51
|
Yang Z, Yuan H, He H, Qi S, Zhu X, Hu X, Jin M, Zhang XX, Yuan ZG. Unlocking the role of EIF5A: A potential diagnostic marker regulating the cell cycle and showing negative correlation with immune infiltration in lung adenocarcinoma. Int Immunopharmacol 2024; 126:111227. [PMID: 37977067 DOI: 10.1016/j.intimp.2023.111227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Despite EIF5A upregulation related to tumor progression in LUAD (lung adenocarcinoma), the underlying mechanisms remain elusive. In addition, there are few comprehensive analyses of EIF5A in LUAD. METHODS We investigated the EIF5A expression level in LUAD patients using data from the TCGA and GEO databases. We employed qRT-PCR and western blot to verify EIF5A expression in cell lines, while immunohistochemistry was utilized for clinical sample analysis. We analyzed EIF5A expression in tumor-infiltrating immune cells using the TISCH database and assessed its association with immune infiltration in LUAD using the "ESTIMATE" R package. Bioinformatics approaches were developed to discover the EIF5A-related genes and explore EIF5A potential mechanisms in LUAD. Proliferation ability was verified through CCK-8, clone formation, and EdU assays, while flow cytometry assessed apoptosis and cell cycle. Western blot was used to detect the expression of pathway-related proteins. RESULTS EIF5A was significantly upregulated in LUAD. Moreover, we constructed a MAZ-hsa-miR-424-3p-EIF5A transcriptional network. We explored the potential mechanism of EIF5A in LUAD and further investigated the cAMP signaling pathway and the cell cycle. Finally, we proved that EIF5A silencing induced G1/S Cell Cycle arrest, promoted apoptosis, and inhibited proliferation via the cAMP/PKA/CREB signaling pathway. CONCLUSION EIF5A serves as a prognostic biomarker with a negative correlation to immune infiltrates in LUAD. It regulated the cell cycle in LUAD by inhibiting the cAMP/PKA/CREB signaling pathway.
Collapse
Affiliation(s)
- Zipeng Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Hao Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Houjing He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Shuting Qi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Xiaojing Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Xiaoyu Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Mengyuan Jin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Xiu-Xiang Zhang
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China.
| | - Zi-Guo Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, Guangdong Province 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China.
| |
Collapse
|
52
|
Patel SA, Hassan MK, Dixit M. Oncogenic activation of EEF1A2 expression: a journey from a putative to an established oncogene. Cell Mol Biol Lett 2024; 29:6. [PMID: 38172654 PMCID: PMC10765684 DOI: 10.1186/s11658-023-00519-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Protein synthesis via translation is a central process involving several essential proteins called translation factors. Although traditionally described as cellular "housekeepers," multiple studies have now supported that protein initiation and elongation factors regulate cell growth, apoptosis, and tumorigenesis. One such translation factor is eukaryotic elongation factor 1 alpha 2 (EEF1A2), a member of the eukaryotic elongation factor family, which has a canonical role in the delivery of aminoacyl-tRNA to the A-site of the ribosome in a guanosine 5'-triphosphate (GTP)-dependent manner. EEF1A2 differs from its closely related isoform, EEF1A1, in tissue distribution. While EEF1A1 is present ubiquitously, EEF1A2 replaces it in specialized tissues. The reason why certain specialized tissues need to essentially switch EEF1A1 expression altogether with EEF1A2 remains to be answered. Abnormal "switch on" of the EEF1A2 gene in normal tissues is witnessed and is seen as a cause of oncogenic transformation in a wide variety of solid tumors. This review presents the journey of finding increased expression of EEF1A2 in multiple cancers, establishing molecular mechanism, and exploring it as a target for cancer therapy. More precisely, we have compiled studies in seven types of cancers that have reported EEF1A2 overexpression. We have discussed the effect of aberrant EEF1A2 expression on the oncogenic properties of cells, signaling pathways, and interacting partners of EEF1A2. More importantly, in the last part, we have discussed the unique potential of EEF1A2 as a therapeutic target. This review article gives an up-to-date account of EEF1A2 as an oncogene and can draw the attention of the scientific community, attracting more research.
Collapse
Affiliation(s)
- Saket Awadhesbhai Patel
- School of Biological Sciences, National Institute of Science Education and Research, Room No. 204, P.O. Jatni, Khurda, Bhubaneswar, Odisha, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Md Khurshidul Hassan
- School of Biological Sciences, National Institute of Science Education and Research, Room No. 204, P.O. Jatni, Khurda, Bhubaneswar, Odisha, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Manjusha Dixit
- School of Biological Sciences, National Institute of Science Education and Research, Room No. 204, P.O. Jatni, Khurda, Bhubaneswar, Odisha, 752050, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India.
