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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; 11:3587. [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
| | - 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
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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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63
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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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64
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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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Musial C, Knap N, Zaucha R, Bastian P, Barone G, Lo Bosco G, Lo-Celso F, Konieczna L, Belka M, Bączek T, Gammazza AM, Kuban-Jankowska A, Cappello F, Nussberger S, Gorska-Ponikowska M. Induction of 2-hydroxycatecholestrogens O-methylation: A missing puzzle piece in diagnostics and treatment of lung cancer. Redox Biol 2022; 55:102395. [PMID: 35841627 PMCID: PMC9289866 DOI: 10.1016/j.redox.2022.102395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/15/2022] [Accepted: 07/02/2022] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is one of the most common cancers worldwide, causing nearly one million deaths each year. Herein, we present the effect of 2-methoxyestradiol (2-ME), the endogenous metabolite of 17β-estradiol (E2), on non-small cell lung cancer (NSCLC) cells. We observed that 2-ME reduced the viability of lung adenocarcinoma in two-dimensional (2D) and three-dimensional (3D) spheroidal A549 cell culture models. Molecular modeling was carried out aiming to visualize amino acid residues within binding pockets of the acyl-protein thioesterases, namely 1 (APT1) and 2 (APT2), and thus to identify which ones were more likely involved in the interaction with 2-ME. Our findings suggest that 2-ME acts as an APT1 inhibitor enhancing protein palmitoylation and oxidative stress phenomena in the lung cancer cell. In order to support our data, metabolomics of blood serum from NSCLC patients was also performed. Moreover, computational analysis suggests that 2-ME as compared to other estrogen metabolism intermediates is relatively safe in terms of its possible non-receptor bioactivity within healthy human cells due to a very low electrophilic potential and hence no substantial risk of spontaneous covalent modification of biologically protective nucleophiles. We propose that 2-ME can be used as a selective tumor biomarker in the course of certain types of lung cancers and possibly as a therapeutic adjuvant or neoadjuvant.
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Affiliation(s)
- Claudia Musial
- Department of Medical Chemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland
| | - Narcyz Knap
- Department of Medical Chemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland
| | - Renata Zaucha
- Department of Clinical Oncology and Radiotherapy, Medical University of Gdansk, 80-214, Gdansk, Poland
| | - Paulina Bastian
- Department of Medical Chemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128, Palermo, Italy
| | - Giosuè Lo Bosco
- Department of Mathematics and Computer Science, University of Palermo, 90133, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy
| | - Fabrizio Lo-Celso
- Department of Physics and Chemistry 'Emilio Segrè', University of Palermo, 90128, Palermo, Italy
| | - Lucyna Konieczna
- Department of Pharmaceutical Chemistry, Medical University of Gdansk, 80-416, Gdansk, Poland
| | - Mariusz Belka
- Department of Pharmaceutical Chemistry, Medical University of Gdansk, 80-416, Gdansk, Poland
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Medical University of Gdansk, 80-416, Gdansk, Poland
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
| | - Alicja Kuban-Jankowska
- Department of Medical Chemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland
| | - Francesco Cappello
- Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy; Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
| | - Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, 70569, Stuttgart, Germany
| | - Magdalena Gorska-Ponikowska
- Department of Medical Chemistry, Medical University of Gdansk, Debinki 1, 80-211, Gdansk, Poland; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy; Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, 70569, Stuttgart, Germany.
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66
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Wang F, Lin H, Su Q, Li C. Cuproptosis-related lncRNA predict prognosis and immune response of lung adenocarcinoma. World J Surg Oncol 2022; 20:275. [PMID: 36050740 PMCID: PMC9434888 DOI: 10.1186/s12957-022-02727-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) accounts for 50% of lung cancers, with high mortality and poor prognosis. Long non-coding RNA (lncRNA) plays a vital role in the progression of tumors. Cuproptosis is a newly discovered form of cell death that is highly investigated. Therefore, in the present study, we aimed to investigate the role of cuproptosis-related lncRNA signature in clinical prognosis prediction and immunotherapy and the relationship with drug sensitivity. MATERIAL AND METHODS Genomic and clinical data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and cuproptosis-related genes were obtained from cuproptosis-related studies. The prognostic signature was constructed by co-expression analysis and Cox regression analysis. Patients were divided into high and low risk groups, and then, a further series of model validations were carried out to assess the prognostic value of the signature. Subsequently, lncRNAs were analyzed for gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes Enrichment (KEGG), immune-related functions, and tumor mutation burden (TMB). Finally, we used tumor immune dysfunction and exclusion (TIDE) algorithms on immune escape and immunotherapy of cuproptosis-related lncRNAs, thereby identifying its sensitivity toward potential drugs for LUAD. RESULTS A total of 16 cuproptosis-related lncRNAs were obtained, and a prognostic signature was developed. We found that high-risk patients had worse overall survival (OS) and progression-free survival (PFS) and higher mortality. Independent prognostic analyses, ROC, C-index, and nomogram showed that the cuproptosis-related lncRNAs can accurately predict the prognosis of patients. The nomogram and heatmap showed a distinct distribution of the high- and low-risk cuproptosis-related lncRNAs. Enrichment analysis showed that the biological functions of lncRNAs are associated with tumor development. We also found that immune-related functions, such as antiviral activity, were suppressed in high-risk patients who had mutations in oncogenes. OS was poorer in patients with high TMB. TIDE algorithms showed that high-risk patients have a greater potential for immune escape and less effective immunotherapy. CONCLUSION To conclude, the 16 cuproptosis-related lncRNAs can accurately predict the prognosis of patients with LUAD and may provide new insights into clinical applications and immunotherapy.
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Affiliation(s)
- Fangwei Wang
- grid.412594.f0000 0004 1757 2961Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nan’ning, China
| | - Hongsheng Lin
- grid.256607.00000 0004 1798 2653Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nan’ning, China
| | - Qisheng Su
- grid.412594.f0000 0004 1757 2961Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nan’ning, China
| | - Chaoqian Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nan'ning, China.
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PRIM2 Promotes Cell Cycle and Tumor Progression in p53-Mutant Lung Cancer. Cancers (Basel) 2022; 14:cancers14143370. [PMID: 35884433 PMCID: PMC9320259 DOI: 10.3390/cancers14143370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The mutation or inactivation of tumor suppressor genes is a key driving force during tumorigenesis, among which, p53 mutation is a common feature of human cancer. Therefore, exploring the potential role of p53 mutation in the occurrence and development of tumors is a powerful support for tumor diagnosis and treatment. In this study, we found that PRIM2 expression was abnormally elevated in p53-mutated lung cancer patients, and the elevated PRIM2 promoted DNA replication, enhanced mismatch repair, activated cell cycle, and promoted lung cancer progression. Here, we first report that the expression of PRIM2 is regulated by p53, and is identified as a biomarker of lung cancer malignancy and survival prognosis. Abstract p53 is a common tumor suppressor, and its mutation drives tumorigenesis. What is more, p53 mutations have also been reported to be indicative of poor prognosis in lung cancer, but the detailed mechanism has not been elucidated. In this study, we found that DNA primase subunit 2 (PRIM2) had a high expression level and associated with poor prognosis in lung cancer. Furthermore, we found that PRIM2 expression was abnormally increased in lung cancer cells with p53 mutation or altered the p53/RB pathway based on database. We also verified that PRIM2 expression was elevated by mutation or deletion of p53 in lung cancer cell lines. Lastly, silence p53 increased the expression of RPIM2. Thus, these data suggest that PRIM2 is a cancer-promoting factor which is regulated by the p53/RB pathway. The p53 tumor-suppressor gene integrates numerous signals that control cell proliferation, cell cycle, and cell death; and the p53/RB pathway determines the cellular localization of transcription factor E2F, which regulates the expression of downstream targets. Next, we explored the role of PRIM2 in lung cancer and found that knockdown of PRIM2 induced cell cycle arrest, increased DNA damage, and increased cell senescence, leading to decreased lung cancer cell proliferation. Lastly, the positive correlation between PRIM2 and E2F/CDK also indicated that PRIM2 was involved in promoting cell cycle mediated by p53/RB pathway. These results confirmed that the expression of PRIM2 is regulated by the p53/RB pathway in lung cancer cells, promotes DNA replication and mismatch repair, and activates the cell cycle. Overall, we found that frequent p53 mutations increased PRIM2 expression, activated the cell cycle, and promoted lung cancer progression.
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68
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Zhang S, Zhang R, Guo D, Han Y, Song G, Yang F, Chen Y. Molecular mechanism of Pulmonary diseases caused by exposure to urban PM 2.5 in Chengdu-Chongqing Economic Circle, China. ENVIRONMENT INTERNATIONAL 2022; 165:107292. [PMID: 35594815 DOI: 10.1016/j.envint.2022.107292] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Chengdu-Chongqing Economic Circle (CD-CQ Economic Circle) is one of China's four major economic circles and five major urban agglomerations located in Southwest China's Sichuan Basin. The CD-CQ Economic Circle, with its strong economic development and dense population, suffers from severe PM2.5 pollution, which is known to cause chronic and acute respiratory ailments. This study examined the lung disease-related hub genes, functions, and pathways that are affected by PM2.5 in summer and winter in the two central megacities of Chengdu and Chongqing. PM2.5 frequently activates lung disease-associated hub genes, most notably the transcription factor TP53. TP53 interacts with the majority of lung disease-related genes and regulates important and commonly occurring biological functions and pathways, including gland development, aging, reactive oxygen species metabolic process, the response to oxygen levels, and fluid shear stress, among others. Thus, PM2.5 has been shown to target TP53 for regulating lung disease genes/functions/pathways, thereby influencing the occurrence and progression of lung illnesses. Notably, PM2.5 may be associated with small cell carcinoma of the lung due to the high number of lung disease genes, hub genes, critical functions, and pathways enriched in this kind of cancer. These findings shed fresh light on the molecular pathophysiology of PM2.5 pollution on the respiratory system in the CD-CQ Economic Circle and aid in the development of novel techniques for mitigating PM2.5 pollution-associated respiratory illness.
