cancer subtypes: TTF1 for adenocarcinoma, p40 for squamous cell carcinoma. Although they generally display a mutually exclusive expression, some exceptions exist simultaneously lacking or (very rarely) expressing both markers, either pattern being associated to poor prognosis. Hence, we quantitatively analyzed the relationship between their coordinated activity and prognosis. By analyzing the respective downstream transcriptional programs of the two genes, we defined a simple quantitative index summarizing the amount of mutual exclusivity between their activities, called Mean Absolute Activity (MAA). Systematic analysis of the MAA index in a dataset of 1018 NSCLC samples replicated on a validation dataset of 275 showed that the loss of imbalance between TTF-1 and p40 corresponds to a steady, progressive reduction in both overall and recurrence-free survival. Coherently, samples correspondent to more balanced activities were enriched for pathways related to increased malignancy and invasiveness. Importantly, multivariate analysis showed that the prognostic significance of the proposed index MAA is independent of other clinical variables including stage, sex, age and smoke exposure. These results hold irrespectively of tumor morphology across NSCLC subtypes, providing a unifying description of different expression patterns.
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Affiliation(s)
- Martina Vescio
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
- CardioTech, IRCCS Centro Cardiologico Monzino, Milan, Italy
| | - Matteo Bulloni
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Inter-Hospital Pathology Division, IRCCS MultiMedica, Milan, Italy
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy.
- CardioTech, IRCCS Centro Cardiologico Monzino, Milan, Italy.
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14
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Mendoza RP, Chen‐Yost HI, Wanjari P, Wang P, Symes E, Johnson DN, Reeves W, Mueller J, Antic T, Biernacka A. Lung adenocarcinomas with isolated TP53 mutation: A comprehensive clinical, cytopathologic and molecular characterization. Cancer Med 2024; 13:e6873. [PMID: 38164123 PMCID: PMC10824142 DOI: 10.1002/cam4.6873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/14/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND TP53 mutation is present in about 50.8% of lung adenocarcinomas, frequently in combination with other genetic alterations. However, a rare subset harbors the TP53 mutation alone. METHODS Next-generation sequencing was performed in 840 lung adenocarcinomas diagnosed by fine needle aspiration. Fourteen cases (1.7%) showed isolated TP53 alteration and were subjected to a comprehensive analysis. RESULTS The average age at diagnosis was 65 years (range 48-79); 9 males and 5 females. All were smokers with an average pack-year of 41 (range 10-70). Nine had metastases, mostly in the brain (n = 2) and pleura (n = 2). After a follow-up period of up to 102 months, 9 died, 4 were alive with disease, and 1 was lost to follow-up. The median survival was 13 months. Most tumors exhibited poor differentiation, composed of solid sheets with moderate to severe atypia, increased mitotic activity, and necrotic background. Half were positive for TTF-1 and showed p53 overexpression. PD-L1 was positive in 6 cases. Most alterations were missense mutations in exons 5-8, and this mutation type was associated with p53 overexpression. Tumors with combined missense mutation and truncated protein had higher PD-L1 expression and significantly shorter overall survival, along with a trend towards an increase in tumor mutational burden (TMB). CEBPA deletion of undetermined significance was the most common copy number alteration. CONCLUSION Isolated TP53 mutation was seen in association with smoking, high-grade cytomorphologic features, adverse prognosis, and recurrent CEBPA deletions. These tumors tend to have strong PD-L1 expression and high TMB, suggesting potential benefit from immune checkpoint inhibitors. Hence, the recognition of this molecular group has prognostic and therapeutic implications.
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Affiliation(s)
- Rachelle P. Mendoza
- Department of PathologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | | | - Pankhuri Wanjari
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
| | - Peng Wang
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
| | - Emily Symes
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
| | - Daniel N. Johnson
- Department of PathologyOSF Little Company of Mary Medical CenterEvergreen ParkIllinoisUSA
| | - Ward Reeves
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
| | - Jeffrey Mueller
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
| | - Tatjana Antic
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
| | - Anna Biernacka
- Department of PathologyThe University of Chicago HospitalsChicagoIllinoisUSA
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15
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Moes-Sosnowska J, Szpechcinski A, Chorostowska-Wynimko J. Clinical significance of TP53 alterations in advanced NSCLC patients treated with EGFR, ALK and ROS1 tyrosine kinase inhibitors: An update. Tumour Biol 2024; 46:S309-S325. [PMID: 37840519 DOI: 10.3233/tub-230034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The development of targeted therapies for non-small cell lung cancer (NSCLC), such as the epidermal growth factor receptor (EGFR), anaplastic lymphoma receptor tyrosine kinase (ALK), and ROS proto-oncogene 1 (ROS1), has improved patients' prognosis and significantly extended progression-free survival. However, it remains unclear why some patients do not benefit from the treatment as much or have a rapid disease progression. It is considered that, apart from the oncogenic driver gene, molecular alterations in a number of caretaker and gatekeeper genes significantly impact the efficacy of targeted therapies. The tumor protein 53 (TP53) gene is one of the most frequently mutated genes in NSCLC. To date, numerous studies have investigated the influence of various TP53 alterations on patient prognosis and responsiveness to therapies targeting EGFR, ALK, or ROS1. This review focuses on the latest data concerning the role of TP53 alterations as prognostic and/or predictive biomarkers for EGFR, ALK, and ROS1 tyrosine kinase inhibitors (TKIs) in advanced NSCLC patients. Since the presence of TP53 mutations in NSCLC has been linked to its decreased responsiveness to EGFR, ALK, and ROS1 targeted therapy in most of the referenced studies, the review also discusses the impact of TP53 mutations on treatment resistance. It seems plausible that assessing the TP53 mutation status could aid in patient stratification for optimal clinical decision-making. However, drawing meaningful conclusions about the clinical value of the TP53 co-mutations in EGFR-, ALK- or ROS1-positive NSCLC is hampered mainly by an insufficient knowledge regarding the functional consequences of the TP53 alterations. The integration of next-generation sequencing into the routine molecular diagnostics of cancer patients will facilitate the detection and identification of targetable genetic alterations along with co-occurring TP53 variants. This advancement holds the potential to accelerate understanding of the biological and clinical role of p53 in targeted therapies for NSCLC.
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Affiliation(s)
- Joanna Moes-Sosnowska
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Adam Szpechcinski
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
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16
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Zeng P, Wang F, Zhang J, Ur Rashid H, Li X, Zhang P, Luo Y, Wu X. Integrating network pharmacology and experimental verification to investigate the pharmacological mechanisms of Buzhong Yiqi decoction in the treatment of non-small cell lung cancer. Chem Biol Drug Des 2024; 103:e14414. [PMID: 38230796 DOI: 10.1111/cbdd.14414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024]
Abstract
Among all types of cancers, non-small cell lung cancer (NSCLC) exhibits the highest mortality rate with a five-year survival rate below 17% for patients. The Buzhong Yiqi decoction (BZYQD), traditional Chinese medicine (TCM) formula, has been reported to exhibit clinical efficacy in the treatment of NSCLC. Nevertheless, the underlying molecular mechanism remains elusive. This study aimed to assess the mechanistic actions exerted by BZYQD against NSCLC using network pharmacological analysis and experimental validation. The public databases were searched for active compounds in BZYQD, their potential targets, and NSCLC-related targets. The protein-protein interaction (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the core targets and signaling pathways of BZYQD against NSCLC. After screening, this study validated the results of predictions through in vitro experiments and public databases. We found 192 common targets between BZYQD and NSCLC. KEGG analysis showed that the anti-NSCLC effects of BZYQD were mediated through the PI3K-AKT signaling pathway. The results of in vitro experiment indicated that BZYQD could inhibit cell viability and proliferation of A549 and H1299 cells apart from inducing cell apoptosis. In addition, western blot results substantiated that BZYQD could treat NSCLC by inhibiting the activation of the PI3K-AKT signaling pathway. The current study investigated the pharmacological mechanism of BZYQD against NSCLC via network pharmacology and in vitro analyses. Overall, the results revealed that BZYQD could be a promising therapeutic agent for the treatment of NSCLC in the future. Still, more experimental investigations are needed to confirm the applicability of BZYQD for clinical trials.
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Affiliation(s)
- Panke Zeng
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Feng Wang
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Jianing Zhang
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Haroon Ur Rashid
- Center for Chemical, Pharmaceutical and Food Sciences, Federal University of Pelotas (UFPel), Pelotas, Brazil
| | - Xin Li
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Pengfei Zhang
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yunru Luo
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xinyu Wu
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
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17
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Jiang T, Lu Y, Yang W, Xu J, Zhu M, Huang Y, Bao F, Zheng S, Li Y. To Explore the Mechanism of Maiwei Dihuang Decoction in the Treatment of Non-small Cell Lung Cancer based on Network Pharmacology Combined with LC-MS. Curr Comput Aided Drug Des 2024; 20:590-597. [PMID: 37612858 DOI: 10.2174/1573409920666230823161355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
OBJECTIVE To explore the mechanism of Maiwei Dihuang decoction in the treatment of non-small cell lung cancer (NSCLC) by using network pharmacology and LC-MS technology. METHODS The effective components in Maiwei Dihuang decoction were detected by liquid chromatography- mass spectrometry (LC-MS). Use the SuperPred database to collect the relevant targets of the active ingredients of Mai Wei Di Tang, and then collect the relevant targets of nonsmall cell lung cancer from GeneCards, DisgenNET and OMIM databases. On this basis, PPI network construction, GO enrichment analysis and KEGG pathway annotation analysis were carried out for target sites. Finally, AutoDock Vina is used for molecular docking. RESULTS We further screened 16 effective Chinese herbal compounds through LC-MS combined with ADME level. On this basis, we obtained 77 core targets through protein interaction network analysis. Through GO, KEGG analysis and molecular docking results, we finally screened out the potential targets of Maiwei Dihuang Decoction for NSCLC: TP53, STAT3, MAPK3. CONCLUSION Maiwei Dihuang decoction may play a role in the treatment of NSCLC by coregulating TP53/STAT3/MAPK3 signal pathway.