| |
Collapse
|
53
|
Zeng L, Li L, Liao X, Zhang L, Yin C, Chen X, Sun J. Population-based high-dimensional analyses identify multiple intrinsic characters for cancer vaccines against lung squamous cell carcinoma. Med Oncol 2024; 41:42. [PMID: 38170412 DOI: 10.1007/s12032-023-02214-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/12/2023] [Indexed: 01/05/2024]
Abstract
In lung squamous cell carcinoma (LUSC), current cancer vaccines show promising effects, despite a lack of benefit for a large number of patients. We first identified the tumor antigens into shared and private antigens, and determined the population by clustering analysis in public datasets. For vaccine development, The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) were collected. WGCNA method was furthermore applied to construct a consensus gene co-expression network based on TCGA and CPTAC datasets. The main analyses in bulk sequencing included survival, clinical features, tumor microenvironment (TME), and pathways enrichment. In addition, single-cell RNA (scRNA) analysis of cancer epithelium dissected consensus subtype. We identified the ideal population for cancer vaccines, and candidate neoantigens including AOC1, COL5A2, LGI2, and POSTN. According to subtype analysis, Lung squamous 1 (LSQ1) type exhibited a higher tumor mutational load (TMB) and copy number but no immune infiltration, whereas lung squamous 2 (LSQ2) tumors had a higher global methylation level and more fibroblasts but had less stemness. Meanwhile, trajectory analysis further revealed that the evolution of TME influenced prognosis. We emphasized specific pathways or targets with the potential for combination immunotherapy by consensus network and single-cell RNA analyses. Anti-androgen therapy has been validated in vitro experiments of LUSC as proof of concept. In conclusion, LSQ1 was linked to immune exclusion and might be utilized for vaccination, while LSQ2 was linked to immune dysfunction and could be used for programmed cell death protein 1 (PD1) blocking therapy.
Collapse
Affiliation(s)
- Longjin Zeng
- Department of Basic Medicine, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Lingchen Li
- Department of Medical Affairs, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China
| | - Xingyun Liao
- Department of Oncology, Affiliated Tumor Hospital, Chongqing, 400037, People's Republic of China
| | - Lincheng Zhang
- Department of Basic Medicine, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Chenrui Yin
- Department of Basic Medicine, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Xiewan Chen
- Department of Basic Medicine, Army Medical University, Chongqing, 400038, People's Republic of China
| | - Jianguo Sun
- Cancer Institute, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China.
| |
Collapse
|
54
|
He Q, Sun C, Pan Y. Whole‑exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras-mutant cancer with extensive regional mutation clusters in its genome. Sci Rep 2024; 14:100. [PMID: 38167599 PMCID: PMC10762126 DOI: 10.1038/s41598-023-50703-2] [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: 02/08/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024] Open
Abstract
Lewis lung carcinoma (LLC), as a widely used preclinical cancer model, has still not been genetically and genomically characterized. Here, we performed a whole-exome sequencing analysis on the LLC cell line to elucidate its molecular characteristics and etiologies. Our data showed that LLC originated from a male mouse belonging to C57BL/6L (a transitional strain between C57BL/6J and C57BL/6N) and contains substantial somatic SNV and InDel mutations (> 20,000). Extensive regional mutation clusters are present in its genome, which were caused mainly by the mutational processes underlying the SBS1, SBS5, SBS15, SBS17a, and SBS21 signatures during frequent structural rearrangements. Thirty three deleterious mutations are present in 30 cancer genes including Kras, Nras, Trp53, Dcc, and Cacna1d. Cdkn2a and Cdkn2b are biallelically deleted from the genome. Five pathways (RTK/RAS, p53, cell cycle, TGFB, and Hippo) are oncogenically deregulated or affected. The major mutational processes in LLC include chromosomal instability, exposure to metabolic mutagens, spontaneous 5-methylcytosine deamination, defective DNA mismatch repair, and reactive oxygen species. Our data also suggest that LLC is a lung cancer similar to human lung adenocarcinoma. This study lays a molecular basis for the more targeted application of LLC in preclinical research.
Collapse
Affiliation(s)
- Quan He
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Cuirong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| |
Collapse
|
55
|
Zhao H, Su Y, Lyu Z, Tian L, Xu P, Lin L, Han W, Fu P. Non-invasively Discriminating the Pathological Subtypes of Non-small Cell Lung Cancer with Pretreatment 18F-FDG PET/CT Using Deep Learning. Acad Radiol 2024; 31:35-45. [PMID: 37117141 DOI: 10.1016/j.acra.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 04/30/2023]
Abstract
RATIONALE AND OBJECTIVES To develop an end-to-end deep learning (DL) model for non-invasively predicting non-small cell lung cancer (NSCLC) pathological subtypes based on 18F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) images, and to explore the potential value of DL technology. MATERIALS AND METHODS Preoperative 18F-FDG PET/CT images of 189 patients with NSCLC were retrospectively collected. The whole cohort was randomly divided into a training cohort, a validation cohort, and an internal/extended test cohort at the ratio of 6:2:2 after preprocessing the images. In the training and validation cohorts, seven DL models-Shufflenet, VGG16, Googlenet, Inception v3, Resnet50, Densenet201, and Mobilenet v2-were trained and optimized. The generalization ability and clinical utility of the optimal model were evaluated in the internal and extended test cohorts. Moreover, Spearman's correlation analysis was used to evaluate the correlation between DL features and traditional radiological features such as tumor size and maximum standardized uptake values (SUVmax). RESULTS Some DL features were significantly correlated with SUVmax and tumor size (P < 0.05). The Mobilenet v2 model achieved the best performance during the model development and validation phases. In the internal test group (area under the receiver operating characteristic curve [AUC]: 0.744, area under the precision-recall curve [AP]: 0.759) and extended test group (AUC: 0.767, AP: 0.768), the Mobilenet v2 model showed good generalization ability and reproducibility. Meanwhile, the decision curve analysis revealed that patients can benefit from the decisions made based on the Mobilenet v2 model. CONCLUSION DL models offer great potential for classifying NSCLC pathological subtypes. Specifically, the Mobilenet v2 model performs well at end-to-end non-invasive pathological subtype stratification of NSCLC.