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Affiliation(s)
- Shumin Zhang
- School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan, China; Research Center for Atmospheric Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Ronghua Zhang
- School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan, China
| | - Dongmei Guo
- School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan, China
| | - Yan Han
- Research Center for Atmospheric Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Guiqin Song
- School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan, China
| | - Fumo Yang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Yang Chen
- Research Center for Atmospheric Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
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69
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The Therapeutic Potential of the Restoration of the p53 Protein Family Members in the EGFR-Mutated Lung Cancer. Int J Mol Sci 2022; 23:ijms23137213. [PMID: 35806218 PMCID: PMC9267050 DOI: 10.3390/ijms23137213] [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: 06/09/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Despite the recent development of precision medicine and targeted therapies, lung cancer remains the top cause of cancer-related mortality worldwide. The patients diagnosed with metastatic disease have a five-year survival rate lower than 6%. In metastatic disease, EGFR is the most common driver of mutation, with the most common co-driver hitting TP53. EGFR-positive patients are offered the frontline treatment with tyrosine kinase inhibitors, yet the development of resistance and the lack of alternative therapies make this group of patients only fit for clinical trial participation. Since mutant p53 is the most common co-driver in the metastatic setting, therapies reactivating the p53 pathway might serve as a promising alternative therapeutic approach in patients who have developed a resistance to tyrosine kinase inhibitors. This review focuses on the molecular background of EGFR-mutated lung cancer and discusses novel therapeutic options converging on the reactivation of p53 tumor suppressor pathways.
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70
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Benesova L, Ptackova R, Halkova T, Semyakina A, Svaton M, Fiala O, Pesek M, Minarik M. Detection and Quantification of ctDNA for Longitudinal Monitoring of Treatment in Non-Small Cell Lung Cancer Patients Using a Universal Mutant Detection Assay by Denaturing Capillary Electrophoresis. Pathol Oncol Res 2022; 28:1610308. [PMID: 35837614 PMCID: PMC9274771 DOI: 10.3389/pore.2022.1610308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022]
Abstract
Background: Observation of anticancer therapy effect by monitoring of minimal residual disease (MRD) is becoming an important tool in management of non-small cell lung cancer (NSCLC). The approach is based on periodic detection and quantification of tumor-specific somatic DNA mutation in circulating tumor DNA (ctDNA) extracted from patient plasma. For such repetitive testing, complex liquid-biopsy techniques relying on ultra-deep NGS sequencing are impractical. There are other, cost-effective, methods for ctDNA analysis, typically based on quantitative PCR or digital PCR, which are applicable for detecting specific individual mutations in hotspots. While such methods are routinely used in NSCLC therapy prediction, however, extension to cover broader spectrum of mutations (e.g., in tumor suppressor genes) is required for universal longitudinal MRD monitoring. Methods: For a set of tissue samples from 81 NSCLC patients we have applied a denaturing capillary electrophoresis (DCE) for initial detection of somatic mutations within 8 predesigned PCR amplicons covering oncogenes and tumor suppressor genes. Mutation-negative samples were then subjected to a large panel NGS sequencing. For each patient mutation found in tissue was then traced over time in ctDNA by DCE. Results: In total we have detected a somatic mutation in tissue of 63 patients. For those we have then prospectively analyzed ctDNA from collected plasma samples over a period of up to 2 years. The dynamics of ctDNA during the initial chemotherapy therapy cycles as well as in the long-term follow-up matched the clinically observed response. Conclusion: Detection and quantification of tumor-specific mutations in ctDNA represents a viable complement to MRD monitoring during therapy of NSCLC patients. The presented approach relying on initial tissue mutation detection by DCE combined with NGS and a subsequent ctDNA mutation testing by DCE only represents a cost-effective approach for its routine implementation.
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Affiliation(s)
- Lucie Benesova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Renata Ptackova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Anastasiya Semyakina
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czechia
| | - Martin Svaton
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Ondrej Fiala
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Milos Pesek
- Department of Pneumology and Phtiseology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Marek Minarik
- Elphogene, Prague, Czechia
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Marek Minarik,
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71
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Nkosi D, Miller CA, Jajosky AN, Oltvai ZN. Incidental discovery of acute myeloid leukemia during liquid biopsy of a lung cancer patient. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006201. [PMID: 35732498 PMCID: PMC9235846 DOI: 10.1101/mcs.a006201] [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: 02/08/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Liquid biopsy is considered an alternative to standard next-generation sequencing (NGS) of solid tumor samples when biopsy tissue is inadequate for testing or when testing of a peripheral blood sample is preferred. A common assumption of liquid biopsies is that the NGS data obtained on circulating cell-free DNA is a high-fidelity reflection of what would be found by solid tumor testing. Here, we describe a case that challenges this widely held assumption. A patient diagnosed with lung carcinoma showed pathogenic IDH1 and TP53 mutations by liquid biopsy NGS at an outside laboratory. Subsequent in-house NGS of a metastatic lymph node fine-needle aspiration (FNA) sample revealed two pathogenic EGFR mutations. Morphologic and immunophenotypic assessment of the patient's blood sample identified acute myeloid leukemia, with in-house NGS confirming and identifying pathogenic IDH1, TP53, and BCOR mutations, respectively. This case, together with a few similar reports, demonstrates that caution is needed when interpreting liquid biopsy NGS results, especially if they are inconsistent with the presumptive diagnosis. Our case suggests that routine parallel sequencing of peripheral white blood cells would substantially increase the fidelity of the obtained liquid biopsy results.
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Affiliation(s)
- Dingani Nkosi
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Caroline A Miller
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Audrey N Jajosky
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Zoltán N Oltvai
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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72
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Chen Z, Xiong H, Shen H, You Q. Autophagy characteristics and establishment of autophagy prognostic models in lung adenocarcinoma and lung squamous cell carcinoma. PLoS One 2022; 17:e0266070. [PMID: 35333893 PMCID: PMC8956171 DOI: 10.1371/journal.pone.0266070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC), which makes up the majority of lung cancers, remains one of the deadliest malignancies in the world. It has a poor prognosis due to its late detection and lack of response to chemoradiaiton. Therefore, it is urgent to find a new prognostic marker. Methods We evaluated biological function and immune cell infiltration in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients from TCGA and GEO databases between different clusters based on autophagy related hub genes. Autophagy scores were used to assess the degree of autophagy in each individual by using component analysis. Results Three different clusters were obtained. Gene set variation analysis, single-sample gene set enrichment analysis and survive analysis showed differences among these three clusters. We demonstrated that the autophagy score of each patient could predict tumor stage and prognosis. Patients with a high autophagy score had a better prognosis, higher immune infiltration, and were more sensitive to immunotherapy and conventional chemotherapy. Conclusion It was uncovered that autophagy played an irreplaceable role in NSCLC. Quantified autophagy scores for each NSCLC patient would help guide effective treatment strategies.
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Affiliation(s)
- Zhubei Chen
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University Medical School, Nantong, China
| | - Hui Xiong
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University Medical School, Nantong, China
| | - Hao Shen
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University Medical School, Nantong, China
| | - Qingsheng You
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- * E-mail:
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73
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Yang L, Guo G, Yu X, Wen Y, Lin Y, Zhang R, Zhao D, Huang Z, Wang G, Yan Y, Zhang X, Chen D, Xing W, Wang W, Zeng W, Zhang L. Mutation-Derived Long Noncoding RNA Signature Predicts Survival in Lung Adenocarcinoma. Front Oncol 2022; 12:780631. [PMID: 35372012 PMCID: PMC8965709 DOI: 10.3389/fonc.2022.780631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genomic instability is one of the representative features of cancer evolution. Recent research has revealed that long noncoding RNAs (lncRNAs) play a critical role in maintaining genomic instability. Our work proposed a gene signature (GILncSig) based on genomic instability-derived lncRNAs to probe the possibility of lncRNA signatures as an index of genomic instability, providing a potential new approach to identify genomic instability-related cancer biomarkers. Methods Lung adenocarcinoma (LUAD) gene expression data from an RNA-seq FPKM dataset, somatic mutation information and relevant clinical materials were downloaded from The Cancer Genome Atlas (TCGA). A prognostic model consisting of genomic instability-related lncRNAs was constructed, termed GILncSig, to calculate the risk score. We validated GILncSig using data from the Gene Expression Omnibus (GEO) database. In this study, we used R software for data analysis. Results Through univariate and multivariate Cox regression analyses, five genomic instability-associated lncRNAs (LINC01671, LINC01116, LINC01214, lncRNA PTCSC3, and LINC02555) were identified. We constructed a lncRNA signature (GILncSig) related to genomic instability. LUAD patients were classified into two risk groups by GILncSig. The results showed that the survival rate of LUAD patients in the low-risk group was higher than that of those in the high-risk group. Then, we verified GILncSig in the GEO database. GILncSig was associated with the genomic mutation rate of LUAD. We also used GILncSig to divide TP53 mutant-type patients and TP53 wild-type patients into two groups and performed prognostic analysis. The results suggested that compared with TP53 mutation status, GILncSig may have better prognostic significance. Conclusions By combining the lncRNA expression profiles associated with somatic mutations and the corresponding clinical characteristics of LUAD, a lncRNA signature (GILncSig) related to genomic instability was established.