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Affiliation(s)
- Tao Jiang
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Yang Lu
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Wanzhi Yang
- Department of Pharmacy, Anqing First People's Hospital of Anhui Medical University, Anhui Province, China
| | - Jinhong Xu
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Mingxing Zhu
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Yong Huang
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Fang Bao
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Shengqi Zheng
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
| | - Yongxia Li
- Department of Pharmacy, Navy Anqing Hospital, Anqing, Anhui Province, China
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Choi DH, Jung HA, Park S, Sun JM, Ahn JS, Ahn MJ, Lee SH. Effectiveness and safety of amivantamab in EGFR exon 20 insertion (E20I) mutations in non-small cell lung cancer (NSCLC). Transl Lung Cancer Res 2023; 12:2448-2459. [PMID: 38205202 PMCID: PMC10775014 DOI: 10.21037/tlcr-23-643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Background In non-small cell lung cancer (NSCLC), the epidermal growth factor receptor (EGFR) mutation is a representative oncogenic driver mutation. Only about 12% of EGFR mutation patients have the exon 20 insertion mutation, which is the third most frequent mutation among EGFR mutation NSCLC. Amivantamab, an EGFR and MET proto-oncogene, receptor tyrosine kinase (MET) bispecific antibody, was approved for NSCLC patients with the EGFR exon 20 insertion (E20I) mutation. In this study, we described the real-world, single-center efficacy and safety data of amivantamab in E20I mutation patients. Methods This study included metastatic NSCLC patients with EGFR E20I mutations. From January 2018 to June 2022, patients with EGFR E20I mutations who were treated with amivantamab were analyzed at Samsung Medical Center as part of the clinical trial or the early access program (EAP). We collected the patients' characteristics [age, sex, smoking history, location of mutation, sites of metastasis, programmed death-ligand 1 (PD-L1) expression status, etc.] and analyzed progression-free survival (PFS) and overall survival (OS) stratified by PD-L1 expression status, co-mutation such as tumor protein p53 (TP53), and metastasis sites. Results A total of 42 patients were analyzed, of which 16 patients were enrolled in the phase 1 study, and 26 patients received amivantamab through EAP. There were 14 (33%) patients with partial remission, 18 (43%) patients with stable disease, and 10 (24%) patients with disease progression. The objective response rate (ORR) was 33%, and the disease control rate (DCR) was 76%. PFS was analyzed by dividing the near and far loop for 31 patients whose mutation location was known. The two groups had no statistically significant difference in PFS [median (range): 11.8 (2.3-21.3) vs. 11.3 (3.4-19.2) months, P=0.69]. For 29 patients with TP53 mutation data, there was no significant difference in PFS between the two groups [median (range): 5.9 (0-18.0) vs. 12.6 (6.9-18.3) months, P=0.11]. When analyzing PFS in 37 patients with PD-L1 expression data, PD-L1 (+) patients showed a poor prognosis [median (range): 11.3 (5.0-17.6) vs. 19.5 (5.3-33.7) months, P=0.04; hazard ratio (HR), 0.44; 95% confidence interval (CI): 0.20-0.98]. Conclusions The efficacy of amivantamab was confirmed for the real-world population for EGFR E20I-mutated NSCLC. PD-L1 status could be a poor predictive factor, which should be further validated.
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Affiliation(s)
- Dae-Ho Choi
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyun Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Mu Sun
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Duabil AJN, Cooper CR, Aldujaily E, Halford SER, Hirschberg S, Katugampola SD, Jones GDD. Investigations of the novel checkpoint kinase 1 inhibitor SRA737 in non-small cell lung cancer and colorectal cancer cells of differing tumour protein 53 gene status. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1210-1226. [PMID: 38214010 PMCID: PMC10776598 DOI: 10.37349/etat.2023.00193] [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: 06/10/2023] [Accepted: 10/16/2023] [Indexed: 01/13/2024] Open
Abstract
Aim In response to DNA damage the serine/threonine-specific protein kinase checkpoint kinase 1 (CHK1) is activated allowing cells to enter S phase (S) and G2 phase (G2) cell-cycle arrest. CHK1 inhibitors are expected to prevent cells from entering such arrest, thereby enhancing DNA damage-induced cytotoxicity. In contrast, normal cells with intact ataxia-telangiectasia mutated (ATM), CHK2 and tumour suppressor protein 53 (P53) signalling are still able to enter cell-cycle arrest using the functioning G1/S checkpoint, thereby being rescued from enhanced cytotoxicity. The main objective of this work is to investigate the in vitro effects of the novel CHK1 inhibitor SRA737 on pairs of non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) cell lines, all with genetic aberrations rendering them susceptible to replication stress but of differing tumour protein 53 (TP53) gene status, focusing on DNA damage induction and the subsequent effects on cell proliferation and viability. Methods NSCLC cell lines H23 [TP53 mutant (MUT)] and A549 [TP53 wild-type (WT)] and CRC cell lines HT29 (TP53 MUT) and HCT116 (TP53 WT) were incubated with differing micromolar concentrations of SRA737 for 24 h and then analysed using alkaline comet and phosphorylated H2A.X variant histone (γH2AX)-foci assays to assess mostly DNA single strand break and double strand break damage, respectively. Cell-counting/trypan blue staining was also performed to assess cell proliferation/viability. Results Clear concentration-dependent increases in comet formation and γH2AX-foci/cell were noted for the TP53 MUT cells with no or lower increases being noted in the corresponding TP53 WT cells. Also, greater anti-proliferative and cell killing effects were noted in the TP53 MUT cells than in the TP53 WT cells. Conclusions This study's data suggests that P53 status/functioning is a key factor in determining the sensitivity of NSCLC and CRC cancer cells towards CHK1 inhibition, even in circumstances conducive to high replicative stress.
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Affiliation(s)
- Ali JN Duabil
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, LE1 7RH Leics, UK
- Department of Surgery, Faculty of Medicine, University of Kufa, Najaf, Iraq
| | - Christian R Cooper
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, LE1 7RH Leics, UK
- MRC Oxford Institute for Radiation Oncology, University of Oxford, OX3 7DQ Oxon, UK
| | - Esraa Aldujaily
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, LE1 7RH Leics, UK
- Department of Pathology & Forensic Medicine, Faculty of Medicine, University of Kufa, Najaf, Iraq
| | - Sarah ER Halford
- Cancer Research UK Centre for Drug Development, London E20 1JQ, UK
| | | | | | - George DD Jones
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, LE1 7RH Leics, UK
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Sun X, Meng F, Nong M, Fang H, Lu C, Wang Y, Zhang P. Single-cell dissection reveals the role of aggrephagy patterns in tumor microenvironment components aiding predicting prognosis and immunotherapy on lung adenocarcinoma. Aging (Albany NY) 2023; 15:14333-14371. [PMID: 38095634 PMCID: PMC10756128 DOI: 10.18632/aging.205306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is one of the leading malignant cancers. Aggrephagy plays a critical role in key genetic events for various cancers; yet, how aggrephagy functions within the tumor microenvironment (TME) in LUAD remains to be elucidated. METHODS In this study, by sequential non-negative matrix factorization (NMF) algorithm, pseudotime analysis, cell-cell interaction analysis, and SCENIC analysis, we have shown that aggrephagy genes demonstrated various patterns among different cell types in LUAD TME. LUAD and Immunotherapy cohorts from public repository were used to determine the prognosis and immune response of aggrephagy TME subtypes. The aggrephagy-deprived prognostic score (ADPS) was quantified based on machine learning algorithms. RESULTS The cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), and CD8+ T cells have various aggrephagy patterns, which enhance the intensity of intercellular communication and transcription factor activation. Furthermore, based on the signatures of the newly defined aggrephagy cell subtypes and expression profiles of large cohorts in LUAD patients, we determine that DYNC1I2+CAF-C1, DYNLL1+CAF-C2, PARK7+CAF-C3, VIM+Mac-C1, PARK7+Mac-C2, VIM+CD8+T_cells-C1, UBA52+CD8+T_cells-C2, TUBA4A+CD8+T_ cells-C3, and TUBA1A+CD8+T_cells-C4 are crucial prognostic factors for LUAD patients. The developed ADPS could predict survival outcomes and immunotherapeutic response across ten cohorts (n = 1838), and patients with low ADPS owned a better prognosis, lower genomic alterations, and are more sensitive to immunotherapy. Meanwhile, based on PRISM, CTRP, and CMAP databases, PLK inhibitor BI-2536, may be a potential agent for patients with high ADPS. CONCLUSIONS Taken together, our novel and systematic single-cell analysis has revealed the unique role of aggrephagy in remodeling the TME of LUAD. As a newly demonstrated biomarker, the ADPS facilitates the clinical management and individualized treatment of LUAD.
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Affiliation(s)
- Xinti Sun
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Fei Meng
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Minyu Nong
- School of Clinical Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Hao Fang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chenglu Lu
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yan Wang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Peng Zhang
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
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21
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Ye B, Chen P, Lin C, Zhang C, Li L. Study on the material basis and action mechanisms of sophora davidii (Franch.) skeels flower extract in the treatment of non-small cell lung cancer. JOURNAL OF ETHNOPHARMACOLOGY 2023; 317:116815. [PMID: 37400006 DOI: 10.1016/j.jep.2023.116815] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sophora davidii (Franch.) Skeels Flower (SDF) is a characteristic folk medicine in Yunnan and Guizhou, which can be used to prevent the occurrence of tumors. The extract of SDF (SDFE) is confirmed to be antitumor by pre-experiment. However, effective components and anticancer mechanisms of SDFE are still unclear. AIM OF THE STUDY The purpose of this study was to explore the material basis and action mechanisms of SDFE in the treatment of non-small cell carcinoma (NSCLC). MATERIALS AND METHODS UHPLC-Q-Exactive-Orbitrap-MS/MS was used to identify the chemical components of SDFE. The network pharmacology was applied to screen out the main active components, core genes and related signaling pathways of SDFE in treatment of NSCLC. Molecular docking was used to predict the affinity of major components and core targets. The database was applied to predict the mRNA and protein expression levels of core targets in NSCLC. Finally, the experiments in vitro were performed by CCK-8, flow cytometry and western blot (WB). RESULTS In this study, 98 chemical components were identified by UHPLC-Q-Exactive- Orbitrap-MS/MS. 5 main active components (namely quercetin, genistein, luteolin, kaempferol, isorhamnetin), 10 core genes (namely TP53, AKT1, STAT3, SRC, MAPK3, EGFR, JUN, EP300, TNF, PIK3R1) and 20 pathways were screened out through network pharmacology. The 5 active ingredients were molecularly docked with the core genes, and most the LibDockScore values were higher than 100. The data collected from the database indicated that TP53, AKT1 and PIK3R1 were closely related to the occurrence of NSCLC. The results of experiment in vitro showed that SDFE promoted NSCLC cells apoptosis by down-regulating the phosphorylation of PI3K, AKT and MDM2, up-regulating the phosphorylation of P53, inhibiting the expression of Bcl-2 and up-regulating the expression of Bax. CONCLUSION The combination of network pharmacology, molecular docking, database validation, and in vitro experimental validation effectively demonstrates that SDFE can promote cell apoptosis by regulating PI3K-AKT/MDM2-P53 signaling pathway, so as to treat NSCLC.
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Affiliation(s)
- Baibai Ye
- Gannan Medical University, Ganzhou, 341000, China.
| | - Ping Chen
- Gannan Medical University, Ganzhou, 341000, China.
| | - Cheng Lin
- Gannan Medical University, Ganzhou, 341000, China.
| | - Chenning Zhang
- Department of Pharmacy, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, 441100, China.
| | - Linfu Li
- Gannan Medical University, Ganzhou, 341000, China.