Collapse
Affiliation(s)
- Hongyue Zhao
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yexin Su
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhehao Lyu
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lin Tian
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Xu
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lin Lin
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wei Han
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Fu
- Department of Nuclear Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| |
Collapse
|
56
|
Chen Q, Wang J, Wang X, Yin Y, Wang X, Song Z, Xing B, Li Y, Zhang J, Qin J, Jiang R. Influence of Tumor Cavitation on Assessing the Clinical Benefit of Anti-PD1 or PD-L1 Inhibitors in Advanced Lung Squamous Cell Carcinoma. Clin Lung Cancer 2024; 25:29-38. [PMID: 38008641 DOI: 10.1016/j.cllc.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/28/2023]
Abstract
PURPOSE A considerable portion of lung squamous cell cancer (LUSC) displays radiographic signs of cavitation. The cavitation of lesions is not accounted for in the prevailing Evaluation Criteria of Response Evaluation Criteria in Solid Tumors (RECIST) v1.1 or iRECIST in lung cancer. We hypothesized that cavitation might alter response assessment in these patients. PATIENTS AND METHODS We performed a retrospective radiologic review of 785 patients with stage IV LUSC treated with PD-1/PD-L1 antibody combined with platinum-based doublet chemotherapy. 131 patients exhibited cavitation lesions pre- or after-treatment. Response was assessed by RECIST v1.1 and a modified Evaluation Criteria in Solid Tumors (mRECIST) guidelines in which the longest diameter of any cavity was subtracted from the overall longest diameter of that lesion to measure target lesions. The response rate and PFS and OS between mRECIST and RECIST v1.1 were compared. Survival curves of different response categories in each criterion were prepared using the method of Kaplan-Meier and log-rank tests. Weighted κ statistics were used to assess interobserver reproducibilities and to compare response rates. The chi-square test confirmed the relationship between PD-L1 expression and post-treatment cavitation. RESULTS Notable cavitation of pulmonary lesions was seen in 16.7% of 785 patients treated with immunotherapy combined with platinum-based chemotherapy. Using the mRECIST for response assessment resulted in a higher response rate than RECIST v1.1 (66% vs. 57%). mRECIST might better identify patients with PFS and OS benefits who have cavitation. The chi-square test revealed a marginally significant difference between PD-L1 expression and tumor cavitation. Interobserver reproducibility of mRECIST for tumor cavitation evaluation was acceptable (the weighted k coefficients for mRECIST criteria was 0.821). CONCLUSION Cavitation lesions at baseline and after checkpoint treatment are common in LUSC patients. mRECIST records a significantly higher response rate than RECIST for these LUSC patients. Response assessment might be improved by incorporating cavitation into volume assessment for target lesions. These results may inform further modifications to RECIST V1.1 to better reflect efficacy with immunotherapy.
Collapse
Affiliation(s)
- Qin Chen
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, PR China; Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, PR China; Tianjin's Clinical Research Center for Cancer, Tianjin, PR China; Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China
| | - Jing Wang
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, PR China; Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, PR China; Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
| | - Xinyue Wang
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, PR China; Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, PR China; Tianjin's Clinical Research Center for Cancer, Tianjin, PR China
| | - Yan Yin
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China
| | - Xuan Wang
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Medical University, Tianjin, PR China
| | - Zhenchun Song
- Medical Radiology Department, Tianjin Chest Hospital, Tianjin, PR China
| | - Bin Xing
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China
| | - Yajing Li
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China
| | - Jingjing Zhang
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China
| | - Jianwen Qin
- Department of Respiratory and Critical Medicine, Tianjin Chest Hospital, Tianjin, PR China.
| | - Richeng Jiang
- Department of Thoracic Oncology, Tianjin Lung Cancer Center, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, PR China; Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, PR China; Tianjin's Clinical Research Center for Cancer, Tianjin, PR China; Cancer Precise Diagnosis Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, PR China; Center for Precision Cancer Medicine & Translational Research, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China.