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Affiliation(s)
- Longjun Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongbin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongtai Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Xing
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weidong Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weian Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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74
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Martin-Fernandez ML. Fluorescence Imaging of Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Resistance in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14030686. [PMID: 35158954 PMCID: PMC8833717 DOI: 10.3390/cancers14030686] [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: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Lung cancer is the leading cause of cancer-related deaths, with a low (<21%) 5-year survival rate. Lung cancer is often driven by the misfunction of molecules on the surface of cells of the epithelium, which orchestrate mechanisms by which these cells grow and proliferate. Beyond common non-specific treatments, such as chemotherapy or radiotherapy, among molecular-specific treatments, a number of small-molecule drugs that block cancer-driven molecular activity have been developed. These drugs initially have significant success in a subset of patients, but these patients systematically develop resistance within approximately one year of therapy. Substantial efforts towards understanding the mechanisms of resistance have focused on the genomics of cancer progression, the response of cells to the drugs, and the cellular changes that allow resistance to develop. Fluorescence microscopy of many flavours has significantly contributed to the last two areas, and is the subject of this review. Abstract Non-small cell lung cancer (NSCLC) is a complex disease often driven by activating mutations or amplification of the epidermal growth factor receptor (EGFR) gene, which expresses a transmembrane receptor tyrosine kinase. Targeted anti-EGFR treatments include small-molecule tyrosine kinase inhibitors (TKIs), among which gefitinib and erlotinib are the best studied, and their function more often imaged. TKIs block EGFR activation, inducing apoptosis in cancer cells addicted to EGFR signals. It is not understood why TKIs do not work in tumours driven by EGFR overexpression but do so in tumours bearing classical activating EGFR mutations, although the latter develop resistance in about one year. Fluorescence imaging played a crucial part in research efforts to understand pro-survival mechanisms, including the dysregulation of autophagy and endocytosis, by which cells overcome the intendedly lethal TKI-induced EGFR signalling block. At their core, pro-survival mechanisms are facilitated by TKI-induced changes in the function and conformation of EGFR and its interactors. This review brings together some of the main advances from fluorescence imaging in investigating TKI function and places them in the broader context of the TKI resistance field, highlighting some paradoxes and suggesting some areas where super-resolution and other emerging methods could make a further contribution.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
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75
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Duan L, Perez RE, Calhoun S, Maki CG. RBL2/DREAM-mediated repression of the Aurora kinase A/B pathway determines therapy responsiveness and outcome in p53 WT NSCLC. Sci Rep 2022; 12:1049. [PMID: 35058503 PMCID: PMC8776870 DOI: 10.1038/s41598-022-05013-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/28/2021] [Indexed: 01/03/2023] Open
Abstract
Wild-type p53 is a stress-responsive transcription factor and potent tumor suppressor. P53 activates or represses genes involved in cell cycle progression or apoptosis in order to arrest the cell cycle or induce cell death. Transcription repression by p53 is indirect and requires repressive members of the RB-family (RB1, RBL1, RBL2) and formation of repressor complexes of RB1-E2F and RBL1/RBL2-DREAM. Many aurora kinase A/B (AURKA/B) pathway genes are repressed in a p53-DREAM-dependent manner. We found heightened expression of RBL2 and reduced expression of AURKA/B pathway genes is associated with improved outcomes in p53 wild-type but not p53 mutant non-small cell lung cancer (NSCLC) patients. Knockdown of p53, RBL2, or the DREAM component LIN37 increased AURKA/B pathway gene expression and reduced paclitaxel and radiation toxicity in NSCLC cells. In contrast, pharmacologic inhibition of AURKA/B or knockdown of AURKA/B pathway components increased paclitaxel and IR sensitivity. The results support a model in which p53-RBL2-DREAM-mediated repression of the AURKA/B pathway contributes to tumor suppression, improved tumor therapy responses, and better outcomes in p53 wild-type NSCLCs.
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Affiliation(s)
- Lei Duan
- Department of Anatomy and Cell Biology, Rush University Medical Center, 600 S. Paulina Ave, AcFac 507, Chicago, IL, 60612, USA. .,Rush University Medical Center, Chicago, IL, 60612, USA.
| | - Ricardo E Perez
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Sarah Calhoun
- Department of Anatomy and Cell Biology, Rush University Medical Center, 600 S. Paulina Ave, AcFac 507, Chicago, IL, 60612, USA.,Rush University Medical Center, Chicago, IL, 60612, USA
| | - Carl G Maki
- Department of Anatomy and Cell Biology, Rush University Medical Center, 600 S. Paulina Ave, AcFac 507, Chicago, IL, 60612, USA. .,Rush University Medical Center, Chicago, IL, 60612, USA.
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Miri MR, Zare A, Saberzadeh J, Baghban N, Nabipour I, Tamadon A. Anti-lung Cancer Marine Compounds: A Review. Ther Innov Regul Sci 2022; 56:191-205. [PMID: 35025082 DOI: 10.1007/s43441-022-00375-3] [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: 10/28/2021] [Accepted: 01/03/2022] [Indexed: 12/24/2022]
Abstract
Lung cancer is one of the most common and lethal cancers in human beings. Lung cancer has been divided into two major types: small cell lung cancer (SCLC) and non-small cell lung carcinoma (NSCLC). Current drugs suffer from various side effects, and the insufficient efficacy of present treatments creates a desire for better more efficient new drugs. This review compares the diversity of marine-derived bioactive compounds from different marine species. Some of the natural products from marine resources are in different stages of clinical trials. By the way, most of them have been studied in vitro and in vivo. Additionally, in this review, the mechanisms of action of marine-derived anti-lung cancer components on lung cancer cell lines have been reviewed. In addition, considering growing rate and the high costs of cancer research, attention must be paid to some aspects of targeting and developing anti-lung cancer drug. In better words, like the other therapeutic strategies that have their particular challenges and weak points, several challenges about marine-derived anti-lung cancer components which exist for scientists for doing research are explained. Moreover, as the attentions in the field of cancer therapy are focused on designing and developing new anticancer strategies for the treatment of cancer in the future, the application of marine-derived anti-lung cancer components in the field of future cancer therapy and their role in future anticancer strategies are briefly discussed.
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Affiliation(s)
- Mohammad Reza Miri
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Afshin Zare
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Jamileh Saberzadeh
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Baghban
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran.
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Pathak AK, Husain N, Shukla S, Pandey RK, Kant S, Bala L. Impact of glutathione S transferases P1 (Ile105Val) variants on the risk of GSTp, phosphorylated c-Jun kinase, and P53 phenotypic expression and their implications on overall survival outcomes in non-small cell lung cancer patients treated with chemotherapy. Mutat Res 2022; 824:111775. [PMID: 35124341 DOI: 10.1016/j.mrfmmm.2022.111775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/18/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
AIM This study focused on GST-M1, T1 null, and P1 Ile105Val variant genotypes associated with the risk of altered expression of GSTp, pJNK, and P53 in NSCLC patients. These markers and overall survival (OS) were correlated with a key set of clinicopathological characteristics. METHODS Genotyping of GST- M1, T1 (+/-), and P1 (Ile105Val) was performed using PCR-RFLP.The expression of GSTp, pJNK, and P53 phenotypes was assessed by immunohistochemistry. The Spearman test was used to examine the correlation between GSTp, pJNK, and P53. Kaplan-Meier test was used for OS analysis. RESULTS GSTP1 Val/Val and Ile/Val genotypes notably increased GSTp expression by 1.8 and 1.7 fold, respectively (p = 0.04,p = 0.06). GSTP1 Val/Val and Ile/Val genotypes considerably reduced P53 expression by 0.61 and 0.57 fold, respectively (p = 0.03& p = 0.05), respectively. GSTp, pJNK, and P53 were significantly co-expressed (p < 0.001). GSTp and pJNK expression showed a moderate negative correlation (ρ = -0.32, p = 0.046). In contrast, GSTp and P53 expression exhibited a strong negative correlation (ρ = -0.53, p < 0.0001). There was no correlation between P53 and pJNK expression(ρ = 0.07, p = 0.54). The patient's median OS was 8.9 months, and it was significantly related to pack-years, stage, metastasis, and GSTM1(-/-) genotypes (p > 0.05). SQCLC showed poor OS than ADC (5.7 months vs.9.1 months, p = 0.2). Stage IV and metastasis significantly reduced the OS (p = 0.001). The tumour size and lymph nodes reflected poor OS (p = 0.07&p = 0.06). Gemcitabine+Cisplatin and Gefitinib showed a slightly higher rate of survival (9.3 months and 8.1 months) than Pemtrexe+Cisplatin treatment (7.0 months,p = 0.8). Multivariate analysis revealed that pack-years and GSTp were independent predictors for OS (p = 0.03). CONCLUSION GSTp, pJNK, and P53 showed interconnected cascading. Age, pack-year, stage, and GSTp were found to be significant predictive factors for OS.Pack-years, GSTp independent OS predictor.