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22
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Nasuh S, Balci SO, Bozgeyik I, Ikeda MA, Tekayev M, Saadat KASM. ARID3A and ARID3B exert direct regulatory control over the long non-coding RNAs (lncRNAs) MALAT1 and NORAD within the context of non-small cell lung cancer (NSCLC). Pathol Res Pract 2023; 252:154948. [PMID: 37977034 DOI: 10.1016/j.prp.2023.154948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Lung cancer, known for its high mortality rates and poor prognosis, remains one of the most prevalent cancer types. Early detection and effective treatment methods are crucial for improving survival rates. Non-small cell lung cancer (NSCLC) accounts for approximately 85 % of all lung cancer cases. Long non-coding RNAs (lncRNAs), which play vital roles in various biological processes, have been implicated in the development of cancer and can impact key therapeutic targets in different cancer types. In NSCLC, the dysregulation of specific lncRNAs, such as MALAT1 and NORAD, has been associated with neoplastic initiation, progression, metastasis, tumor angiogenesis, chemoresistance, and genomic instability. Both MALAT1 and NORAD directly regulate the expression of the transcription factor E2F1, thereby influencing cell cycle progression. Additionally, MALAT1 has been reported to affect the expression of p53 target genes, leading to cell cycle progression through the repression of p53 promoter activity. NORAD, on the other hand, is indirectly regulated by p53. The AT-rich interaction domain (ARID) family of DNA-binding proteins, particularly ARID3A and ARID3B, are involved in various biological processes such as cell proliferation, differentiation, and development. They also play significant roles in E2F-dependent transcription and are transcriptional targets of p53. The intricate balance between promoting cellular proliferation through the pRB-E2F pathway and inducing growth arrest through the p53 pathway underscores the crucial regulatory role of ARID3A, ARID3B, and their interaction with lncRNAs MALAT1 and NORAD. In this study, we aimed to investigate the potential interactive and functional connections among ARID3A, ARID3B, MALAT1, and NORAD in NSCLC, considering their involvement in the pRB-E2F and p53 pathways. Our findings strongly suggest that ARID3A and ARID3B play a regulatory role in controlling MALAT1 and NORAD in NSCLC. Specifically, our study demonstrates that the activities of MALAT1 and NORAD were markedly increased upon the overexpression of ARID3A and ARID3B. Therefore, we can conclude that ARID3A and ARID3B likely contribute significantly to the oncogenic functions of MALAT1 and NORAD in NSCLC. Consequently, targeting ARID3A and ARID3B could hold promise as a therapeutic approach in NSCLC, given their direct control over the expression of MALAT1 and NORAD.
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Affiliation(s)
- Sedin Nasuh
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey
| | - Sibel Oguzkan Balci
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey
| | - Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine Adiyaman University, Adiyaman 02040, Turkey
| | - Masa-Aki Ikeda
- Department of Regenerative and Reconstructive Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Muhammetnur Tekayev
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey; Department of Histology and Embryology, Hamidiye Faculty of Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences, Istanbul 34668, Turkey
| | - Khandakar A S M Saadat
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey.
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Li H, Lei Y, Li G, Huang Y. Identification of tumor-suppressor genes in lung squamous cell carcinoma through integrated bioinformatics analyses. Oncol Res 2023; 32:187-197. [PMID: 38188687 PMCID: PMC10767242 DOI: 10.32604/or.2023.030656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/20/2023] [Indexed: 01/09/2024] Open
Abstract
Lung cancer is a prevalent malignancy, and fatalities of the disease exceed 400,000 cases worldwide. Lung squamous cell carcinoma (LUSC) has been recognized as the most common pathological form of lung cancer. The comprehensive understanding of molecular features related to LUSC progression has great significance in LUSC prognosis assessment and clinical management. In this study, we aim to identify a panel of signature genes closely associated with LUSC, which can provide novel insights into the progression of LUSC. Gene expression profiles were retrieved from public resources including gene expression omnibus (GEO) and the cancer genome atlas (TCGA) database. Differentially expressed genes (DEGs) between LUSC specimens and normal lung tissues were identified by bioinformatics analyses. A total of 66 DEGs were identified based on two cohorts of data. CytoHubba plugin of Cytoscape software was utilized for the further analyses of the top 10 candidate hub genes including OGN, ABI3BP, MAMDC2, FGF7, FAM107A, SPARCL1, DCN, COL14A1, and MFAP4 and CHRDL1, which showed significant downregulation in LUSC. Two LUSC cell lines were used to validate the functions of CHRDL1 and FAM107A through overexpression experiment. Together, our data revealed novel candidate tumor-suppressor genes in LUSC, suggesting previously unappreciated mechanisms in the progression of LUSC.
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Affiliation(s)
- Heng Li
- The 2nd Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Tumor Hospital, Kunming, 650118, China
| | - Youming Lei
- Department of Geriatric Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Gaofeng Li
- The 2nd Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Tumor Hospital, Kunming, 650118, China
| | - Yunchao Huang
- The 1st Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Tumor Hospital, Kunming, 650118, China
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Zhu L, Zhou D, Chen Y, Guo T, Chen W, Pan X. Correlation Analysis of the TP53 Mutation With Clinical Characteristics in the Prognosis of Non-Small Cell Lung Cancer. Clin Med Insights Oncol 2023; 17:11795549231184918. [PMID: 37823008 PMCID: PMC10563498 DOI: 10.1177/11795549231184918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/12/2023] [Indexed: 10/13/2023] Open
Abstract
Background Non-small cell lung cancer (NSCLC) with TP53 mutations has a worse prognosis. It was generally more resistant to chemotherapy and radiation. Our aim was to investigate the correlation between the TP53 co-mutated gene and clinical features, and prognostic value in patients with NSCLC. Methods Seventy-three patients with a diagnosis of NSCLC at our hospital were recruited. They were divided into the TP53 mutation status (minor) (TP53 MU) and TP53 wild-type (major) (TP53 WT) groups according to their clinical characteristics after their mutation data and clinical information were collected. Serum markers were compared between groups using Mann-Whitney U test. Other clinical factors were compared between groups using χ2 test and Fisher exact test. The log-rank test was used to compare survival curves. Results Of the 73 patients with NSCLC, 37 (50.68%) were found to carry TP53 mutation. TP53 MU and TP53 WT groups (n = 36) showed a significant difference in the number of smokers, incidence of squamous cell carcinoma, EGFR mutation, and number of advanced patients (P < .05), while gender, age, lymph node metastasis, and KRAS mutation did not differ significantly between the 2 groups. The survival curves in the TP53/KRAS and the TP53/EGFR co-mutation groups suggest that patients with NSCLC may have a shorter progression-free survival (PFS) if they carry one of the 2 types of co-mutation. Conclusions TP53 gene mutations are more common in patients with NSCLC and squamous cell carcinoma. New predictive markers for NSCLC prognosis may be TP53/KRAS and TP53/EGFR co-mutations.
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Affiliation(s)
- Lihuan Zhu
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Dongsheng Zhou
- Department of Radiology, Fujian Provincial Hospital and Provincial Clinical College, Fujian Medical University, Fuzhou, China
| | - Yiyong Chen
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Tianxing Guo
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Wenshu Chen
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
| | - Xiaojie Pan
- Department of Thoracic Surgery, Fujian Provincial Hospital and Provincial Clinical College of Fujian Medical University, Fuzhou, China
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Paudel KR, Rajput R, De Rubis G, Raju Allam VSR, Williams KA, Singh SK, Gupta G, Salunke P, Hansbro PM, Gerlach J, Dua K. In vitro anti-cancer activity of a polyherbal preparation, VEDICINALS®9, against A549 human lung adenocarcinoma cells. Pathol Res Pract 2023; 250:154832. [PMID: 37774532 DOI: 10.1016/j.prp.2023.154832] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE Non-small cell lung cancer (NSCLC) is among the leading causes of morbidity and mortality worldwide. Despite the availability of several treatment options, the five-year survival rate of NSCLC is extremely low (<20%). This underlines the necessity of more effective therapeutic alternatives. In this context, plant-derived extracts and bioactive molecules extracted from plants, known collectively as phytoceuticals, represent an extremely variegated source of bioactive compounds with potent anticancer potential. In the present study, we tested the in vitro anticancer activity of a polyherbal preparation, VEDICINALS®9, containing nine different bioactive principles extracted by medicinal plants. METHODS The anticancer activity of VEDICINALS®9 was investigated by measuring its impact on A549 human NSCLC cell proliferation (MTT assay and trypan blue staining), migration (wound healing assay and transwell chamber assay) and by measuring the impact on the expression of cancer-related proteins (Human XL Oncology Protein Array). RESULTS We show that VEDICINALS®9 at a concentration of 0.2% v/v has potent anticancer effect, significantly inhibiting A549 cell proliferation and migration. Mechanistically, this was achieved by downregulating the expression of proteins involved in cancer cell proliferation (Axl, FGF basic, enolase 2, progranulin, survivin) and migration (Dkk-1, cathepsins B and D, BCL-x, amphiregulin, CapG, u-plasminogen activator). Furthermore, treatment with VEDICINALS®9 resulted in increased expression of the oncosuppressor protein p53 and of the angiogenesis inhibitor endostatin. CONCLUSIONS Taken together, our results provide proof of principle of the potent anticancer activity of the polyherbal preparation VEDICINALS®9, highlighting its enormous potential as an alternative or adjuvant therapy for lung cancer.
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Affiliation(s)
- Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia
| | - Rashi Rajput
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Gabriele De Rubis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Venkata Sita Rama Raju Allam
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (BMC), Uppsala University, Uppsala, Sweden
| | - Kylie Anne Williams
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Sachin Kumar Singh
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jaipur, Rajasthan, India; Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | | | - Philip Michael Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia
| | | | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia.