| |
Collapse
|
57
|
Luo Q, Li X, Meng Z, Rong H, Li Y, Zhao G, Zhu H, Cen L, Liao Q. Identification of hypoxia-related gene signatures based on multi-omics analysis in lung adenocarcinoma. J Cell Mol Med 2024; 28:e18032. [PMID: 38013642 PMCID: PMC10826438 DOI: 10.1111/jcmm.18032] [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: 05/11/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common type of lung cancer and one of the malignancies with the highest incidence rate and mortality worldwide. Hypoxia is a typical feature of tumour microenvironment (TME), which affects the progression of LUAD from multiple molecular levels. However, the underlying molecular mechanisms behind LUAD hypoxia are not fully understood. In this study, we estimated the level of hypoxia by calculating a score based on 15 hypoxia genes. The hypoxia scores were relatively high in LUAD patients with poor prognosis and were bound up with tumour node metastasis (TNM) stage, tumour size, lymph node, age and gender. By comparison of high hypoxia score group and low hypoxia score group, 1820 differentially expressed genes were identified, among which up-regulated genes were mainly about cell division and proliferation while down-regulated genes were primarily involved in cilium-related biological processes. Besides, LUAD patients with high hypoxia scores had higher frequencies of gene mutations, among which TP53, TTN and MUC16 had the highest mutation rates. As for DNA methylation, 1015 differentially methylated probes-related genes were found and may play potential roles in tumour-related neurobiological processes and cell signal transduction. Finally, a prognostic model with 25 multi-omics features was constructed and showed good predictive performance. The area under curve (AUC) values of 1-, 3- and 5-year survival reached 0.863, 0.826 and 0.846, respectively. Above all, our findings are helpful in understanding the impact and molecular mechanisms of hypoxia in LUAD.
Collapse
Affiliation(s)
- Qineng Luo
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Xing Li
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Zixing Meng
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Hao Rong
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Yanguo Li
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Guofang Zhao
- Department of Thoracic SurgeryHwa Mei HospitalUniversity of Chinese Academy of SciencesNingboZhejiangP. R. China
| | - Huangkai Zhu
- Department of Thoracic SurgeryHwa Mei HospitalUniversity of Chinese Academy of SciencesNingboZhejiangP. R. China
| | - Lvjun Cen
- The First Affiliated HospitalNingbo UniversityNingboZhejiangP. R. China
| | - Qi Liao
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
- The First Affiliated HospitalNingbo UniversityNingboZhejiangP. R. China
| |
Collapse
|
58
|
Oi I, Ito T, Saito Z, Imakita T, Kanai O, Fujita K, Tachibana H, Mio T. Kristen rat sarcoma virus (KRAS) G12F-positive non-small cell lung cancer mimicking KRAS G12C positivity: A case report. Thorac Cancer 2024; 15:271-273. [PMID: 38010032 PMCID: PMC10803219 DOI: 10.1111/1759-7714.15171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023] Open
Abstract
Searching for driver gene alteration is a prerequisite for chemotherapy of non-small cell lung cancer. Due to its high sensitivity and concordance rate, the Amoy Dx Pan Lung Cancer PCR panel has been approved and is widely used in Japan. In this report, we describe a case in which a positive result for Kristen rat sarcoma virus (KRAS) exon2 p.G12F, a rare KRAS mutation, may have led to a false-positive result for KRAS exon2 p.G12C on AMOY. Genetic analysis in this case was performed by LC-SCRUM-Asia.
Collapse
Affiliation(s)
- Issei Oi
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Takanori Ito
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Zentaro Saito
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Takuma Imakita
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Osamu Kanai
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Kohei Fujita
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Hiromasa Tachibana
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| | - Tadashi Mio
- Division of Respiratory Medicine, Center of Respiratory DiseasesNational Hospital Organization Kyoto Medical CenterKyotoJapan
| |
Collapse
|
59
|
Ouyang H, Wu S, Li W, Grey MJ, Wu W, Hansen SH. p120 RasGAP and ZO-2 are essential for Hippo signaling and tumor-suppressor function mediated by p190A RhoGAP. Cell Rep 2023; 42:113486. [PMID: 37995182 PMCID: PMC10809936 DOI: 10.1016/j.celrep.2023.113486] [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: 10/11/2022] [Revised: 10/19/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
ARHGAP35, which encodes p190A RhoGAP (p190A), is a major cancer gene. p190A is a tumor suppressor that activates the Hippo pathway. p190A was originally cloned via direct binding to p120 RasGAP (RasGAP). Here, we determine that interaction of p190A with the tight-junction-associated protein ZO-2 is dependent on RasGAP. We establish that both RasGAP and ZO-2 are necessary for p190A to activate large tumor-suppressor (LATS) kinases, elicit mesenchymal-to-epithelial transition, promote contact inhibition of cell proliferation, and suppress tumorigenesis. Moreover, RasGAP and ZO-2 are required for transcriptional modulation by p190A. Finally, we demonstrate that low ARHGAP35 expression is associated with shorter survival in patients with high, but not low, transcript levels of TJP2 encoding ZO-2. Hence, we define a tumor-suppressor interactome of p190A that includes ZO-2, an established constituent of the Hippo pathway, and RasGAP, which, despite strong association with Ras signaling, is essential for p190A to activate LATS kinases.