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Affiliation(s)
- Anumesh K Pathak
- Department of Pathology, Dr. Ram ManoharLohia Institute of Medical Sciences, Lucknow 226010, India; Department of Biochemistry, Babu Banarasi Das University, Lucknow 226018, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram ManoharLohia Institute of Medical Sciences, Lucknow 226010, India.
| | - Saumya Shukla
- Department of Pathology, Dr. Ram ManoharLohia Institute of Medical Sciences, Lucknow 226010, India
| | - Rahul Kumar Pandey
- Department of Pathology, Dr. Ram ManoharLohia Institute of Medical Sciences, Lucknow 226010, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Lucknow 226003, India
| | - Lakshmi Bala
- Department of Biochemistry, Babu Banarasi Das University, Lucknow 226018, India
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Plummer R, Dean E, Arkenau HT, Redfern C, Spira AI, Melear JM, Chung KY, Ferrer-Playan J, Goddemeier T, Locatelli G, Dong J, Fleuranceau-Morel P, Diaz-Padilla I, Shapiro GI. A phase 1b study evaluating the safety and preliminary efficacy of berzosertib in combination with gemcitabine in patients with advanced non-small cell lung cancer. Lung Cancer 2022; 163:19-26. [PMID: 34894455 DOI: 10.1016/j.lungcan.2021.11.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Berzosertib (formerly M6620, VX-970) is an intravenous, highly potent and selective, first-in-class ataxia telangiectasia and Rad3-related (ATR) protein kinase inhibitor. We assessed the safety, tolerability, preliminary efficacy, and pharmacokinetics (PK) of berzosertib plus gemcitabine in an expansion cohort of patients with advanced non-small cell lung cancer (NSCLC). The association of efficacy with TP53 status and other tumor markers was also explored. MATERIALS AND METHODS Adult patients with advanced histologically confirmed NSCLC received berzosertib 210 mg/m2 (days 2 and 9) and gemcitabine 1000 mg/m2 (days 1 and 8) at the recommended phase 2 dose established in the dose escalation part of the study. RESULTS Thirty-eight patients received at least one dose of study treatment. The most common treatment-emergent adverse events were fatigue (55.3%), anemia (52.6%), and nausea (39.5%). Gemcitabine had no apparent effect on the PK of berzosertib. The objective response rate (ORR) was 10.5% (4/38, 90% confidence interval [CI]: 3.7-22.5%). In the exploratory analysis, the ORR was 30.0% (3/10, 90% CI: 9.0-61.0%) in patients with high loss of heterozygosity (LOH) and 11.0% (1/9, 90% CI: 1.0-43.0%) in patients with low LOH. The ORR was 33.0% (2/6, 90% CI: 6.0-73.0%) in patients with high tumor mutational burden (TMB), 12.5% (2/16, 90% CI: 2.0-34.0%) in patients with intermediate TMB, and 0% (0/3, 90% CI: 0.0-53.6%) in patients with low TMB. CONCLUSIONS Berzosertib plus gemcitabine was well tolerated in patients with advanced, pre-treated NSCLC. Based on the observed clinical efficacy, future clinical trials should involve genomically selected patients.
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Affiliation(s)
- Ruth Plummer
- Newcastle University and Northern Centre for Cancer Care, Newcastle Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom.
| | - Emma Dean
- The University of Manchester and The Christie NHS Foundation Trust, Manchester, United Kingdom.
| | | | | | - Alexander I Spira
- Virginia Cancer Specialists Research Institute and US Oncology Research, Fairfax, VA, United States
| | | | - Ki Y Chung
- Prisma Health, Greenville, SC, United States.
| | - Jordi Ferrer-Playan
- Ares Trading SA, Eysins, Switzerland, an affiliate of Merck KGaA, Darmstadt, Germany
| | | | | | - Jennifer Dong
- EMD Serono Research & Development Institute, Inc., Billerica, MA, United States
| | | | - Ivan Diaz-Padilla
- Ares Trading SA, Eysins, Switzerland, an affiliate of Merck KGaA, Darmstadt, Germany
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States.
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Alhebshi H, Tian K, Patnaik L, Taylor R, Bezecny P, Hall C, Muller PAJ, Safari N, Creamer DPM, Demonacos C, Mutti L, Bittar MN, Krstic-Demonacos M. Evaluation of the Role of p53 Tumour Suppressor Posttranslational Modifications and TTC5 Cofactor in Lung Cancer. Int J Mol Sci 2021; 22:ijms222413198. [PMID: 34947995 PMCID: PMC8707832 DOI: 10.3390/ijms222413198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Mutations in the p53 tumor suppressor are found in over 50% of cancers. p53 function is controlled through posttranslational modifications and cofactor interactions. In this study, we investigated the posttranslationally modified p53, including p53 acetylated at lysine 382 (K382), p53 phosphorylated at serine 46 (S46), and the p53 cofactor TTC5/STRAP (Tetratricopeptide repeat domain 5/ Stress-responsive activator of p300-TTC5) proteins in lung cancer. Immunohistochemical (IHC) analysis of lung cancer tissues from 250 patients was carried out and the results were correlated with clinicopathological features. Significant associations between total or modified p53 with a higher grade of the tumour and shorter overall survival (OS) probability were detected, suggesting that mutant and/or modified p53 acts as an oncoprotein in these patients. Acetylated at K382 p53 was predominantly nuclear in some samples and cytoplasmic in others. The localization of the K382 acetylated p53 was significantly associated with the gender and grade of the disease. The TTC5 protein levels were significantly associated with the grade, tumor size, and node involvement in a complex manner. SIRT1 expression was evaluated in 50 lung cancer patients and significant positive correlation was found with p53 S46 intensity, whereas negative TTC5 staining was associated with SIRT1 expression. Furthermore, p53 protein levels showed positive association with poor OS, whereas TTC5 protein levels showed positive association with better OS outcome. Overall, our results indicate that an analysis of p53 modified versions together with TTC5 expression, upon testing on a larger sample size of patients, could serve as useful prognostic factors or drug targets for lung cancer treatment.
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Affiliation(s)
- Hasen Alhebshi
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
| | - Kun Tian
- Institute of Biological Anthropology, School of Basical Medical Science, Jinzhou Medical University, Jinzhou 121001, China;
| | - Lipsita Patnaik
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Rebecca Taylor
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Pavel Bezecny
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Callum Hall
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester SK10 4TG, UK; (C.H.); (P.A.J.M.)
| | - Patricia Anthonia Johanna Muller
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester SK10 4TG, UK; (C.H.); (P.A.J.M.)
| | - Nazila Safari
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
| | - Delta Patricia Menendez Creamer
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Stopford Building, 3.124 Oxford Road, Manchester M13 9PT, UK;
| | - Luciano Mutti
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
| | - Mohamad Nidal Bittar
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool FY3 8NR, UK; (L.P.); (R.T.); (P.B.); (M.N.B.)
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Cockcroft Building 305, Manchester M5 4WT, UK; (H.A.); (N.S.); (D.P.M.C.)
- Correspondence:
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80
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Zhao Z, Wan J, Guo M, Wang Y, Yang Z, Zhou F, Li Z, Ming L. Expression and prognostic significance of m6A-related genes in TP53-mutant non-small-cell lung cancer. J Clin Lab Anal 2021; 36:e24118. [PMID: 34812534 PMCID: PMC8761469 DOI: 10.1002/jcla.24118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background TP53 is an important tumor suppressor gene on human 17th chromosome with its mutations more than 60% in tumor cells. Lung cancer is the highest incidence malignancy in men around the world. N‐6 methylase (m6A) is an enzyme that plays an important role in mRNA splicing, translation, and stabilization. However, its role in TP53‐mutant non‐small‐cell lung cancer (NSCLC) remains unknown. Method First, we investigated 17 common m6A regulators' prognostic values in NSCLC. Then, after the establishment of risk signature, we explored the diagnostic value of m6A in TP53‐mutant NSCLC. Finally, gene set enrichment analysis (GSEA), gene ontology (GO) enrichment analysis, and differential expression analysis were used to reveal the possible mechanism of m6A regulators affecting TP53‐mutant NSCLC patients. Results Study showed that nine m6A regulators (YTHDC2, METTL14, FTO, METTL16, YTHDF1, HNRNPA2B1, RBM15, KIAA1429, and WTAP) were expressed differently between TP53‐mutant and wild‐type NSCLC (p < 0.05); and ALKBH5 and HNRNPA2B1 were associated with the prognostic of TP53‐mutant patients. After construction of the risk signature combined ALKBH5 and HNRNPA2B1, we divided patients with TP53 mutations into high‐ and low‐risk groups, and there was a significant survival difference between two groups. Finally, 338 differentially expression genes (DEGs) were found between high‐ and low‐risk groups. GO enrichment analysis, PPI network, and GSEA enrichment analysis showed that m6A may affect the immune environment in extracellular and change the stability of mRNA. Conclusion In conclusion, m6A regulators can be used as prognostic predictors in TP53‐mutant patients.
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Affiliation(s)
- Zhuochen Zhao
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Junhu Wan
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Manman Guo
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Yangxia Wang
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Zhengwu Yang
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Fuyou Zhou
- The Department of Thoracic Surgery, Anyang Cancer Hospital, Henan, China
| | - Zhuofang Li
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Liang Ming
- The Clinical Laboratory of the First Affiliated Hospital of Zhengzhou University, Henan, China
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81
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Šutić M, Vukić A, Baranašić J, Försti A, Džubur F, Samaržija M, Jakopović M, Brčić L, Knežević J. Diagnostic, Predictive, and Prognostic Biomarkers in Non-Small Cell Lung Cancer (NSCLC) Management. J Pers Med 2021; 11:1102. [PMID: 34834454 PMCID: PMC8624402 DOI: 10.3390/jpm11111102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Despite growing efforts for its early detection by screening populations at risk, the majority of lung cancer patients are still diagnosed in an advanced stage. The management of lung cancer has dramatically improved in the last decade and is no longer based on the "one-fits-all" paradigm or the general histological classification of non-small cell versus small cell lung cancer. Emerging options of targeted therapies and immunotherapies have shifted the management of lung cancer to a more personalized treatment approach, significantly influencing the clinical course and outcome of the disease. Molecular biomarkers have emerged as valuable tools in the prognosis and prediction of therapy response. In this review, we discuss the relevant biomarkers used in the clinical management of lung tumors, from diagnosis to prognosis. We also discuss promising new biomarkers, focusing on non-small cell lung cancer as the most abundant type of lung cancer.
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Affiliation(s)
- Maja Šutić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
| | - Ana Vukić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
| | - Jurica Baranašić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
| | - Asta Försti
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany;
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Feđa Džubur
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (F.D.); (M.S.); (M.J.)
- Clinical Department for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Miroslav Samaržija
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (F.D.); (M.S.); (M.J.)
- Clinical Department for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Marko Jakopović
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (F.D.); (M.S.); (M.J.)