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Guo X, Dong L, Liu H, Chen X. TP53, NOTCH2, and STK11 Mutations in a Rare Tumor of non-Small Cell Lung Carcinoma with Diffuse Coexpression of TTF1 and p40 in the Same Tumor Cells. Int J Surg Pathol 2023; 31:1041-1047. [PMID: 36253711 DOI: 10.1177/10668969221126105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Introduction. Five cases of non-small cell lung carcinoma (NSCLC) with diffuse coexpression of TTF1 and p40 in the same tumor cells (hereafter referred to as TTF1/P40-NSCLC) have been reported since 2015. It was considered a new entity of NSCLC occurred in aged male smokers with poorly differentiated carcinomas and a similar molecular signature harboring a TP53 mutation. Methods. We report an extremely rare tumor of TTF1/P40-NSCLC. Morphological observation and immunohistochemical examination were performed, clinical and molecular features were summarized, and a review of the relevant literature was provided. Results. The tumor showed a solid growth pattern with patchy necrosis, and glandular and squamous pattern were not obvious. The tumor cells proliferated within the bronchial epithelium. Spreading through air spaces of tumor cells were observed. A peculiar immunohistochemical phenotype of diffuse and strong positivity for TTF1 (8G7G3/1) and p40 in the same tumor cells was detected. Additionally, the tumor cells were positive for KRT7 and KRT20, while negative for PD-L1 (22C3). Negative P53 (null) Immunohistochemistry (IHC) staining indicated mutational status and the Ki67 index was 80%. Molecular investigation was performed using whole exome sequencing, and TP53, NOTCH2, and STK11 mutations were detected. The patient remained alive over a follow-up period of 22 months without tumor recurrence or metastasis. Conclusions. We describe an unusual tumor of TTF1/P40-NSCLC harboring TP53, NOTCH2 and STK11 mutations. These gene mutations may be helpful in providing additional therapeutic possibilities. Our report offers further insight into this rare tumor.
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Affiliation(s)
- Xingmei Guo
- Department of Pathology, The Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hengan Liu
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoyan Chen
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Li X, Chen J, Meng J. Comprehensive analysis of the prognostic values and immune implication of ESYT3 in lung adenocarcinoma. Medicine (Baltimore) 2023; 102:e34557. [PMID: 37657044 PMCID: PMC10476797 DOI: 10.1097/md.0000000000034557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/12/2023] [Indexed: 09/03/2023] Open
Abstract
Few studies have reported the association between ESYT3 and tumors. The purpose of this study was to investigate the molecular features and potential roles of ESYT3 in lung adenocarcinoma (LUAD). In the present study, GEPIA, UALCAN, TCGA databases, and KM Plotter were primarily used to study ESYT3 mRNA expression profiles and prognostic values in patients with LUAD. Then we evaluated co-expressed genes of ESYT3 by cBioPortal online tools and performed enrichment analysis using Metascape. Moreover, the relationship between ESYT3 and immune infiltrating cells was explored via TIMER2, and MethSurv database was used to conduct methylation analysis. We found ESYT3 was downregulated in LUAD tissues based on TCGA and GEPIA databases. Low expression of ESYT3 mRNA was observed to be significantly correlated with N classification and stage classification. GEPIA2, UALCAN databases and KM Plotter showed that low expression levels of ESYT3 was associated with poor survival in LUAD patients. The enrichment analysis indicated that co-expressed genes of ESYT3 were highly enriched in cell division. Then, our study showed ESYT3 was correlated with immune infiltration and immune checkpoints. Additionally, hypomethylation was associated with low ESYT3 expression and poor prognosis in LUAD. In conclusion, this study suggested ESYT3 could be a potential prognostic marker and a promising therapeutic target in LUAD.
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Affiliation(s)
- Xuedong Li
- Medical Science Laboratory, Liuzhou Worker’s Hospital, Liuzhou, Guangxi, China
| | - Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Jie Meng
- Medical Science Laboratory, Liuzhou Worker’s Hospital, Liuzhou, Guangxi, China
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28
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Kim JW, Kim MJ, Han TH, Lee JY, Kim S, Kim H, Oh KJ, Kim WK, Han BS, Bae KH, Ban HS, Bae SH, Lee SC, Lee H, Lee EW. FSP1 confers ferroptosis resistance in KEAP1 mutant non-small cell lung carcinoma in NRF2-dependent and -independent manner. Cell Death Dis 2023; 14:567. [PMID: 37633973 PMCID: PMC10460413 DOI: 10.1038/s41419-023-06070-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/02/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Ferroptosis, a type of cell death induced by lipid peroxidation, has emerged as a novel anti-cancer strategy. Cancer cells frequently acquire resistance to ferroptosis. However, the underlying mechanisms are poorly understood. To address this issue, we conducted a thorough investigation of the genomic and transcriptomic data derived from hundreds of human cancer cell lines and primary tissue samples, with a particular focus on non-small cell lung carcinoma (NSCLC). It was observed that mutations in Kelch-like ECH-associated protein 1 (KEAP1) and subsequent nuclear factor erythroid 2-related factor 2 (NRF2, also known as NFE2L2) activation are strongly associated with ferroptosis resistance in NSCLC. Additionally, AIFM2 gene, which encodes ferroptosis suppressor protein 1 (FSP1), was identified as the gene most significantly correlated with ferroptosis resistance, followed by multiple NRF2 targets. We found that inhibition of NRF2 alone was not sufficient to reduce FSP1 protein levels and promote ferroptosis, whereas FSP1 inhibition effectively sensitized KEAP1-mutant NSCLC cells to ferroptosis. Furthermore, we found that combined inhibition of FSP1 and NRF2 induced ferroptosis more intensely. Our findings imply that FSP1 is a crucial suppressor of ferroptosis whose expression is partially dependent on NRF2 and that synergistically targeting both FSP1 and NRF2 may be a promising strategy for overcoming ferroptosis resistance in cancer.
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Affiliation(s)
- Jong Woo Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Min-Ju Kim
- Department of Pharmacy, College of Pharmacy and Research Institute for Drug Development, Pusan National University, Busan, 46241, Republic of Korea
| | - Tae-Hee Han
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Ji-Yoon Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sangok Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyerin Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Won Kon Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Baek-Soo Han
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
- Biodefense Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyun Seung Ban
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Soo Han Bae
- Severance Biomedical Science Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | - Haeseung Lee
- Department of Pharmacy, College of Pharmacy and Research Institute for Drug Development, Pusan National University, Busan, 46241, Republic of Korea.
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Yao N, Pan J, Chen X, Li P, Li Y, Wang Z, Yao T, Qian L, Yi D, Wu Y. Discovery of potential biomarkers for lung cancer classification based on human proteome microarrays using Stochastic Gradient Boosting approach. J Cancer Res Clin Oncol 2023; 149:6803-6812. [PMID: 36807761 DOI: 10.1007/s00432-023-04643-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023]
Abstract
PURPOSE Early identification of lung cancer (LC) will considerably facilitate the intervention and prevention of LC. The human proteome micro-arrays approach can be used as a "liquid biopsy" to diagnose LC to complement conventional diagnosis, which needs advanced bioinformatics methods such as feature selection (FS) and refined machine learning models. METHODS A two-stage FS methodology by infusing Pearson's Correlation (PC) with a univariate filter (SBF) or recursive feature elimination (RFE) was used to reduce the redundancy of the original dataset. The Stochastic Gradient Boosting (SGB), Random Forest (RF), and Support Vector Machine (SVM) techniques were applied to build ensemble classifiers based on four subsets. The synthetic minority oversampling technique (SMOTE) was used in the preprocessing of imbalanced data. RESULTS FS approach with SBF and RFE extracted 25 and 55 features, respectively, with 14 overlapped ones. All three ensemble models demonstrate superior accuracy (ranging from 0.867 to 0.967) and sensitivity (0.917 to 1.00) in the test datasets with SGB of SBF subset outperforming others. The SMOTE technique has improved the model performance in the training process. Three of the top selected candidate biomarkers (LGR4, CDC34, and GHRHR) were highly suggested to play a role in lung tumorigenesis. CONCLUSION A novel hybrid FS method with classical ensemble machine learning algorithms was first used in the classification of protein microarray data. The parsimony model constructed by the SGB algorithm with the appropriate FS and SMOTE approach performs well in the classification task with higher sensitivity and specificity. Standardization and innovation of bioinformatics approach for protein microarray analysis need further exploration and validation.
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Affiliation(s)
- Ning Yao
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
- Chongqing Center for Disease Control and Prevention, No.8 Changjiang 2nd Street, Yuzhong District, Chongqing, 400042, China
| | - Jianbo Pan
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Xicheng Chen
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Pengpeng Li
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Yang Li
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Zhenyan Wang
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Tianhua Yao
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Li Qian
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China
| | - Dong Yi
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China.
| | - Yazhou Wu
- Department of Health Statistics, College of Preventive Medicine, Army Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China.
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Xu D, Qian W, Yang Z, Zhang Z, Sun P, Wan Q, Yin Y, Hu Y, Gong L, Zhang B, Yang X, Pu Z, Lu P, Zou J. Acetylation halts missense mutant p53 aggregation and rescues tumor suppression in non-small cell lung cancers. iScience 2023; 26:107003. [PMID: 37534137 PMCID: PMC10391690 DOI: 10.1016/j.isci.2023.107003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 08/04/2023] Open
Abstract
TP53 mutations are ubiquitous with tumorigenesis in non-small cell lung cancers (NSCLC). By analyzing the TCGA database, we reported that TP53 missense mutations are correlated with chromosomal instability and tumor mutation burden in NSCLC. The inability of wild-type nor mutant p53 expression can't predict survival in lung cancer cohorts, however, an examination of primary NSCLC tissues found that acetylated p53 did yield an association with improved survival outcomes. Molecularly, we demonstrated that acetylation drove the ubiquitination and degradation of mutant p53 but enhanced stability of wild-type p53. Moreover, acetylation of a missense p53 mutation prevented the gain of oncogenic function observed in typical TP53 mutant-expressing cells and enhanced tumor suppressor functions. Consequently, acetylation inducer targeting of missense mutant p53 may be a viable therapeutic goal for NSCLC treatment and may improve the accuracy of current efforts to utilize p53 mutations in a prognostic manner.
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Affiliation(s)
- Daxing Xu
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Wei Qian
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhenkun Yang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhenhao Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi, Jiangsu 214023, China
| | - Quan Wan
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu 214023, China
| | - Ying Yin
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Yaling Hu
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Lingli Gong
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Bo Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Xusheng Yang
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Peihua Lu
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Department of Medical Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
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Karaağaç M, Geredeli Ç, Yıldırım MS, Altınok T, Dede İ, İnal A, Zamani AG, Kaya B, Demirkazık A, Artaç M. The XRCC1 and TP53 gene polymorphisms are associated with advanced-stage disease and early distant metastasis at diagnosis in non-small cell lung cancer. J Cancer Res Ther 2023; 19:1248-1254. [PMID: 37787291 DOI: 10.4103/jcrt.jcrt_1657_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Background Studies on single nucleotide polymorphisms (SNPs) in non-small cell lung cancer (NSCLC) suggest that DNA repair capacity may have prognostic implications for disease recurrence and survival. However, there is no study investigating the relationship between SNPs and the risk of metastasis at the time of initial diagnosis in patients with NSCLC. Objective This study aimed to investigate the potential predictive value of SNPs in detecting the risk of metastasis at the time of initial diagnosis and poor prognosis in patients with NSCLC. Material and Methods In this prospective cohort study, we evaluated 275 patients with NSCLC. Analysis of SNPs from peripheral blood cells was performed by a polymerase chain reaction. Excision repair cross-complementing group 1 (ERCC1)- Asn118Asn, excision repair cross-complementing group 2 (ERCC2)-Lys751Gln, X-ray repair cross-complementing group 1 (XRCC1)-Arg399Gln, and tumor protein 53 (TP53)-Arg72Pro polymorphisms were evaluated in conjunction with the development of metastasis. Results The ERCC1 normal genotype, ERCC2 heterozygote genotype, XRCC1 normal genotype, and TP53 normal genotype were associated with a higher stage and more advanced-stage disease at the time of initial diagnosis (P = 0.027, 0.005, <0.001, and 0.006, respectively). Also, XRCC1 normal genotype and TP53 normal genotype were associated with the risk of metastasis at the time of initial diagnosis (P = <0.001 and 0.002, respectively). Moreover, the XRCC1 normal genotype was associated with the risk of brain metastasis at the time of initial diagnosis (P = 0.031). Conclusions We showed that SNPs are related to a higher stage and more advanced-stage disease at the time of initial diagnosis in patients with NSCLC, and XRCC1 and TP53 gene polymorphisms are associated with the risk of metastasis. These results may contribute to the identification of high-risk groups and may help to earlier diagnosis and treatment in patients with NSCLC.