Collapse
Affiliation(s)
- Hanyue Ouyang
- GI Cell Biology Laboratory, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Shuang Wu
- Department of Radiation Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wangji Li
- GI Cell Biology Laboratory, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael J Grey
- GI Cell Biology Laboratory, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Wenchao Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Steen H Hansen
- GI Cell Biology Laboratory, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
60
|
Mukhopadhyay S, Huang HY, Lin Z, Ranieri M, Li S, Sahu S, Liu Y, Ban Y, Guidry K, Hu H, Lopez A, Sherman F, Tan YJ, Lee YT, Armstrong AP, Dolgalev I, Sahu P, Zhang T, Lu W, Gray NS, Christensen JG, Tang TT, Velcheti V, Khodadadi-Jamayran A, Wong KK, Neel BG. Genome-Wide CRISPR Screens Identify Multiple Synthetic Lethal Targets That Enhance KRASG12C Inhibitor Efficacy. Cancer Res 2023; 83:4095-4111. [PMID: 37729426 PMCID: PMC10841254 DOI: 10.1158/0008-5472.can-23-2729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/22/2023]
Abstract
Non-small lung cancers (NSCLC) frequently (∼30%) harbor KRAS driver mutations, half of which are KRASG12C. KRAS-mutant NSCLC with comutated STK11 and/or KEAP1 is particularly refractory to conventional, targeted, and immune therapy. Development of KRASG12C inhibitors (G12Ci) provided a major therapeutic advance, but resistance still limits their efficacy. To identify genes whose deletion augments efficacy of the G12Cis adagrasib (MRTX-849) or adagrasib plus TNO155 (SHP2i), we performed genome-wide CRISPR/Cas9 screens on KRAS/STK11-mutant NSCLC lines. Recurrent, potentially targetable, synthetic lethal (SL) genes were identified, including serine-threonine kinases, tRNA-modifying and proteoglycan synthesis enzymes, and YAP/TAZ/TEAD pathway components. Several SL genes were confirmed by siRNA/shRNA experiments, and the YAP/TAZ/TEAD pathway was extensively validated in vitro and in mice. Mechanistic studies showed that G12Ci treatment induced gene expression of RHO paralogs and activators, increased RHOA activation, and evoked ROCK-dependent nuclear translocation of YAP. Mice and patients with acquired G12Ci- or G12Ci/SHP2i-resistant tumors showed strong overlap with SL pathways, arguing for the relevance of the screen results. These findings provide a landscape of potential targets for future combination strategies, some of which can be tested rapidly in the clinic. SIGNIFICANCE Identification of synthetic lethal genes with KRASG12C using genome-wide CRISPR/Cas9 screening and credentialing of the ability of TEAD inhibition to enhance KRASG12C efficacy provides a roadmap for combination strategies. See related commentary by Johnson and Haigis, p. 4005.
Collapse
Affiliation(s)
- Suman Mukhopadhyay
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Hsin-Yi Huang
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Ziyan Lin
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, United States
| | - Michela Ranieri
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Shuai Li
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Soumyadip Sahu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yingzhuo Liu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yi Ban
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Kayla Guidry
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Alfonso Lopez
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Fiona Sherman
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yi Jer Tan
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yeuan Ting Lee
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Amanda P. Armstrong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Priyanka Sahu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | - Wenchao Lu
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | | | - Tracy T. Tang
- Vivace Therapeutics, Inc., San Mateo, California, United States
| | - Vamsidhar Velcheti
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, United States
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| |
Collapse
|
61
|
Vokes NI, Galan Cobo A, Fernandez-Chas M, Molkentine D, Treviño S, Druker V, Qian Y, Patel S, Schmidt S, Hong L, Lewis J, Rinsurongkawong W, Rinsurongkawong V, Lee JJ, Negrao MV, Gibbons DL, Vaporciyan A, Le X, Wu J, Zhang J, Rigney U, Iyer S, Dean E, Heymach JV. ATM Mutations Associate with Distinct Co-Mutational Patterns and Therapeutic Vulnerabilities in NSCLC. Clin Cancer Res 2023; 29:4958-4972. [PMID: 37733794 PMCID: PMC10690143 DOI: 10.1158/1078-0432.ccr-23-1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/16/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
PURPOSE Ataxia-telangiectasia mutated (ATM) is the most frequently mutated DNA damage repair gene in non-small cell lung cancer (NSCLC). However, the molecular correlates of ATM mutations and their clinical implications have not been fully elucidated. EXPERIMENTAL DESIGN Clinicopathologic and genomic data from 26,587 patients with NSCLC from MD Anderson, public databases, and a de-identified nationwide (US-based) NSCLC clinicogenomic database (CGDB) were used to assess the co-mutation landscape, protein expression, and mutational processes in ATM-mutant tumors. We used the CGDB to evaluate ATM-associated outcomes in patients treated with immune checkpoint inhibitors (ICI) with or without chemotherapy, and assessed the effect of ATM loss on STING signaling and chemotherapy sensitivity in preclinical models. RESULTS Nonsynonymous mutations in ATM were observed in 11.2% of samples (2,980/26,587) and were significantly associated with mutations in KRAS, but mutually exclusive with EGFR (q < 0.1). KRAS mutational status constrained the ATM co-mutation landscape, with strong mutual exclusivity with TP53 and KEAP1 within KRAS-mutated samples. Those ATM mutations that co-occurred with TP53 were more likely to be missense mutations and associate with high mutational burden, suggestive of non-functional passenger mutations. In the CGDB cohort, dysfunctional ATM mutations associated with improved OS only in patients treated with ICI-chemotherapy, and not ICI alone. In vitro analyses demonstrated enhanced upregulation of STING signaling in ATM knockout cells with the addition of chemotherapy. CONCLUSIONS ATM mutations define a distinct subset of NSCLC associated with KRAS mutations, increased TMB, decreased TP53 and EGFR co-occurrence, and potential increased sensitivity to ICIs in the context of DNA-damaging chemotherapy.