- Clinical Department for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Luka Brčić
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria;
| | - Jelena Knežević
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
- Faculties for Dental Medicine and Health, University of Osijek, 31000 Osijek, Croatia
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82
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Zeng D, Hu Z, Yi Y, Valeria B, Shan G, Chen Z, Zhan C, Lin M, Lin Z, Wang Q. Differences in genetics and microenvironment of lung adenocarcinoma patients with or without TP53 mutation. BMC Pulm Med 2021; 21:316. [PMID: 34635074 PMCID: PMC8507221 DOI: 10.1186/s12890-021-01671-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background Differences in genetics and microenvironment of LUAD patients with or without TP53 mutation were analyzed to illustrate the role of TP53 mutation within the carcinogenesis of LUAD, which will provide new concepts for the treatment of LUAD. Methods
In this study, we used genetics and clinical info from the TCGA database, including somatic mutations data, RNA-seq, miRNA-seq, and clinical data. More than one bioinformatics tools were used to analyze the unique genomic pattern of TP53-related LUAD. Results According to TP53 gene mutation status, we divided the LUAD patients into two groups, including 265 in the mutant group (MU) and 295 in the wild-type group (WT). 787 significant somatic mutations were detected between the groups, including mutations in titin (TTN), type 2 ryanodine receptor (RYR2) and CUB and Sushi multiple domains 3(CSMD3), which were up-regulated in the MU. However, no significant survival difference was observed. At the RNA level, we obtained 923 significantly differentially expressed genes; in the MU, α-defensin 5(DEFA5), pregnancy-specific glycoprotein 5(PSG5) and neuropeptide Y(NPY) were the most up-regulated genes, glucose-6-phosphatase (G6PC), alpha-fetoprotein (AFP) and carry gametocidal (GC) were the most down-regulated genes. GSVA analysis revealed 30 significant pathways. Compared with the WT, the expression of 12 pathways in the mutant group was up-regulated, most of which pointed to cell division. There were significant differences in tumor immune infiltrating cells, such as Macrophages M1, T cells CD4 memory activated, Mast cells resting, and Dendritic cells resting. In terms of immune genes, a total of 35 immune-related genes were screened, of which VGF (VGF nerve growth factor inducible) and PGC (peroxisome proliferator-activated receptor gamma coactivator) were the most significant up-regulated and down-regulated genes, respectively. Research on the expression pattern of immunomodulators found that 9 immune checkpoint molecules and 6 immune costimulatory molecules were considerably wholly different between the two groups. Conclusions Taking the mutant group as a reference, LUAD patients in the mutant group had significant differences in somatic mutations, mRNA-seq, miRNA-seq, immune infiltration, and immunomodulators, indicating that TP53 mutation plays a crucial role in the occurrence and development of LUAD. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01671-8.
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Affiliation(s)
- Dejun Zeng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yanjun Yi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Besskaya Valeria
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Guangyao Shan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Miao Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Zongwu Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
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83
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Lu J, Zhong R, Lou Y, Hu M, Yang Z, Wang Y, Chen Y, Zou B, Zhang W, Wang H, Han B. TP53 Mutation Status and Biopsy Lesion Type Determine the Immunotherapeutic Stratification in Non-Small-Cell Lung Cancer. Front Immunol 2021; 12:732125. [PMID: 34603310 PMCID: PMC8485033 DOI: 10.3389/fimmu.2021.732125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023] Open
Abstract
Immunotherapy, a chemotherapy-free process, has emerged as a promising therapeutic strategy to prolong the overall survival (OS) of patients with non-small-cell lung cancer (NSCLC). However, effective stratification factors for immunotherapy remain unclear. The purpose of this study was to discuss the potential stratification factors of NSCLC immunotherapy using immune checkpoint inhibitors (ICIs) by integrating genomic profiling and tumor lesion–type information. In this study, 344 patients with NSCLC, whose clinical and tissue (including metastatic and primary lesions) mutation information was available, were included. The potential gene mutation status for predicting the outcomes of immunotherapy was screened by comparing the difference in mutation frequency between responders and non-responders. Our results indicated that the potential predictors of immunotherapy were significantly different, especially between patients with TP53(+) (including metastatic and primary lesions) and TP53(−) (including metastatic and primary lesions). According to this classification, patients with NSCLC who suggested immunotherapy had a higher OS than those who did not (25 months vs. 7 months, P < 0.0001, hazard ratio = 0.39). Collectively, this study provides a new perspective for screening immunotherapy predictors in NSCLC, suggesting that the TP53 mutation status and source of biopsy tissue should be considered during the development of immunotherapy biomarkers.
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Affiliation(s)
- Jun Lu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Translational Medical Research Platform for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Runbo Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Lou
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Minjuan Hu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyu Yang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Chen
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Benkun Zou
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huimin Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Translational Medical Research Platform for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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84
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Contribution of p53 in sensitivity to EGFR tyrosine kinase inhibitors in non-small cell lung cancer. Sci Rep 2021; 11:19667. [PMID: 34608255 PMCID: PMC8490392 DOI: 10.1038/s41598-021-99267-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022] Open
Abstract
The emergence of resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) with activating EGFR mutations is a major hindrance to treatment. We investigated the effects of p53 in primary sensitivity and acquired resistance to EGFR-TKIs in NSCLC cells. Changes in sensitivity to EGFR-TKIs were determined using p53 overexpression or knockdown in cells with activating EGFR mutations. We investigated EMT-related molecules, morphologic changes, and AXL induction to elucidate mechanisms of acquired resistance to EGFR-TKIs according to p53 status. Changes in p53 status affected primary sensitivity as well as acquired resistance to EGFR-TKIs according to cell type. Firstly, p53 silencing did not affect primary and acquired resistance to EGFR-TKIs in PC-9 cells, but it led to primary resistance to EGFR-TKIs through AXL induction in HCC827 cells. Secondly, p53 silencing in H1975 cells enhanced the sensitivity to osimertinib through the emergence of mesenchymal-to-epithelial transition, and the emergence of acquired resistance to osimertinib in p53 knockout cells was much slower than in H1975 cells. Furthermore, two cell lines (H1975 and H1975/p53KO) demonstrated the different mechanisms of acquired resistance to osimertinib. Lastly, the introduction of mutant p53-R273H induced the epithelial-to-mesenchymal transition and exerted resistance to EGFR-TKIs in cells with activating EGFR mutations. These findings indicate that p53 mutations can be associated with primary or acquired resistance to EGFR-TKIs. Thus, the status or mutations of p53 may be considered as routes to improving the therapeutic effects of EGFR-TKIs in NSCLC.
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85
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Ngai TW, Elfar GA, Yeo P, Phua N, Hor JH, Chen S, Ho YS, Cheok CF. Nitro-Deficient Niclosamide Confers Reduced Genotoxicity and Retains Mitochondrial Uncoupling Activity for Cancer Therapy. Int J Mol Sci 2021; 22:10420. [PMID: 34638761 PMCID: PMC8508655 DOI: 10.3390/ijms221910420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
Niclosamide is an oral anthelmintic drug, approved for use against tapeworm infections. Recent studies suggest however that niclosamide may have broader clinical applications in cancers, spurring increased interest in the functions and mechanisms of niclosamide. Previously, we reported that niclosamide targets a metabolic vulnerability in p53-deficient tumours, providing a basis for patient stratification and personalised treatment strategies. In the present study, we functionally characterised the contribution of the aniline 4'-NO2 group on niclosamide to its cellular activities. We demonstrated that niclosamide induces genome-wide DNA damage that is mechanistically uncoupled from its antitumour effects mediated through mitochondrial uncoupling. Elimination of the nitro group in ND-Nic analogue significantly reduced γH2AX signals and DNA breaks while preserving its antitumour mechanism mediated through a calcium signalling pathway and arachidonic acid metabolism. Lipidomics profiling further revealed that ND-Nic-treated cells retained a metabolite profile characteristic of niclosamide-treated cells. Notably, quantitative scoring of drug sensitivity suggests that elimination of its nitro group enhanced the target selectivity of niclosamide against p53 deficiency. Importantly, the results also raise concern that niclosamide may impose a pleiotropic genotoxic effect, which limits its clinical efficacy and warrants further investigation into alternative drug analogues that may ameliorate any potential unwanted side effects.
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Affiliation(s)
- Tsz Wai Ngai
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; (T.W.N.); (G.A.E.); (P.Y.); (N.P.); (J.H.H.)
| | - Gamal Ahmed Elfar
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; (T.W.N.); (G.A.E.); (P.Y.); (N.P.); (J.H.H.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
| | - Pearlyn Yeo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; (T.W.N.); (G.A.E.); (P.Y.); (N.P.); (J.H.H.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
| | - Nicholas Phua
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; (T.W.N.); (G.A.E.); (P.Y.); (N.P.); (J.H.H.)
| | - Jin Hui Hor
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; (T.W.N.); (G.A.E.); (P.Y.); (N.P.); (J.H.H.)
| | - Shuwen Chen
- Analytical Science and Technology (Metabolomics), Bioprocessing Technology Institute, 20 Biopolis Way, Centros #06-01, Singapore 138668, Singapore; (S.C.); (Y.S.H.)
| | - Ying Swan Ho
- Analytical Science and Technology (Metabolomics), Bioprocessing Technology Institute, 20 Biopolis Way, Centros #06-01, Singapore 138668, Singapore; (S.C.); (Y.S.H.)
| | - Chit Fang Cheok
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; (T.W.N.); (G.A.E.); (P.Y.); (N.P.); (J.H.H.)