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Affiliation(s)
- Mustafa Karaağaç
- Department of Medical Oncology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Çağlayan Geredeli
- Department of Medical Oncology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Mahmut Selman Yıldırım
- Department of Medical Oncology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Tamer Altınok
- Department of Thoracic Surgery, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - İsa Dede
- Department of Medical Oncology, Medical Faculty, Ankara University, Ankara, Turkey
| | - Ali İnal
- Department of Medical Oncology, Medical Faculty, Dicle University, Diyarbakir, Turkey
| | - Ayşe Gül Zamani
- Department of Medical Oncology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Buğra Kaya
- Department of Nuclear Medicine, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ahmet Demirkazık
- Department of Medical Oncology, Medical Faculty, Ankara University, Ankara, Turkey
| | - Mehmet Artaç
- Department of Medical Oncology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
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Duan Y, Du Y, Mu Y, Gu Z, Wang C. Expression, prognostic value and mechanism of SP100 family in pancreatic adenocarcinoma. Aging (Albany NY) 2023; 15:5569-5591. [PMID: 37354211 PMCID: PMC10333092 DOI: 10.18632/aging.204811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/23/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Pancreatic adenocarcinoma (PAAD) is one of the most aggressive malignancies with a very poor prognosis. Exploring more therapeutic targets and prognostic biomarkers is of great significance to improve the prognosis of PAAD patients. Increasing evidence supports that the speckled protein (SP) 100 family is associated with human cancer and immune disorders. However, the function of the SP100 family members in PAAD is still unclear. METHODS R, Cytoscape, cBioPortal, and other software and online databases were used to comprehensively analyze the expression characteristics, prognostic value, and oncogenic mechanism of the SP100 family in PAAD. RESULTS The high expression of SP100 family members in PAAD was significantly correlated with poor clinicopathological features and poor prognosis of PAAD patients. Mechanistically, TP53 mutations were significantly associated with the expression levels of the SP100 family members, which were significantly coexpressed with M6A methylation regulators and were activated in multiple oncogenic pathways, including the EMT pathways. Moreover, we found that their expression levels were significantly correlated with the sensitivity of multiple traditional chemotherapeutic drugs. CONCLUSION The SP100 family is closely related to the occurrence and development of PAAD and can be used as a new biomarker and therapeutic target for patients with PAAD.
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Affiliation(s)
- Yunjie Duan
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongxing Du
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongrun Mu
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongting Gu
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chengfeng Wang
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
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Ye W, Li M, Luo K. Therapies Targeting Immune Cells in Tumor Microenvironment for Non-Small Cell Lung Cancer. Pharmaceutics 2023; 15:1788. [PMID: 37513975 PMCID: PMC10384189 DOI: 10.3390/pharmaceutics15071788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
The tumor microenvironment (TME) plays critical roles in immune modulation and tumor malignancies in the process of cancer development. Immune cells constitute a significant component of the TME and influence the migration and metastasis of tumor cells. Recently, a number of therapeutic approaches targeting immune cells have proven promising and have already been used to treat different types of cancer. In particular, PD-1 and PD-L1 inhibitors have been used in the first-line setting in non-small cell lung cancer (NSCLC) with PD-L1 expression ≥1%, as approved by the FDA. In this review, we provide an introduction to the immune cells in the TME and their efficacies, and then we discuss current immunotherapies in NSCLC and scientific research progress in this field.
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Affiliation(s)
- Wei Ye
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510091, China
| | - Meiye Li
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510091, China
| | - Kewang Luo
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510091, China
- People's Hospital of Longhua, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen 518109, China
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Zhou F, Gao H, Shang L, Li J, Zhang M, Wang S, Li R, Ye L, Yang S. Oridonin promotes endoplasmic reticulum stress via TP53-repressed TCF4 transactivation in colorectal cancer. J Exp Clin Cancer Res 2023; 42:150. [PMID: 37337284 DOI: 10.1186/s13046-023-02702-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/09/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The incidence of colorectal cancer and cancer death rate are increasing every year, and the affected population is becoming younger. Traditional Chinese medicine therapy has a unique effect in prolonging survival time and improving the prognosis of patients with colorectal cancer. Oridonin has been reported to have anti-cancer effects in a variety of tumors, but the exact mechanism remains to be investigated. METHODS Cell Counting Kit-8 assay (CCK8) and 5-Ethynyl-2'-deoxyuridine (EdU) staining assay, Tranwell, and Wound healing assays were performed to measure cell proliferation, invasion, and migration capacities, respectively. The protein and mRNA expression levels of various molecules were reflected by Western blot and Reverse Transcription quantitative Polymerase Chain Reaction (qRT-PCR). Transcription Factor 4 (TCF4) and its target genes were analyzed by Position Weight Matrices (PWMs) software and the Gene Expression Omnibus (GEO) database. Immunofluorescence (IF) was performed to visualize the expression and position of Endoplasmic Reticulum (ER) stress biomarkers. The morphology of the ER was demonstrated by the ER tracker-red. Reactive Oxygen Species (ROS) levels were measured using a flow cytometer (FCM) or fluorescent staining. Calcium ion (Ca2+) concentration was quantified by Fluo-3 AM staining. Athymic nude mice were modeled with subcutaneous xenografts. RESULTS Oridonin inhibited the proliferation, invasion, and migration of colorectal cancer, and this effect was weakened in a concentration-dependent manner by ER stress inhibitors. In addition, oridonin-induced colorectal tumor cells showed increased expression of ER stress biomarkers, loose morphology of ER, increased vesicles, and irregular shape. TCF4 was identified as a regulator of ER stress by PWMs software and GEO survival analysis. In vitro and in vivo experiments confirmed that TCF4 inhibited ER stress, reduced ROS production, and maintained Ca2+ homeostasis. In addition, oridonin also activated TP53 and inhibited TCF4 transactivation, further exacerbating the elevated ROS levels and calcium ion release in tumor cells and inhibiting tumorigenesis in colorectal cancer cells in vivo. CONCLUSIONS Oridonin upregulated TP53, inhibited TCF4 transactivation, and induced ER stress dysregulation in tumor cells, promoting colorectal cancer cell death. Therefore, TCF4 may be one of the important nodes for tumor cells to regulate ER stress and maintain protein synthesis homeostasis. And the inhibition of the TP53/TCF4 axis plays a key role in the anti-cancer effects of oridonin.
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Affiliation(s)
- Fangyuan Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Haiyang Gao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Luorui Shang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Jinxiao Li
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Mengqi Zhang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Shuhan Wang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Runze Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Lin Ye
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China.
| | - Shenglan Yang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China.
- Clinical Nutrition Department, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province, 1277 Jiefang Avenue, Wuhan, 430022, China.
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Geng X, Chi W, Lin X, Niu Z, Jiang Q, Sui Y, Jiang J. Determining the mechanism of action of the Qishan formula against lung adenocarcinoma by integration of network pharmacology, molecular docking, and proteomics. Medicine (Baltimore) 2023; 102:e33384. [PMID: 37000102 PMCID: PMC10063309 DOI: 10.1097/md.0000000000033384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/21/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the main pathological type of lung cancer. Qishan formula (QSF) is reportedly efficacious against LUAD. However, its mechanisms of action currently remain elusive. Therefore, network pharmacology, molecular docking techniques and proteomics were used to verify the potential pharmacological effects of QSF in the treatment of LUAD. METHODS The active ingredients and potential targets of QSF were obtained from the TCMSP, chemical source network and construct a drug-component-target networks using Cytoscape v3.7.2. Data for disease targets were obtained from 5 databases: TCGA, OMIM, DrugBank, DisGeNET, and GeneCards. Drug disease cross targets were used to construct protein-protein interaction networks for selecting the core targets using the STRING database and enrichment pathway networks using the DAVID database. Finally, TMT quantitative proteomics was used to identify the possible core targets and action pathways. Molecular docking to verify the affinity between components and targets. RESULTS Network pharmacology identified core components of QSF against LUAD included baicalein, methylophiopogonone B, quercetin, kaempferol, isorhamnetin, and luteolin, which can act on 10 key targets (SRC, TP53, PIK3R1, MAPK3, STAT3, MAKP1, HSP90AA1, PIK3CA, HRAS, and AKT1). QSF might play a therapeutic role in LUAD by regulating biological processes such as signal transduction, protein phosphorylation, cell proliferation, and apoptosis, as well as the PI3K/AKT, MAPK, FoxO, and other signaling pathways. Proteomics identified 207 differentially expressed proteins, and by integrating with network pharmacology and molecular docking results we found that 6 core components of QSF may target TP53 against LUAD through the PI3K/AKT signaling pathway. CONCLUSION QSF is a multitarget recipe potentially exerting pleiotropic effects in LUAD.