Collapse
Affiliation(s)
- Natalie I. Vokes
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ana Galan Cobo
- Department of Molecular Diagnostics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - David Molkentine
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Santiago Treviño
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vitaly Druker
- Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Yu Qian
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sonia Patel
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie Schmidt
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeff Lewis
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Waree Rinsurongkawong
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcelo V. Negrao
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L. Gibbons
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiuning Le
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Una Rigney
- Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sonia Iyer
- Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - John V. Heymach
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| |
Collapse
|
62
|
Kwantwi LB. Genetic alterations shape innate immune cells to foster immunosuppression and cancer immunotherapy resistance. Clin Exp Med 2023; 23:4289-4296. [PMID: 37910258 DOI: 10.1007/s10238-023-01240-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
Cancer immunotherapy, particularly immune checkpoint inhibitors, has opened a new avenue for cancer treatment following the durable clinical benefits. Despite the clinical successes across several cancer types, primary or acquired resistance might eventually lead to cancer progression in patients with clinical responses. Hence, to broaden the clinical applicability of these treatments, a detailed understanding of the mechanisms limiting the efficacy of cancer immunotherapy is needed. Evidence provided thus far has implicated immunosuppressive innate immune cells infiltrating the tumor microenvironment as key players in immunotherapy resistance. According to the available data, genetic alterations can shape the innate immune response to promote immunotherapy resistance and tumor progression. Herein, this review has discussed the current understanding of the underlying mechanisms where genetic alterations modulate the innate immune milieu to drive immunosuppression and immunotherapy resistance.
Collapse
Affiliation(s)
- Louis Boafo Kwantwi
- Department of Pathology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, USA.
| |
Collapse
|
63
|
Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS OPEN 2023; 16:9-16. [PMID: 38204702 PMCID: PMC10775106 DOI: 10.1016/j.xjon.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Cameron N. Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G. Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tetsuhiko Asao
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
64
|
Tan KT, Slevin MK, Leibowitz ML, Garrity-Janger M, Li H, Meyerson M. Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569101. [PMID: 38077026 PMCID: PMC10705422 DOI: 10.1101/2023.11.30.569101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Alterations in the structure and location of telomeres are key events in cancer genome evolution. However, previous genomic approaches, unable to span long telomeric repeat arrays, could not characterize the nature of these alterations. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeat arrays, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. Analysis of lung adenocarcinoma genome sequences identified somatic neotelomere and telomere-spanning fusion alterations. These results provide a framework for systematic study of telomeric repeat arrays in cancer genomes, that could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
Collapse
Affiliation(s)
- Kar-Tong Tan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Michael K. Slevin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mitchell L. Leibowitz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Max Garrity-Janger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Lead contact
| |
Collapse
|
65
|
Liu SX, Wang C, Lin RB, Ding WY, Roy G, Wang HB, Yang T, Liu Q, Luo YL, Jin SL, Zeng MS, Zhao B, Zhong Q. Super-enhancer driven SOX2 promotes tumor formation by chromatin re-organization in nasopharyngeal carcinoma. EBioMedicine 2023; 98:104870. [PMID: 37967508 PMCID: PMC10679863 DOI: 10.1016/j.ebiom.2023.104870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a malignant head and neck cancer with a high incidence in Southern China and Southeast Asia. Patients with remote metastasis and recurrent NPC have poor prognosis. Thus, a better understanding of NPC pathogenesis may identify novel therapies to address the unmet clinical needs. METHODS H3K27ac ChIP-seq and HiChIP was applied to understand the enhancer landscapes and the chromosome interactions. Whole genome sequencing was conducted to analyze the relationship between genomic variations and epigenetic dysregulation. CRISPRi and JQ1 treatment were used to evaluate the transcriptional regulation of SOX2 SEs. Colony formation assay, survival analysis and in vivo subcutaneous patient-derived xenograft assays were applied to explore the function and clinical relevance of SOX2 in NPC. FINDINGS We globally mapped the enhancer landscapes and generated NPC enhancer connectomes, linking NPC specific enhancers and SEs. We found five overlapped genes, including SOX2, among super-enhancer regulated genes, survival related genes and NPC essential genes. The mRNA expression of SOX2 was repressed when applying CRISPRi targeting different SOX2 SEs or JQ1 treatment. Next, we identified a genetic variation (Chr3:181422197, G > A) in SOX2 SE which is correlated with higher expression of SOX2 and poor survival. In addition, SOX2 was highly expressed in NPC and is correlated with short survival in patients with NPC. Knock-down of SOX2 suppressed tumor growth in vitro and in vivo. INTERPRETATION Our study demonstrated the super-enhancer landscape with chromosome interactions and identified super-enhancer driven SOX2 promotes tumorigenesis, suggesting that SOX2 is a potential therapeutic target for patients with NPC. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
Collapse
Affiliation(s)
- Shang-Xin Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Chong Wang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ruo-Bin Lin
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Wei-Yue Ding
- School of Mathematics, Harbin Institute of Technology, Harbin, PR China
| | - Gaurab Roy
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Hong-Bo Wang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Ting Yang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Qian Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China; Department of Ultrasound Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Yi-Ling Luo
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Shui-Lin Jin
- School of Mathematics, Harbin Institute of Technology, Harbin, PR China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China; Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Guangzhou, PR China.