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
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86
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Lu J, Zhang Y, Lou Y, Yan B, Zou B, Hu M, Wang Y, Chen Y, Yang Z, Wang H, Zhang W, Han B. ctDNA-Profiling-Based UBL Biological Process Mutation Status as a Predictor of Atezolizumab Response Among TP53-Negative NSCLC Patients. Front Genet 2021; 12:723670. [PMID: 34557222 PMCID: PMC8452871 DOI: 10.3389/fgene.2021.723670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/09/2021] [Indexed: 01/01/2023] Open
Abstract
Atezolizumab, an immune checkpoint inhibitor, has been approved for use in clinical practice in non-small cell lung cancer (NSCLC) patients, but potential biomarkers for response stratification still need further screening. In the present study, a total of 399 patients with high-quality ctDNA profiling results were included. The mutation status of ubiquitin-like conjugation (UBL) biological process genes (including ABL1, APC, LRP6, FUBP1, KEAP1, and TOP2A) and clinical information were further integrated. The results suggested that the patients with the clinical characteristics of male or history of smoking had a higher frequency of UBL mutation positivity [UBL (+)]; the patients who were UBL (+) had shorter progression-free survival (PFS) (1.69 vs. 3.22 months, p = 0.0007) and overall survival (8.61 vs. 16.10 months, p < 0.0001) than those patients with UBL mutation negativity [UBL (–)]; and more promising predictive values were shown in the smoker subgroup and ≤ 3 metastasis subgroup. More interestingly, we found the predictor has more performance in TP53-negative cohorts [training in an independent POPLAR and OAK cohorts (n = 200), and validation in an independent MSKCC cohort (n = 127)]. Overall, this study provides a predictor, UBL biological process gene mutation status, not only for identifying NSCLC patients who may respond to atezolizumab therapy but also for screening out the potential NSCLC responders who received other immune checkpoint inhibitors.
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Affiliation(s)
- Jun Lu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Translational Medical Research Platform for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanwei Zhang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Lou
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Yan
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Benkun Zou
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Minjuan Hu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Chen
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyu Yang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huimin Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.,Translational Medical Research Platform for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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87
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Qu H, Zhou M, Yan Z, Wang H, Rustgi VK, Zhang S, Gevaert O, Metaxas DN. Genetic mutation and biological pathway prediction based on whole slide images in breast carcinoma using deep learning. NPJ Precis Oncol 2021; 5:87. [PMID: 34556802 PMCID: PMC8460699 DOI: 10.1038/s41698-021-00225-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
Breast carcinoma is the most common cancer among women worldwide that consists of a heterogeneous group of subtype diseases. The whole-slide images (WSIs) can capture the cell-level heterogeneity, and are routinely used for cancer diagnosis by pathologists. However, key driver genetic mutations related to targeted therapies are identified by genomic analysis like high-throughput molecular profiling. In this study, we develop a deep-learning model to predict the genetic mutations and biological pathway activities directly from WSIs. Our study offers unique insights into WSI visual interactions between mutation and its related pathway, enabling a head-to-head comparison to reinforce our major findings. Using the histopathology images from the Genomic Data Commons Database, our model can predict the point mutations of six important genes (AUC 0.68-0.85) and copy number alteration of another six genes (AUC 0.69-0.79). Additionally, the trained models can predict the activities of three out of ten canonical pathways (AUC 0.65-0.79). Next, we visualized the weight maps of tumor tiles in WSI to understand the decision-making process of deep-learning models via a self-attention mechanism. We further validated our models on liver and lung cancers that are related to metastatic breast cancer. Our results provide insights into the association between pathological image features, molecular outcomes, and targeted therapies for breast cancer patients.
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Affiliation(s)
- Hui Qu
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Mu Zhou
- Sensebrain Research, Princeton, NJ, USA
| | | | - He Wang
- School of Medicine, Yale University, New Haven, CT, USA
| | - Vinod K Rustgi
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Shaoting Zhang
- SenseTime Research and Shanghai AI Laboratory, Shanghai, China.
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Dimitris N Metaxas
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA.
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88
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Yao B, Han X, Pang L, Xu C, Liu S, Cheng X, Chen J. Acquired ALK Resistance Mutations Identified from Liquid Biopsy in an ALK-Rearranged Squamous Cell Lung Cancer Patient Treated with Sequential ALK TKI Therapy: A Case Report. Onco Targets Ther 2021; 14:4329-4333. [PMID: 34376997 PMCID: PMC8349191 DOI: 10.2147/ott.s315832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/21/2021] [Indexed: 12/26/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) rearrangement is extremely rare in lung squamous cell carcinoma (LSCC), and it remains controversial as to whether LSCC patients with ALK rearrangement can benefit from ALK tyrosine kinase inhibitors (TKIs). Here, we report an LSCC patient with ALK rearrangement who was treated with sequential ALK TKI therapies and experienced a clinical benefit of 35 months. Although the use of ALK TKIs showed clinical benefits, targeted next-generation sequencing (NGS) for dynamic monitoring of circulating tumor DNA (ctDNA) from patient plasma revealed the accumulation of ALK resistance mutations, which could provide valuable information in designing the treatment strategy. Our study highlights the importance of dynamic monitoring of ctDNA using NGS to discover tumor evolution to guide treatment decision-making and provides meaningful insights into the potential treatment options for ALK-positive LSCC patients.
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Affiliation(s)
- Bin Yao
- Department of Radiotherapy and Chemotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Xue Han
- Department of Research and Development, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China
| | - Linrong Pang
- Department of Radiotherapy and Chemotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Caihong Xu
- Department of Radiotherapy and Chemotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Sisi Liu
- Department of Research and Development, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China
| | - Xiaochun Cheng
- Department of Radiotherapy and Chemotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Jun Chen
- Department of Radiotherapy and Chemotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
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89
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Erhunmwunsee L, Wing SE, Shen J, Hu H, Sosa E, Lopez LN, Raquel C, Sur M, Ibarra-Noriega P, Currey M, Lee J, Kim JY, Raz DJ, Amini A, Sampath S, Koczywas M, Massarelli E, West HL, Reckamp KL, Kittles RA, Salgia R, Seewaldt VL, Neuhausen SL, Gray SW. The Association between Polluted Neighborhoods and TP53-Mutated Non-Small Cell Lung Cancer. Cancer Epidemiol Biomarkers Prev 2021; 30:1498-1505. [PMID: 34088750 PMCID: PMC8338883 DOI: 10.1158/1055-9965.epi-20-1555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/13/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Poor patients often reside in neighborhoods of lower socioeconomic status (SES) with high levels of airborne pollutants. They also have higher mortality from non-small cell lung cancer (NSCLC) than those living in wealthier communities. We investigated whether living in polluted neighborhoods is associated with somatic mutations linked with lower survival rates, i.e., TP53 mutations. METHODS In a retrospective cohort of 478 patients with NSCLC treated at a comprehensive cancer center between 2015 and 2018, we used logistic regression to assess associations between individual demographic and clinical characteristics, including somatic TP53 mutation status and environmental risk factors of annual average particulate matter (PM2.5) levels, and neighborhood SES. RESULTS 277 patients (58%) had somatic TP53 mutations. Of those, 45% lived in neighborhoods with "moderate" Environmental Protection Agency-defined PM2.5 exposure, compared with 39% of patients without TP53 mutations. We found significant associations between living in neighborhoods with "moderate" versus "good" PM2.5 concentrations and minority population percentage [OR, 1.06; 95% confidence interval (CI), 1.04-1.08]. There was a significant association between presence of TP53 mutations and PM2.5 exposure (moderate versus good: OR, 1.66; 95% CI, 1.02-2.72) after adjusting for patient characteristics, other environmental factors, and neighborhood-level SES. CONCLUSIONS When controlling for individual- and neighborhood-level confounders, we find that the odds of having a TP53-mutated NSCLC are increased in areas with higher PM2.5 exposure. IMPACT The link between pollution and aggressive biology may contribute to the increased burden of adverse NSCLC outcomes in individuals living in lower SES neighborhoods.
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Affiliation(s)
- Loretta Erhunmwunsee
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California.
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Sam E Wing
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Jenny Shen
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Hengrui Hu
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Ernesto Sosa
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Lisa N Lopez
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Catherine Raquel
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Melissa Sur
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Pilar Ibarra-Noriega
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Madeline Currey
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Janet Lee
- Vital Research, Los Angeles, California
| | - Jae Y Kim
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Dan J Raz
- Department of Surgery, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Arya Amini
- Department of Radiation Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Sagus Sampath
- Department of Radiation Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Marianna Koczywas
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Erminia Massarelli
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Howard L West
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Karen L Reckamp
- Department of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Ravi Salgia
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Victoria L Seewaldt
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Susan L Neuhausen
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Stacy W Gray
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California
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90
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Non-Small Cell Lung Cancer Harboring Concurrent EGFR Genomic Alterations: A Systematic Review and Critical Appraisal of the Double Dilemma. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2020016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The molecular pathways which promote lung cancer cell features have been broadly explored, leading to significant improvement in prognostic and diagnostic strategies. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have dramatically altered the treatment approach for patients with metastatic non-small cell lung cancer (NSCLC). Latest investigations by using next-generation sequencing (NGS) have shown that other oncogenic driver mutations, believed mutually exclusive for decades, could coexist in EGFR-mutated NSCLC patients. However, the exact clinical and pathological role of concomitant genomic aberrations needs to be investigated. In this systematic review, we aimed to summarize the recent data on the oncogenic role of concurrent genomic alterations, by specifically evaluating the characteristics, the pathological significance, and their potential impact on the treatment approach.