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Affiliation(s)
- Xue Geng
- Department of Clinical Medicine, Heilongjiang University of Chinese Medicine, Herbin, China
| | - Wencheng Chi
- Department of Clinical Medicine, Heilongjiang University of Chinese Medicine, Herbin, China
- Department of Oncology, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Herbin, China
| | - Xiaoyue Lin
- Department of Clinical Medicine, Heilongjiang University of Chinese Medicine, Herbin, China
| | - Zeji Niu
- Department of Clinical Medicine, Heilongjiang University of Chinese Medicine, Herbin, China
| | - Qinghui Jiang
- Department of Oncology, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Herbin, China
| | - Yutong Sui
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jiakang Jiang
- Department of Clinical Medicine, Heilongjiang University of Chinese Medicine, Herbin, China
- Department of Oncology, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Herbin, China
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Zhong J, Shen X, Zhou J, Yu H, Wang B, Sun J, Wang J, Liu F. Development and validation of a combined hypoxia and ferroptosis prognostic signature for breast cancer. Front Oncol 2023; 13:1077342. [PMID: 36998462 PMCID: PMC10043308 DOI: 10.3389/fonc.2023.1077342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
BackgroundHypoxia is involved in tumor biological processes and disease progression. Ferroptosis, as a newly discovered programmed cell death process, is closely related to breast cancer (BC) occurrence and development. However, reliable prognostic signatures based on a combination of hypoxia and ferroptosis in BC have not been developed.MethodWe set The Cancer Genome Atlas (TCGA) breast cancer cohort as training set and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) BC cohort as the validation set. Least Absolute Shrinkage and Selection Operator (LASSO) and COX regression approaches were used to construct ferroptosis-related genes (FRGs) and hypoxia-related genes (HRGs) prognostic signature (HFRS). The CIBERSORT algorithm and ESTIMATE score were used to explore the relationship between HFRS and tumor immune microenvironment. Immunohistochemical staining was used to detect protein expression in tissue samples. A nomogram was developed to advance the clinical application of HFRS signature.ResultsTen ferroptosis-related genes and hypoxia-related genes were screened to construct the HFRS prognostic signature in TCGA BC cohort, and the predictive capacity was verified in METABRIC BC cohort. BC patients with high-HFRS had shorter survival time, higher tumor stage, and a higher rate of positive lymph node. Moreover, high HFRS was associated with high hypoxia, ferroptosis, and immunosuppression status. A nomogram that was constructed with age, stage, and HFRS signature showed a strong prognostic capability to predict overall survival (OS) for BC patients.ConclusionWe developed a novel prognostic model with hypoxia and ferroptosis-related genes to predict OS, and characterize the immune microenvironment of BC patients, which might provide new cures for clinical decision-making and individual treatment of BC patients.
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Affiliation(s)
- Jianxin Zhong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Xi Shen
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Junjie Zhou
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heping Yu
- Department of Thyroid and Breast Surgery, Wuhan Fourth Hospital, Wuhan, China
| | - Birong Wang
- Department of Thyroid and Breast Surgery, Wuhan Fourth Hospital, Wuhan, China
| | - Jianbin Sun
- Department of Thyroid and Breast Surgery, Wuhan Fourth Hospital, Wuhan, China
| | - Jing Wang
- Department of Thoracic Surgery, Wuhan Fourth Hospital, Wuhan, China
- *Correspondence: Jing Wang, ; Feng Liu,
| | - Feng Liu
- Department of Thyroid and Breast Surgery, Wuhan Fourth Hospital, Wuhan, China
- *Correspondence: Jing Wang, ; Feng Liu,
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Alam M, Hasan GM, Eldin SM, Adnan M, Riaz MB, Islam A, Khan I, Hassan MI. Investigating regulated signaling pathways in therapeutic targeting of non-small cell lung carcinoma. Biomed Pharmacother 2023; 161:114452. [PMID: 36878052 DOI: 10.1016/j.biopha.2023.114452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/19/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Non-small cell lung carcinoma (NSCLC) is the most common malignancy worldwide. The signaling cascades are stimulated via genetic modifications in upstream signaling molecules, which affect apoptotic, proliferative, and differentiation pathways. Dysregulation of these signaling cascades causes cancer-initiating cell proliferation, cancer development, and drug resistance. Numerous efforts in the treatment of NSCLC have been undertaken in the past few decades, enhancing our understanding of the mechanisms of cancer development and moving forward to develop effective therapeutic approaches. Modifications of transcription factors and connected pathways are utilized to develop new treatment options for NSCLC. Developing designed inhibitors targeting specific cellular signaling pathways in tumor progression has been recommended for the therapeutic management of NSCLC. This comprehensive review provided deeper mechanistic insights into the molecular mechanism of action of various signaling molecules and their targeting in the clinical management of NSCLC.
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Affiliation(s)
- Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Sayed M Eldin
- Center of Research, Faculty of Engineering, Future University in Egypt, New Cairo 11835, Egypt
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Muhammad Bilal Riaz
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdnask, Poland; Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ilyas Khan
- Department of Mathematics, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Nishio M, Paz-Ares L, Reck M, Nakagawa K, Garon EB, Popat S, Ceccarelli M, Graham HT, Visseren-Grul C, Novello S. RELAY, Ramucirumab plus Erlotinib (RAM+ERL) in Untreated Metastatic EGFR-Mutant NSCLC (EGFR+ NSCLC): Association between TP53 Status and Clinical Outcome. Clin Lung Cancer 2023:S1525-7304(23)00046-3. [PMID: 37076395 DOI: 10.1016/j.cllc.2023.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND Ramucirumab plus erlotinib (RAM+ERL) demonstrated superior progression-free survival (PFS) in RELAY, a randomised Phase III trial in patients with untreated, metastatic, EGFR-mutated, non-small-cell lung cancer (EGFR+ NSCLC). Here, we present the relationship between TP53 status and outcomes in RELAY. MATERIALS AND METHODS Patients received oral ERL plus intravenous RAM (10 mg/kg IV) or placebo (PBO+ERL) every 2 weeks. Plasma was assessed by Guardant 360 next-generation sequencing and patients with any gene alteration detected at baseline were included in this exploratory analysis. Endpoints included PFS, overall response rate (ORR), disease control rate (DCR), DoR, overall survival (OS), safety, and biomarker analysis. The association between TP53 status and outcomes was evaluated. RESULTS Mutated TP53 was detected in 165 (42.7%; 74 RAM+ERL, 91 PBO+ERL) patients, wild-type TP53 in 221 (57.3%; 118 RAM+ERL, 103 PBO+ERL) patients. Patient and disease characteristics and concurrent gene alterations were comparable between those with mutant and wildtype TP53. Independent of treatment, TP53 mutations, most notably on exon 8, were associated with worse clinical outcomes. In all patients, RAM+ERL improved PFS. While ORR and DCR were comparable across all patients, DoR was superior with RAM+ERL. There were no clinically meaningful differences in the safety profiles between those with baseline TP53 mutation and wild-type. CONCLUSION This analysis indicates that while TP53 mutations are a negative prognostic marker in EGFR+ NSCLC, the addition of a VEGF inhibitor improves outcomes in those with mutant TP53. RAM+ERL is an efficacious first-line treatment option for patients with EGFR+ NSCLC, independent of TP53 status.
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Affiliation(s)
- Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Luis Paz-Ares
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Martin Reck
- Department of Thoracic Oncology, LungenClinic, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Edward B Garon
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sanjay Popat
- Lung Unit, Royal Marsden NHS Trust, London, United Kingdom
| | - Matteo Ceccarelli
- Global Clinical Development, Eli Lilly and Company, Sesto Fiorentino, Florence, Italy
| | | | - Carla Visseren-Grul
- Global Clinical Development, Eli Lilly Netherlands, Utrecht, The Netherlands
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, Turin, Italy
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Cai S, Ding Z, Liu X, Zeng J. Trabectedin induces ferroptosis via regulation of HIF-1α/IRP1/TFR1 and Keap1/Nrf2/GPX4 axis in non-small cell lung cancer cells. Chem Biol Interact 2023; 369:110262. [PMID: 36396105 DOI: 10.1016/j.cbi.2022.110262] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/24/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND OBJECTIVES Non-small cell lung cancer (NSCLC) is a global health concern. NSCLC treatment outcomes are generally poor due to treatment resistance or toxicity. Ferroptosis is a novel cell death triggered by iron accumulation, reactive oxygen species (ROS), and lipid peroxidation. Ferroptosis may kill cancer cells, particularly those resistant to apoptosis. MATERIALS AND METHODS The Cell Counting Kit-8 assay assessed NSCLC cell viability after trabectedin treatment. Flow cytometry with Annexin V-FITC staining evaluated cell death. ROS, iron, lipid peroxidation, and GSH levels were measured using commercial kits. qRT-PCR and western blots evaluated messenger RNA and protein levels. Proteins were inhibited using short interfering RNA transfection and specific inhibitors. RESULTS Trabectedin was cytotoxic to NSCLC cells regardless of p53 status. Trabectedin upregulated iron, ROS, and lipid peroxidation in NSCLC cells, causing ferroptosis. Trabectedin increases iron and ROS levels by upregulating transferrin receptor 1 and the HIF-1/IRP1 axis. In NSCLC cells, trabectedin suppresses glutathione peroxidase 4, followed by the Keap1/Nrf2 axis. CONCLUSIONS Our findings imply that trabectedin may treat NSCLC effectively.
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Affiliation(s)
- Shunv Cai
- Department of Anesthesiology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, People's Republic of China
| | - Zewu Ding
- Department of Anesthesiology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, People's Republic of China
| | - Xinyi Liu
- Department of Anesthesiology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, People's Republic of China
| | - Jian Zeng
- Department of Thoracic Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital). Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, People's Republic of China.
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Cai J, Xie H, Yan Y, Huang Z, Tang P, Cao X, Wang Z, Yang C, Wen J, Tan M, Zhang F, Shen B. A novel cuproptosis-related lncRNA signature predicts prognosis and therapeutic response in bladder cancer. Front Genet 2023; 13:1082691. [PMID: 36685947 PMCID: PMC9845412 DOI: 10.3389/fgene.2022.1082691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Bladder cancer (BC) ranks the tenth in the incidence of global tumor epidemiology. LncRNAs and cuproptosis were discovered to regulate the cell death. Herein, we downloaded transcriptome profiling, mutational data, and clinical data on patients from The Cancer Genome Atlas (TCGA). High- and low-risk BC patients were categorized. Three CRLs (AL590428.1, AL138756.1 and GUSBP11) were taken into prognostic signature through least absolute shrinkage and selection operator (LASSO) Cox regression. Worse OS and PFS were shown in high-risk group (p < 0.05). ROC, independent prognostic analyses, nomogram and C-index were predicted via CRLs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated IncRNAs play a biological role in BC progression. Immune-related functions showed the high-risk group received more benefit from immunotherapy and had stronger immune responses, and the overall survival was better (p < 0.05). Finally, a more effective outcome (p < 0.05) was found from clinical immunotherapy via the TIDE algorithm and many potential anti-tumor drugs were identified. In our study, the cuproptosis-related signature provided a novel tool to predict the prognosis in BC patients accurately and provided a novel strategy for clinical immunotherapy and clinical applications.