| | - Bo Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
| |
Collapse
|
66
|
Zschaeck S, Klinger B, van den Hoff J, Cegla P, Apostolova I, Kreissl MC, Cholewiński W, Kukuk E, Strobel H, Amthauer H, Blüthgen N, Zips D, Hofheinz F. Combination of tumor asphericity and an extracellular matrix-related prognostic gene signature in non-small cell lung cancer patients. Sci Rep 2023; 13:20840. [PMID: 38012155 PMCID: PMC10681996 DOI: 10.1038/s41598-023-46405-4] [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: 08/10/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
One important aim of precision oncology is a personalized treatment of patients. This can be achieved by various biomarkers, especially imaging parameters and gene expression signatures are commonly used. So far, combination approaches are sparse. The aim of the study was to independently validate the prognostic value of the novel positron emission tomography (PET) parameter tumor asphericity (ASP) in non small cell lung cancer (NSCLC) patients and to investigate associations between published gene expression profiles and ASP. This was a retrospective evaluation of PET imaging and gene expression data from three public databases and two institutional datasets. The whole cohort comprised 253 NSCLC patients, all treated with curative intent surgery. Clinical parameters, standard PET parameters and ASP were evaluated in all patients. Additional gene expression data were available for 120 patients. Univariate Cox regression and Kaplan-Meier analysis was performed for the primary endpoint progression-free survival (PFS) and additional endpoints. Furthermore, multivariate cox regression testing was performed including clinically significant parameters, ASP, and the extracellular matrix-related prognostic gene signature (EPPI). In the whole cohort, a significant association with PFS was observed for ASP (p < 0.001) and EPPI (p = 0.012). Upon multivariate testing, EPPI remained significantly associated with PFS (p = 0.018) in the subgroup of patients with additional gene expression data, while ASP was significantly associated with PFS in the whole cohort (p = 0.012). In stage II patients, ASP was significantly associated with PFS (p = 0.009), and a previously published cutoff value for ASP (19.5%) was successfully validated (p = 0.008). In patients with additional gene expression data, EPPI showed a significant association with PFS, too (p = 0.033). The exploratory combination of ASP and EPPI showed that the combinatory approach has potential to further improve patient stratification compared to the use of only one parameter. We report the first successful validation of EPPI and ASP in stage II NSCLC patients. The combination of both parameters seems to be a very promising approach for improvement of risk stratification in a group of patients with urgent need for a more personalized treatment approach.
Collapse
Affiliation(s)
- Sebastian Zschaeck
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Bertram Klinger
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Computational Modelling in Medicine, Instiute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
| | - Jörg van den Hoff
- Helmholtz-Zentrum Dresden-Rossendorf, PET Center, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Paulina Cegla
- Department of Nuclear Medicine, Greater Poland Cancer Centre, Poznan, Poland
| | - Ivayla Apostolova
- Department for Diagnostic and Interventional Radiology and Nuclear Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Division of Nuclear Medicine, Department of Radiology and Nuclear Medicine, Otto Von Guericke University, Magdeburg, Germany
| | - Michael C Kreissl
- Division of Nuclear Medicine, Department of Radiology and Nuclear Medicine, Otto Von Guericke University, Magdeburg, Germany
| | - Witold Cholewiński
- Department of Nuclear Medicine, Greater Poland Cancer Centre, Poznan, Poland
| | - Emily Kukuk
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Helen Strobel
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Holger Amthauer
- Division of Nuclear Medicine, Department of Radiology and Nuclear Medicine, Otto Von Guericke University, Magdeburg, Germany
- Department of Nuclear Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Nils Blüthgen
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Computational Modelling in Medicine, Instiute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
| | - Daniel Zips
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
| | - Frank Hofheinz
- Helmholtz-Zentrum Dresden-Rossendorf, PET Center, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany.
| |
Collapse
|
67
|
Chevalier A, Guo T, Gurevich NQ, Xu J, Yajima M, Campbell JD. Characterization of highly active mutational signatures in tumors from a large Chinese population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.03.23297964. [PMID: 37961450 PMCID: PMC10635259 DOI: 10.1101/2023.11.03.23297964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The majority of mutational signatures have been characterized in tumors from Western countries and the degree to which mutational signatures are similar or different in Eastern populations has not been fully explored. We leveraged a large-scale clinical sequencing cohort of tumors from a Chinese population containing 25 tumor types and found that the highly active mutational signatures were similar to those previously characterized1,2. The aristolochic acid signature SBS22 was observed in four soft tissue sarcomas and the POLE-associated signature SBS10 was observed in a gallbladder carcinoma. In lung adenocarcinoma, the polycyclic aromatic hydrocarbon (PAH) signature SBS4 was significantly higher in males compared to females but not associated with smoking status. The UV-associated signature SBS7 was significantly lower in cutaneous melanomas from the Chinese population compared to a similar American cohort. Overall, these results add to our understanding of the mutational processes that contribute to tumors from the Chinese population.