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91
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Kanaki Z, Voutsina A, Markou A, Pateras IS, Potaris K, Avgeris M, Makrythanasis P, Athanasiadis EI, Vamvakaris I, Patsea E, Vachlas K, Lianidou E, Georgoulias V, Kotsakis A, Klinakis A. Generation of Non-Small Cell Lung Cancer Patient-Derived Xenografts to Study Intratumor Heterogeneity. Cancers (Basel) 2021; 13:cancers13102446. [PMID: 34070013 PMCID: PMC8157865 DOI: 10.3390/cancers13102446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary It is widely thought that tumors are composed of different subpopulations of cancer cells carrying genetic alterations with some of them being common among all cells while others are unique for each subpopulation. This variable genetic profile of tumor cells is a component of what is collectively described as intratumor heterogeneity (ITH). Surviving the immune system and therapies, and establishing metastases are forces of natural selection that act upon ITH and drive tumor evolution and, eventually, the clinical presentation of patients. The aim of this prospective study was to investigate ITH in early-stage operable non-small cell lung cancer. We directly grafted human tumors in immunosuppressed mice and compared the genetic profile of the tumors grown in mice with that of the original human tumors. We identified clinical factors that affected the ability of human tumors to grow as mouse xenografts. Abstract Recent advances in sequencing technologies have allowed the in-depth molecular study of tumors, even at the single cell level. Sequencing efforts have uncovered a previously unappreciated heterogeneity among tumor cells, which has been postulated to be the driving force of tumor evolution and to facilitate recurrence, metastasis, and drug resistance. In the current study, focused on early-stage operable non-small cell lung cancer, we used tumor growth in patient-derived xenograft (PDX) models in mice as a fast-forward tumor evolution process to investigate the molecular characteristics of tumor cells that grow in mice, as well as the parameters that affect the grafting efficiency. We found that squamous cell carcinomas grafted significantly more efficiently compared with adenocarcinomas. Advanced stage, patient age and primary tumor size were positively correlated with grafting. Additionally, we isolated and characterized circulating tumor cells (CTC) from patients’ peripheral blood and found that the presence of CTCs expressing epithelial-to-mesenchymal (EMT) markers correlated with the grafting potential. Interestingly, exome sequencing of the PDX tumor identified genetic alterations in DNA repair and genome integrity genes that were under-represented in the human primary counterpart. In conclusion, through the generation of a PDX biobank of NSCLC, we identified the clinical and molecular properties of tumors that affected growth in mice.
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Affiliation(s)
- Zoi Kanaki
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | - Alexandra Voutsina
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | - Athina Markou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.M.); (E.L.)
| | - Ioannis S. Pateras
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Konstantinos Potaris
- Department of Thoracic Surgery, Sotiria Hospital for Chest Diseases, 11527 Athens, Greece; (K.P.); (K.V.)
| | - Margaritis Avgeris
- Laboratory of Clinical Biochemistry–Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, “P. & A. Kyriakou” Children’s Hospital, 11527 Athens, Greece;
| | - Periklis Makrythanasis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
| | | | - Ioannis Vamvakaris
- Pathology Department, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece;
| | - Eleni Patsea
- Department of Pathology, Metropolitan Hospital, 18547 Cholargos, Greece;
| | - Konstantinos Vachlas
- Department of Thoracic Surgery, Sotiria Hospital for Chest Diseases, 11527 Athens, Greece; (K.P.); (K.V.)
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.M.); (E.L.)
| | | | - Athanasios Kotsakis
- Department of Medical Oncology, General University Hospital of Larissa, 41110 Larissa, Greece;
| | - Apostolos Klinakis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (Z.K.); (A.V.); (P.M.)
- Correspondence:
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92
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Ren K, Sun J, Liu L, Yang Y, Li H, Wang Z, Deng J, Hou M, Qiu J, Zhao W. TP53-Activated lncRNA GHRLOS Regulates Cell Proliferation, Invasion, and Apoptosis of Non-Small Cell Lung Cancer by Modulating the miR-346/APC Axis. Front Oncol 2021; 11:676202. [PMID: 33968785 PMCID: PMC8097184 DOI: 10.3389/fonc.2021.676202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the main type of lung cancer with high mortality worldwide. To improve NSCLC therapy, the exploration of molecular mechanisms involved in NSCLC progression and identification of their potential therapy targeting is important. Long noncoding RNAs (lncRNAs) have shown important roles in regulating various tumors progression, including NSCLC. We found lncRNA GHRLOS was decreased in NSCLC cell lines and tissues which correlated with poor prognosis of NSCLC patients. However, the role and underlying mechanisms of lncRNA GHRLOS in NSCLC progression remains elusive. The expression of lncRNA GHRLOS was examined in NSCLC cell lines and biopsy specimens of patients with NSCLC by quantitative real time polymerase chain reaction (qRT-PCR). The effects of GHRLOS on proliferation, invasion and apoptosis of NSCLC cells were determined by both in vitro and in vivo experiments. The interaction between GHRLOS and TP53 was determined by dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) combined with qRT-PCR analysis. RNA immunoprecipitation (RIP) was conducted to validate the binding between GHRLOS and microRNA-346 (miR-346). Dual-luciferase reporter assays were also carried out to reveal the interaction between miR-346 and the 3’ untranslated region (3’UTR) of adenomatous polyposis coli (APC) mRNA.Our data demonstrated that overexpression of lncRNA GHRLOS suppressed cancer cell proliferation and invasion as well as promoted cell apoptosis by regulating the expression of CDK2, PCNA, E-cadherin, N-cadherin, Bax, and Bcl-2 in NSCLC cells. Moreover, lncRNA GHRLOS was upregulated by the binding of TP53 to the GHRLOS promoter. The binding target of lncRNA GHRLOS was identified to be miR-346. Impressively, overexpression of miR-346 promoted cell proliferation and invasion, as well as inhibited cell apoptosis, however, these effects can be blocked by overexpression of lncRNA GHRLOS both in vitro and in vivo. In summary, this study reveals lncRNA GHRLOS, upregulated by TP53, acts as a molecule sponge of miR-346 to cooperatively modulates expression of APC, a miR-346 target, and potentially inhibits NSCLC progression via TP53/lncRNA GHRLOS/miR-346/APC axis, which represents a novel pathway that could be useful in targeted therapy against NSCLC.
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Affiliation(s)
- Ke Ren
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China.,Development and Regeneration Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Jinghui Sun
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China
| | - Lingling Liu
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China.,Development and Regeneration Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Yuping Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Honghui Li
- Department of Refractive Surgery, Chengdu Aier Eye Hospital, Chengdu, China
| | - Zhichao Wang
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China
| | - Jingzhu Deng
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China
| | - Min Hou
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China
| | - Jia Qiu
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China
| | - Wei Zhao
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
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93
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Kara A, Özgür A, Nalbantoğlu S, Karadağ A. DNA repair pathways and their roles in drug resistance for lung adenocarcinoma. Mol Biol Rep 2021; 48:3813-3825. [PMID: 33856604 DOI: 10.1007/s11033-021-06314-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/24/2021] [Indexed: 01/24/2023]
Abstract
Lung cancer is the leading cancer type of death rate. The lung adenocarcinoma subtype is responsible for almost half of the total lung cancer deaths. Despite the improvements in cancer treatment in recent years, lung adenocarcinoma patients' overall survival rate remains poor. Immunetherapy and chemotherapy are two of the most widely used options for the treatment of cancer. Although many cancer types initially respond to these treatments, the development of resistance is inevitable. The rapid development of drug resistance mainly characterizes lung adenocarcinoma. Despite being the subject of many studies in recent years, the resistance initiation and progression mechanism is still unclear. In this review, we have examined the role of the primary DNA repair pathways (non-homologous end joining (NHEJ) pathway, homologous-recombinant repair (HR) pathway, base excision repair (BER) pathway, and nucleotide excision repair (NER) pathway and transactivation mechanisms of tumor protein 53 (TP53) in drug resistance development. This review suggests that mentioned pathways have essential roles in developing the resistance against chemotherapy and immunotherapy in lung adenocarcinoma patients.
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Affiliation(s)
- Altan Kara
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey.
| | - Aykut Özgür
- Laboratory and Veterinary Health Program, Department of Veterinary Medicine, Artova Vocational School, Tokat Gaziosmanpaşa University, Tokat, Turkey
| | - Sinem Nalbantoğlu
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
| | - Abdullah Karadağ
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
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94
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Kulkarni A, McDermott JR, Kathad U, Modali R, Richard JP, Sharma P, Bhatia K. The acylfulvene alkylating agent, LP-184, retains nanomolar potency in non-small cell lung cancer carrying otherwise therapy-refractory mutations. Oncotarget 2021; 12:791-806. [PMID: 33889302 PMCID: PMC8057270 DOI: 10.18632/oncotarget.27943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/29/2021] [Indexed: 11/25/2022] Open
Abstract
More than 40% of non-small cell lung cancer (NSCLC) patients lack actionable targets and require non-targeted chemotherapeutics. Many become refractory to drugs due to underlying resistance-associated mutations. KEAP1 mutant NSCLCs further activate NRF2 and upregulate its client PTGR1. LP-184, a novel alkylating agent belonging to the acylfulvene class is a prodrug dependent upon PTGR1. We hypothesized that NSCLC with KEAP1 mutations would continue to remain sensitive to LP-184. LP-184 demonstrated highly potent anticancer activity both in primary NSCLC cell lines and in those originating from brain metastases of primary lung cancers. LP-184 activity correlated with PTGR1 transcript levels but was independent of mutations in key oncogenes (KRAS and KEAP1) and tumor suppressors (TP53 and STK11). LP-184 was orders of magnitude more potent in vitro than cisplatin and pemetrexed. Correlative analyses of sensitivity with cell line gene expression patterns indicated that alterations in NRF2, MET, EGFR and BRAF consistently modulated LP-184 sensitivity. These correlations were then extended to TCGA analysis of 517 lung adenocarcinoma patients, out of which 35% showed elevated PTGR1, and 40% of those further displayed statistically significant co-occurrence of KEAP1 mutations. The gene correlates of LP-184 sensitivity allow additional personalization of therapeutic options for future treatment of NSCLC.