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Affiliation(s)
- Jinming Cai
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haoran Xie
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yilin Yan
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengnan Huang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pengfei Tang
- Department of Urology, Shanghai General Hospital Affiliated to Nanjing Medical University, Shanghai, China
| | - Xiangqian Cao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zeyi Wang
- Department of Urology, Shanghai General Hospital Affiliated to Nanjing Medical University, Shanghai, China
| | - Chenkai Yang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiling Wen
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China,*Correspondence: Jiling Wen, ; Mingyue Tan, ; Fang Zhang, ; Bing Shen,
| | - Mingyue Tan
- Department of Urology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,*Correspondence: Jiling Wen, ; Mingyue Tan, ; Fang Zhang, ; Bing Shen,
| | - Fang Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jiling Wen, ; Mingyue Tan, ; Fang Zhang, ; Bing Shen,
| | - Bing Shen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jiling Wen, ; Mingyue Tan, ; Fang Zhang, ; Bing Shen,
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Congur I, Koni E, Onat OE, Tokcaer Keskin Z. Meta-analysis of commonly mutated genes in leptomeningeal carcinomatosis. PeerJ 2023; 11:e15250. [PMID: 37096065 PMCID: PMC10122459 DOI: 10.7717/peerj.15250] [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: 01/26/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Background Leptomeningeal carcinomatosis (LMC) is a rare type of cancer that settles at the meninges through metastasis of non-small cell lung cancer (NSCLC), breast cancer and melanoma. The molecular mechanism underlying LMC is not known, therefore molecular studies investigating the development of LMC are needed. Here, we aimed to identify commonly mutated genes in LMC caused by NSCLC, breast cancer, and melanoma using an in-slico approach and their interactions using integrated bioinformatic approaches/tools in this meta-analysis. Methods We conducted a meta-analysis using information from 16 studies that included different sequencing techniques of patients with LMC caused by three different primary cancers: breast cancer, NSCLC, and melanoma. All studies that assessed mutation information from patients with LMC were searched in PubMed, from their inception to February, 16 2022. Studies that performed NGS on LMC patients with NSCLC, breast cancer, or melanoma were included, while studies that did not apply NGS to CSF samples, did not provide information on altered genes, were reviews, editorials, or conference abstracts, or whose main goal was the detection of malignancies were all excluded. We identified commonly mutated genes in all three types of cancer. Next, we constructed a protein-protein interaction network, then performed pathway enrichment analysis. We searched National Institutes of Health (NIH) and Drug-Gene Interaction Database (DGIdb) to find candidate drugs. Results We found that TP53, PTEN, PIK3CA, IL7R, and KMT2D genes were commonly mutated genes in all three types of cancer via our meta-analysis that consisted out of 16 studies. Our pathway enrichment analysis showed that all five genes were primarily associated with regulation of cell communication and signaling, and cell proliferation. Other enriched pathways included regulation of apoptotic processes of leukocytes and fibroblasts, macroautophagy and growth. According to our drug search we found candidate drugs; Everolimus, Bevacizumab and Temozolomide, which interact with these five genes. Conclusion In conclusion, a total of 96 mutated genes in LMC were investigated via meta-analysis. Our findings suggested vital roles of TP53, PTEN, PIK3CA, KMT2D, and IL7R, which can provide insight into the molecular basis of LMC development and paving the door to the development of new targeted medicine and will encourage molecular biologists to seek biological evidence.
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Affiliation(s)
- Irem Congur
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Ekin Koni
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Onur Emre Onat
- Department of Genome Studies, Institute of Health Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Molecular Biology, Institute of Life Sciences and Biotechnology, Bezmialem Foundation University, Istanbul, Turkey
| | - Zeynep Tokcaer Keskin
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Engineering and Natural Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
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Duan Y, Du Y, Mu Y, Gu Z, Wang C. Prognostic value, immune signature and molecular mechanisms of the SUMO family in pancreatic adenocarcinoma. Front Mol Biosci 2022; 9:1096679. [PMID: 36589239 PMCID: PMC9798011 DOI: 10.3389/fmolb.2022.1096679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) has a high degree of malignancy and a very poor prognosis, and the 5-year overall survival rate of patients is approximately 7%. To improve the prognosis of patients with PAAD, a more comprehensive and in-depth study of the pathogenesis of PAAD and the identification of new diagnostic markers and treatment targets are urgently needed. Increasing evidence supports that the small ubiquitin-like modifier (SUMO) family is closely related to the occurrence and development of a variety of cancers. However, the function of the SUMO family in PAAD is not clear, and related research is very scarce. Methods: R, Cytoscape, cBioPortal, and other software and online databases were used to comprehensively analyze the expression characteristics, prognostic value, and oncogenic mechanism of the SUMO family in PAAD. Results: SUMO family members are highly expressed in PAAD, and high expression of SUMO family members is significantly associated with poor clinicopathological features and poor prognosis in PAAD patients. In addition, SUMO family members are significantly coexpressed with M6A methylation regulators and various oncogenes and play an activating role in various oncogenic pathways, including EMT. Furthermore, it is worth noting that the close association between SUMO family members and TP53 mutation status and the negative regulatory effect of SUMO1/2 on PAAD immunity may represent the potential mechanism by which SUMO family members promote the development of PAAD. Moreover, the coexpression characteristics of SUMO family members and a variety of cancer-promoting immune checkpoint genes, as well as the positive correlation between SUMO4 expression level and the sensitivity of various targeted or chemotherapeutic drugs, including gemcitabine, paclitaxel, and doxorubicin, suggest future clinical directions of this study. Conclusion: The SUMO family is closely related to the occurrence and development of PAAD and can be used as a new biomarker and therapeutic target for patients with PAAD.
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Affiliation(s)
- Yunjie Duan
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongxing Du
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongrun Mu
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongting Gu
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chengfeng Wang
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China,*Correspondence: Chengfeng Wang,
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Buburuzan L, Zamfir (Irofei) MA, Ardeleanu CM, Muresan AH, Vasilescu F, Hudita A, Costache M, Galateanu B, Puscasu A, Filippi A, Motas N. Dual NGS Comparative Analysis of Liquid Biopsy (LB) and Formalin-Fixed Paraffin-Embedded (FFPE) Samples of Non-Small Cell Lung Carcinoma (NSCLC). Cancers (Basel) 2022; 14:cancers14246084. [PMID: 36551569 PMCID: PMC9776679 DOI: 10.3390/cancers14246084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Lung cancer ranks second worldwide after breast cancer and third in Europe after breast and colorectal cancers when both sexes and all ages are considered. In this context, the aim of this study was to emphasize the power of dual analysis of the molecular profile both in tumor tissue and plasma by NGS assay as a liquid biopsy approach with impact on prognosis and therapy modulation in NSCLC patients. NGS analysis was performed both from tissue biopsies and from cfNAs isolated from peripheral blood samples. Out of all 29 different mutations detectable by both NGS panels (plasma and tumor tissue), seven different variants (24.13%; EGFR L858R in two patients, KRAS G13D and Q61H and TP53 G244D, V197M, R213P, and R273H) were detected only in plasma and not in the tumor itself. These mutations were detected in seven different patients, two of them having known distant organ metastasis. Our data show that NGS analysis of cfDNA could identify actionable mutations in advanced NSCLC and, therefore, this analysis could be used to monitor the disease progression and the treatment response and even to modulate the therapy in real time.
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Affiliation(s)
- Laura Buburuzan
- Department of Molecular Biology, Onco Team Diagnostic S.A., 012244 Bucharest, Romania
| | - Maria-Anca Zamfir (Irofei)
- Department of Molecular Biology, Onco Team Diagnostic S.A., 012244 Bucharest, Romania
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania
| | | | - Alin Horatiu Muresan
- Department of Molecular Biology, Onco Team Diagnostic S.A., 012244 Bucharest, Romania
| | - Florina Vasilescu
- Department of Molecular Biology, Onco Team Diagnostic S.A., 012244 Bucharest, Romania
| | - Ariana Hudita
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Bianca Galateanu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania
- Correspondence:
| | - Alexandra Puscasu
- Department of Medical Oncology, Fundeni Clinical Institute, 72437 Bucharest, Romania
| | - Alexandru Filippi
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila Bucharest, 050474 Bucharest, Romania
| | - Natalia Motas
- Faculty of Medicine, University of Medicine and Pharmacy Carol Davila Bucharest, 050474 Bucharest, Romania
- Clinic of Thoracic Surgery, Institute of Oncology Prof. Dr. A. Trestioreanu Bucharest, 022328 București, Romania
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Unraveling the Structural Changes in the DNA-Binding Region of Tumor Protein p53 ( TP53) upon Hotspot Mutation p53 Arg248 by Comparative Computational Approach. Int J Mol Sci 2022; 23:ijms232415499. [PMID: 36555140 PMCID: PMC9779389 DOI: 10.3390/ijms232415499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
The vital tissue homeostasis regulator p53 forms a tetramer when it binds to DNA and regulates the genes that mediate essential biological processes such as cell-cycle arrest, senescence, DNA repair, and apoptosis. Missense mutations in the core DNA-binding domain (109-292) simultaneously cause the loss of p53 tumor suppressor function and accumulation of the mutant p53 proteins that are carcinogenic. The most common p53 hotspot mutation at codon 248 in the DNA-binding region, where arginine (R) is substituted by tryptophan (W), glycine (G), leucine (L), proline (P), and glutamine (Q), is reported in various cancers. However, it is unclear how the p53 Arg248 mutation with distinct amino acid substitution affects the structure, function, and DNA binding affinity. Here, we characterized the pathogenicity and protein stability of p53 hotspot mutations at codon 248 using computational tools PredictSNP, Align GVGD, HOPE, ConSurf, and iStable. We found R248W, R248G, and R248P mutations highly deleterious and destabilizing. Further, we subjected all five R248 mutant-p53-DNA and wt-p53-DNA complexes to molecular dynamics simulation to investigate the structural stability and DNA binding affinity. From the MD simulation analysis, we observed increased RMSD, RMSF, and Rg values and decreased protein-DNA intermolecular hydrogen bonds in the R248-p53-DNA than the wt-p53-DNA complexes. Likewise, due to high SASA values, we observed the shrinkage of proteins in R248W, R248G, and R248P mutant-p53-DNA complexes. Compared to other mutant p53-DNA complexes, the R248W, R248G, and R248P mutant-p53-DNA complexes showed more structural alteration. MM-PBSA analysis showed decreased binding energies with DNA in all five R248-p53-DNA mutants than the wt-p53-DNA complexes. Henceforth, we conclude that the amino acid substitution of Arginine with the other five amino acids at codon 248 reduces the p53 protein's affinity for DNA and may disrupt cell division, resulting in a gain of p53 function. The proposed study influences the development of rationally designed molecular-targeted treatments that improve p53-based therapeutic outcomes in cancer.