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Affiliation(s)
| | | | | | - Rama Modali
- REPROCELL USA Inc., Beltsville, MD 20705, USA
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95
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Zhou YJ, Zheng W, Zeng QH, Ye Y, Wang C, Fang C, Liu CJ, Niu L, Wu LM. Targeted exome sequencing identifies mutational landscape in a cohort of 1500 Chinese patients with non-small cell lung carcinoma (NSCLC). Hum Genomics 2021; 15:21. [PMID: 33845897 PMCID: PMC8042687 DOI: 10.1186/s40246-021-00320-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/10/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Non-small cell lung carcinoma (NSCLC) is one of the most common human cancers, comprising approximately 80-85% of all lung carcinomas. An estimated incidence of NSCLC is approximately 2 million new cases per year worldwide. RESULTS In recent decade, the treatment of NSCLC has made breakthrough progress owing to a large number of targeted therapies which were approved for clinical use. Epidemiology, genetic susceptibility, and molecular profiles in patients are likely to play an important factor in response rates and survival benefits to these targeted treatments and thus warrant further investigation on ethnic differences in NSCLC. In this study, a total number of 1500 Chinese patient samples,1000 formalin fixed paraffin-embedded (FFPE) and 500 blood samples, from patients with NSCLC were analyzed by targeted sequencing to explore mutational landscape in ethnic groups associated with China. CONCLUSIONS Overall, the data presented here provide a comprehensive analysis of NSCLC mutational landscape in Chinese patients and findings are discussed in the context of similar studies on different ethnic groups.
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Affiliation(s)
- Ya-Jun Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Wei Zheng
- Department of Oncology, PLA General Hospital, Beijing, 100037, China
| | - Qing-Hua Zeng
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yang Ye
- Department of Cardiothoracic Surgery, Jingdezhen First People's Hospital, Jingdezhen, 33300, Jiangxi, China
| | - Ce Wang
- CheerLand Clinical Laboratory Co., Ltd., Building 15, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Cheng Fang
- Department of Oncology, The 334 Affiliated Hospital of Nanchang University, Nanchang, 330024, Jiangxi, China
| | - Chao-Jun Liu
- CheerLand Clinical Laboratory Co., Ltd., Building 15, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Li Niu
- CheerLand Clinical Laboratory Co., Ltd., Building 15, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, 102206, China.
| | - Li-Ming Wu
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, No.218, Jixi Road, Hefei, 230022, Anhui, China.
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96
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de Almeida LC, Calil FA, Machado-Neto JA, Costa-Lotufo LV. DNA damaging agents and DNA repair: From carcinogenesis to cancer therapy. Cancer Genet 2021; 252-253:6-24. [DOI: 10.1016/j.cancergen.2020.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 02/09/2023]
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97
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Khanlari M, Wang SA, Fowler NH, Tang G, Saluja K, Muzzafar T, Medeiros LJ, Thakral B. Concurrent TP53 Mutation and Deletion in Refractory Low-grade Follicular Lymphoma. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 21:e626-e629. [PMID: 33867306 DOI: 10.1016/j.clml.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/08/2021] [Accepted: 03/14/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Mahsa Khanlari
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX
| | - Sa A Wang
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX
| | - Nathan H Fowler
- Department of Lymphoma and Myeloma Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX
| | - Guilin Tang
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX
| | - Karan Saluja
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center, Houston, TX
| | - Tariq Muzzafar
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX
| | | | - Beenu Thakral
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX.
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98
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Abolfathi H, Sheikhpour M, Shahraeini SS, Khatami S, Nojoumi SA. Studies in lung cancer cytokine proteomics: a review. Expert Rev Proteomics 2021; 18:49-64. [PMID: 33612047 DOI: 10.1080/14789450.2021.1892491] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Proteins are molecules that have role in the progression of the diseases. Proteomics is a tool that can play an effective role in identifying diagnostic and therapeutic biomarkers for lung cancer. Cytokines are proteins that play a decisive role in activating body's immune system in lung cancer. They can increase the growth of the tumor (oncogenic cytokines) or limit tumor growth (anti-tumor cytokines) by regulating related signaling pathways such as proliferation, growth, metastasis, and apoptosis. AREAS COVERED In the present study, a total of 223 papers including 196 research papers and 27 review papers, extracted from PubMed and Scopus and published from 1997 to present, are reviewed. The most important involved-cytokines in lung cancer including TNF-α, IFN- γ, TGF-β, VEGF and interleukins such as IL-6, IL-17, IL-8, IL-10, IL-22, IL-1β and IL-18 are introduced. Also, the pathological and biological role of such cytokines in cancer signaling pathways is explained. EXPERT OPINION In lung cancer, the cytokine expression changes under the physiological conditions of the immune system, and inflammatory cytokines are associated with the progression of lung cancer. Therefore, the cytokine expression profile can be used in the diagnosis, prognosis, prediction of therapeutic responses, and survival of patients with lung cancer.
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Affiliation(s)
- Hanie Abolfathi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Sadegh Shahraeini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Khatami
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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99
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Hartmann O, Reissland M, Maier CR, Fischer T, Prieto-Garcia C, Baluapuri A, Schwarz J, Schmitz W, Garrido-Rodriguez M, Pahor N, Davies CC, Bassermann F, Orian A, Wolf E, Schulze A, Calzado MA, Rosenfeldt MT, Diefenbacher ME. Implementation of CRISPR/Cas9 Genome Editing to Generate Murine Lung Cancer Models That Depict the Mutational Landscape of Human Disease. Front Cell Dev Biol 2021; 9:641618. [PMID: 33738287 PMCID: PMC7961101 DOI: 10.3389/fcell.2021.641618] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the most common cancer worldwide and the leading cause of cancer-related deaths in both men and women. Despite the development of novel therapeutic interventions, the 5-year survival rate for non-small cell lung cancer (NSCLC) patients remains low, demonstrating the necessity for novel treatments. One strategy to improve translational research is the development of surrogate models reflecting somatic mutations identified in lung cancer patients as these impact treatment responses. With the advent of CRISPR-mediated genome editing, gene deletion as well as site-directed integration of point mutations enabled us to model human malignancies in more detail than ever before. Here, we report that by using CRISPR/Cas9-mediated targeting of Trp53 and KRas, we recapitulated the classic murine NSCLC model Trp53 fl/fl :lsl-KRas G12D/wt . Developing tumors were indistinguishable from Trp53 fl/fl :lsl-KRas G12D/ wt -derived tumors with regard to morphology, marker expression, and transcriptional profiles. We demonstrate the applicability of CRISPR for tumor modeling in vivo and ameliorating the need to use conventional genetically engineered mouse models. Furthermore, tumor onset was not only achieved in constitutive Cas9 expression but also in wild-type animals via infection of lung epithelial cells with two discrete AAVs encoding different parts of the CRISPR machinery. While conventional mouse models require extensive husbandry to integrate new genetic features allowing for gene targeting, basic molecular methods suffice to inflict the desired genetic alterations in vivo. Utilizing the CRISPR toolbox, in vivo cancer research and modeling is rapidly evolving and enables researchers to swiftly develop new, clinically relevant surrogate models for translational research.
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Affiliation(s)
- Oliver Hartmann
- Deregulated Protein Stability and Cancer Laboratory, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
| | - Michaela Reissland
- Deregulated Protein Stability and Cancer Laboratory, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
| | - Carina R. Maier
- Tumour Metabolism and Microenvironment Group, DKFZ Heidelberg, Heidelberg, Germany
| | - Thomas Fischer
- Deregulated Protein Stability and Cancer Laboratory, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
- Klinik und Poliklinik für Strahlentherapie, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Cristian Prieto-Garcia
- Deregulated Protein Stability and Cancer Laboratory, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
- Faculty of Medicine, TICC, Technion Haifa, Haifa, Israel
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Jessica Schwarz
- Cancer Systems Biology Group, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Werner Schmitz
- Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Martin Garrido-Rodriguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Nikolett Pahor
- Deregulated Protein Stability and Cancer Laboratory, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
| | - Clare C. Davies
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Florian Bassermann
- Department of Medicine III, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Amir Orian
- Faculty of Medicine, TICC, Technion Haifa, Haifa, Israel
| | - Elmar Wolf
- Cancer Systems Biology Group, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Almut Schulze
- Tumour Metabolism and Microenvironment Group, DKFZ Heidelberg, Heidelberg, Germany
| | - Marco A. Calzado
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Mathias T. Rosenfeldt
- Mildred Scheel Early Career Center, Würzburg, Germany
- Institut für Pathologie, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Markus E. Diefenbacher
- Deregulated Protein Stability and Cancer Laboratory, Lehrstuhl für Biochemie und Molekularbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
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Uncovering the Anti-Lung-Cancer Mechanisms of the Herbal Drug FDY2004 by Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6644018. [PMID: 33628308 PMCID: PMC7886515 DOI: 10.1155/2021/6644018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 12/24/2022]
Abstract
With growing evidence on the therapeutic efficacy and safety of herbal drugs, there has been a substantial increase in their application in the lung cancer treatment. Meanwhile, their action mechanisms at the system level have not been comprehensively uncovered. To this end, we employed a network pharmacology methodology to elucidate the systematic action mechanisms of FDY2004, an anticancer herbal drug composed of Moutan Radicis Cortex, Persicae Semen, and Rhei Radix et Rhizoma, in lung cancer treatment. By evaluating the pharmacokinetic properties of the chemical compounds present in FDY2004 using herbal medicine-associated databases, we identified its 29 active chemical components interacting with 141 lung cancer-associated therapeutic targets in humans. The functional enrichment analysis of the lung cancer-related targets of FDY2004 revealed the enriched Gene Ontology terms, involving the regulation of cell proliferation and growth, cell survival and death, and oxidative stress responses. Moreover, we identified key FDY2004-targeted oncogenic and tumor-suppressive pathways associated with lung cancer, including the phosphatidylinositol 3-kinase-Akt, mitogen-activated protein kinase, tumor necrosis factor, Ras, focal adhesion, and hypoxia-inducible factor-1 signaling pathways. Overall, our study provides novel evidence and basis for research on the comprehensive anticancer mechanisms of herbal medicines in lung cancer treatment.
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