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Ma Y, Pan H, Liu Y, Zhang Y, Hong S, Huang J, Weng S, Yang Y, Fang W, Huang Y, Xiao S, Wang T, Ding L, Cui L, Zhang L, Zhao H. Ensartinib in advanced ALK-positive non-small cell lung cancer: a multicenter, open-label, two-staged, phase 1 trial. J Thorac Dis 2022; 14:4751-4762. [PMID: 36647478 PMCID: PMC9840022 DOI: 10.21037/jtd-22-1606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]
Abstract
Background Ensartinib, a potent second-generation tyrosine kinase inhibitor (TKI) that targets anaplastic lymphoma kinase (ALK), MET and ROS1, was evaluated in a phase I clinical trial in patients with advanced, ALK-rearranged non-small cell lung cancer (NSCLC). Methods Patients with advanced, ALK or ROS1-positive NSCLC were recruited from 2 centers in China. This study consisted of dose escalation and expansion stages. Patients were treated with oral ensartinib [dosage of escalation stage was from 150, 200, 225 to 250 mg per day, expansion stage was recommended phase II dose (RP2D)] in continuous 28-day cycles. The primary objectives were safety, dose limited toxicity (DLT), maximum tolerated dose (MTD), and RP2D based on tolerability. Key secondary objectives included pharmacokinetic (PK) and anti-tumor activity. Results Forty-eight patients were enrolled, 37 (77.1%) were ALK TKI-naïve, 11 (22.9%) patients had previously received crizotinib, ceritinib or alectinib. Ensartinib was well tolerated and common treatment-related adverse events (TRAEs) included rash (87.5%), transaminase elevation (60.4%), pruritus (45.8%) and creatinine elevation (35.4%). The top 3 grade 3-5 TRAEs were rash (14.6%), elevated alanine aminotransferase (ALT) (12.5%) and aspartate transaminase (AST) (4.2%). Two DLTs were observed in 250 mg, so MTD and RP2D was 225 mg per day. Ensartinib was moderately absorbed (median Tmax: 3.00-4.00 h) and slowly eliminated (mean T1/2: 21.0-30.2 h). The area under the curve (AUC) of ensartinib reached saturation at 200 to 225 mg and no major accumulation after daily administration. For all patients, the objective response rate (ORR) and disease control rates (DCR) were 64.6 % and 81.3%, median progression-free survival (mPFS) was 16.79 months. In subgroup analysis, the ORR and mPFS was 81.3% and 45.5%, 25.73 and 4.14 months in TKI-naïve and -treated ALK+ patients, respectively. The intra-cranial ORR and mPFS for patients with measurable brain metastases were 66.7% and 22.90 months. ALK abundance may predict the efficacy of ensartinib. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed specific signaling pathways enrichment in long and short progression-free survival (PFS) groups. Conclusions Ensartinib was well tolerated under 225 mg (MTD) and demonstrated promising anti-tumor activity in ALK+ NSCLC patients, including those with CNS metastases and those previously TKI-treated. Trial Registration ClinicalTrials.gov NCT02959619.
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Affiliation(s)
- Yuxiang Ma
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China;,Department of Clinical Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Hui Pan
- Department of Clinical Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yu Liu
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China;,Department of Clinical Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yang Zhang
- Department of Clinical Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shaodong Hong
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jianjin Huang
- Department of Medical Oncology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Shanshan Weng
- Department of Medical Oncology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Yunpeng Yang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wenfeng Fang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yan Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shanshan Xiao
- Department of R&D, Hangzhou Repugene Technology Co.,Ltd., Hangzhou, China
| | - Tao Wang
- Department of R&D, Hangzhou Repugene Technology Co.,Ltd., Hangzhou, China
| | - Lieming Ding
- Betta Pharmaceuticals Co., Ltd., China, Hangzhou, China
| | - Lingling Cui
- Betta Pharmaceuticals Co., Ltd., China, Hangzhou, China
| | - Li Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Hongyun Zhao
- Department of Clinical Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Wang Y, Goh KY, Chen Z, Lee WX, Choy SM, Fong JX, Wong YK, Li D, Hu F, Tang HW. A Novel TP53 Gene Mutation Sustains Non-Small Cell Lung Cancer through Mitophagy. Cells 2022; 11:cells11223587. [PMID: 36429016 PMCID: PMC9688643 DOI: 10.3390/cells11223587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lung cancer is the leading cause of cancer death in the world. In particular, non-small-cell lung cancer (NSCLC) represents the majority of the lung cancer population. Advances in DNA sequencing technologies have significantly contributed to revealing the roles, functions and mechanisms of gene mutations. However, the driver mutations that cause cancers and their pathologies remain to be explored. Here, we performed next-generation sequencing (NGS) on tumor tissues isolated from 314 Chinese NSCLC patients and established the mutational landscape in NSCLC. Among 656 mutations, we identified TP53-p.Glu358Val as a driver mutation in lung cancer and found that it activates mitophagy to sustain cancer cell growth. In support of this finding, mice subcutaneously implanted with NSCLC cells expressing TP53-p.Glu358Val developed larger tumors compared to wild-type cells. The pharmaceutical inhibition of autophagy/mitophagy selectively suppresses the cell proliferation of TP53-null or TP53-p.Glu358Val-expressing lung cancer cells. Together, our study characterizes a new TP53 mutation identified from Chinese lung cancer patients and uncovers its roles in regulating mitophagy, providing a new insight into NSCLC treatment.
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Affiliation(s)
- Yuanli Wang
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin 541014, China
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, Qinzhou 535000, China
| | - Kah Yong Goh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Zhencheng Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin 541014, China
- Correspondence: (Z.C.); (H.-W.T.)
| | - Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sze Mun Choy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jia Xin Fong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Yun Ka Wong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Dongxia Li
- School of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| | - Fangrong Hu
- School of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China
| | - Hong-Wen Tang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore
- Correspondence: (Z.C.); (H.-W.T.)
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Wang Y, Wang S, Cui Y, Zhang J, Geng S, Yin H, Zhang S, Li Q, Wang Y. A focused transcriptomic analysis of the TP53-regulated genes identifies the GPI-anchored molecule-like protein (GML) as a favorable prognostic predictor of lung cancer. Genes Dis 2022; 10:396-398. [DOI: 10.1016/j.gendis.2022.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 08/12/2022] [Indexed: 11/06/2022] Open
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Zhang M, Wang Y, Amin A, Khan MA, Yu Z, Liang C. Network Pharmacology Analysis of Bioactive Components and Mechanisms of Action of Qi Wei Wan Formula for Treating Non-Small Cell Lung Carcinoma. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221120215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Astragali Radix (AR) and Schisandrae chinensis Fructus (SCF) have been used individually and in traditional Chinese medicine (TCM) formulas for treating non-small cell lung carcinoma (NSCLC). Qi Wei Wan (QWW), a 2-herb TCM formula composed of AR and SCF, is used to treat blood deficiency, fatigue, and metabolic abnormalities. We speculate that QWW may be more effective in treating NSCLC than AR or SCF alone. We identified 28 bioactive compounds in QWW and 322 targets of these compounds from databases. Network pharmacology analysis was used to identify 248 putative NSCLC-related gene targets of the bioactive compounds in QWW. Common target genes were analyzed to build protein–protein interaction networks. Implicated biological functions and pathways (p53, PI3K-Akt, etc) were identified by Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses. Molecular docking of core target proteins with the key active compounds was also performed. This study identified the potential gene targets and mechanisms involved in the anti-NSCLC effects of QWW.
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Affiliation(s)
- Minghe Zhang
- Division of Life Science and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ye Wang
- Division of Life Science and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Aftab Amin
- Division of Life Science and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Muhammad Ajmal Khan
- Division of Life Science and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhiling Yu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Chun Liang
- Division of Life Science and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- EnKang Pharmaceuticals (Guangzhou), Ltd., Guangzhou, China
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Atitey K. DEGBOE: Discrete time Evolution modeling of Gene mutation through Bayesian inference using qualitative Observation of mutation Events. J Biomed Inform 2022; 134:104197. [PMID: 36084801 PMCID: PMC9809132 DOI: 10.1016/j.jbi.2022.104197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/02/2022] [Accepted: 09/01/2022] [Indexed: 01/05/2023]
Abstract
An important aspect of cancer progression concerns the way in which gene mutations accumulate in cellular lineages. Comprehensive efforts into cataloging cancer genes have revealed that tumors demonstrate variability in genes that accumulate mutations which depend on the presence or absence of other mutations. However, understanding the stochastic process by which mutations arise across the genome is an important open problem of this nature in biology due to modeling discrete variate time-series is the most challenging, and, as yet, least well-developed of all areas of research in time-series. In this paper, a DEGBOE framework is proposed to model the mutation time-series given the sequence data of the gene mutations. The method relates the discrete-time, nonlinear and nonstationary series of gene mutations to the time-varying autoregressive moving average model. It presents the observation as a nonlinear function dependent on two variables: gene mutation, and gene-gene interactions characterizing the effects of the varying presence or absence of other gene mutations on a mutations' occurrence and evolution. DEGBOE is applied to model the dynamics of frequently mutated genes in lung cancer, includingEGFR,KRAS, and TP53. The results of the model are analyzed and compared to the original simulated data of theDNAwalk, and experimental lung cancer mutations data. It identifies the driver role of TP53 mutations in lung cancer progression.
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Affiliation(s)
- Komlan Atitey
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, United States.
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50
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Jiang S, Geng S, Luo X, Zhang C, Yu Y, Cheng M, Zhang S, Shi N, Dong M. Biomarkers of related driver genes predict anti-tumor efficacy of immune checkpoint inhibitors. Front Immunol 2022; 13:995785. [PMID: 36189266 PMCID: PMC9521273 DOI: 10.3389/fimmu.2022.995785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cancer is a disease with high morbidity and mortality in the world. In the past, the main treatment methods for cancer patients were surgery, radiotherapy and chemotherapy. However, with early treatment, the recurrence rate of cancer is higher, and the drug resistance of cancer cells is faster. In recent years, with the discovery of immune escape mechanism of cancer cells, Immunotherapy, especially Immune Checkpoint Inhibitors (ICIs), has made a breakthrough in the treatment of solid tumors, significantly prolonging the overall survival time and disease-free progression in some solid tumors, and its clinical benefits are more prominent than those of traditional anti-tumor drugs, which has become the hope of cancer patients after the failure of multi-line therapy. More and more studies have shown that there is a correlation between cancer driving genes and the clinical benefits of ICIs treatment, and the therapeutic effects and adverse reactions of ICIs can be predicted by the status of driving genes. Therefore, screening potential biomarkers of people who may benefit from immunotherapy in order to maximize the therapeutic benefits is a top priority. This review systematically summarizes the cancer driving genes that may affect the clinical benefits of immune checkpoint inhibitors, and provides accurate scientific basis for clinical practice.
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Affiliation(s)
- Shuai Jiang
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuai Geng
- Department of Pharmacy, Strategic Support Force Medical Center, Beijing, China
| | - Xinyu Luo
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Can Zhang
- Department of Ultrasound Diagnosis, Strategic Support Force Medical Center, Beijing, China
| | - Yang Yu
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mengfei Cheng
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuo Zhang
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ning Shi
- Department of Pharmacy, Strategic Support Force Medical Center, Beijing, China
- *Correspondence: Mei Dong, ; Ning Shi,
| | - Mei Dong
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Mei Dong, ; Ning Shi,
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