Collapse
Affiliation(s)
- Aaron Chevalier
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Tao Guo
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts
| | - Natasha Q. Gurevich
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Jingwen Xu
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts
| | - Masanao Yajima
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts
| | - Joshua D. Campbell
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| |
Collapse
|
68
|
Zheng D, Grandgenett PM, Zhang Q, Baine M, Shi Y, Du Q, Liang X, Wong J, Iqbal S, Preuss K, Kamal A, Yu H, Du H, Hollingsworth MA, Zhang C. radioGWAS: link radiome to genome to discover driver genes with somatic mutations for heterogeneous tumor image phenotype in pancreatic cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.02.23297995. [PMID: 37961101 PMCID: PMC10635263 DOI: 10.1101/2023.11.02.23297995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Addressing the significant level of variability exhibited by pancreatic cancer necessitates the adoption of a systems biology approach that integrates molecular data, biological properties of the tumors, and clinical features of the patients. In this study, a comprehensive multi-omics methodology was employed to examine a distinctive collection patient dataset containing rapid autopsy tumor and normal tissue samples as well as longitudinal imaging with a focus on pancreatic cancer. By performing a whole exome sequencing analysis on tumor and normal tissues to identify somatic gene variants and a radiomics feature analysis to tumor CT images, the genome-wide association approach established a connection between pancreatic cancer driver genes and relevant radiomics features, enabling a thorough and quantitative assessment of the heterogeneity of pancreatic tumors. The significant association between sets of genes and radiomics features revealed the involvement of genes in shaping tumor morphological heterogeneity. Some results of the association established a connection between the molecular level mechanism and their outcomes at the level of tumor structural heterogeneity. Because tumor structure and tumor structural heterogeneity are related to the patients' overall survival, patients who had pancreatic cancer driver gene mutations with an association to a certain radiomics feature have been observed to experience worse survival rates than cases without these somatic mutations. Furthermore, the outcome of the association analysis has revealed potential gene mutations and radiomics feature candidates that warrant further investigation in future research endeavors.
Collapse
|
69
|
Gensheimer MF, Gee H, Shirato H, Taguchi H, Snyder JM, Chin AL, Vitzthum LK, Maxim PG, Wakelee HA, Neal J, Das M, Chang DT, Kidd E, Hancock SL, Shultz DB, Horst KC, Le QT, Wong S, Brown E, Nguyen N, Liang R, Loo BW, Diehn M. Individualized Stereotactic Ablative Radiotherapy for Lung Tumors: The iSABR Phase 2 Nonrandomized Controlled Trial. JAMA Oncol 2023; 9:1525-1534. [PMID: 37707820 PMCID: PMC10502697 DOI: 10.1001/jamaoncol.2023.3495] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/11/2023] [Indexed: 09/15/2023]
Abstract
Importance Stereotactic ablative radiotherapy (SABR) is used for treating lung tumors but can cause toxic effects, including life-threatening damage to central structures. Retrospective data suggested that small tumors up to 10 cm3 in volume can be well controlled with a biologically effective dose less than 100 Gy. Objective To assess whether individualizing lung SABR dose and fractionation by tumor size, location, and histological characteristics may be associated with local tumor control. Design, Setting, and Participants This nonrandomized controlled trial (the iSABR trial, so named for individualized SABR) was a phase 2 multicenter trial enrolling participants from November 15, 2011, to December 5, 2018, at academic medical centers in the US and Japan. Data were analyzed from December 9, 2020, to May 10, 2023. Patients were enrolled in 3 groups according to cancer type: initial diagnosis of non-small cell lung cancer (NSCLC) with an American Joint Committee on Cancer 7th edition T1-3N0M0 tumor (group 1), a T1-3N0M0 new primary NSCLC with a history of prior NSCLC or multiple NSCLCs (group 2), or lung metastases from NSCLC or another solid tumor (group 3). Intervention Up to 4 tumors were treated with once-daily SABR. The dose ranged from 25 Gy in 1 fraction for peripheral tumors with a volume of 0 to 10 cm3 to 60 Gy in 8 fractions for central tumors with a volume greater than 30 cm3. Main outcome Per-group freedom from local recurrence (same-lobe recurrence) at 1 year, with censoring at time of distant recurrence, death, or loss to follow-up. Results In total, 217 unique patients (median [IQR] age, 72 [64-80] years; 129 [59%] male; 150 [69%] current or former smokers) were enrolled (some multiple times). There were 240 treatment courses: 79 in group 1, 82 in group 2, and 79 in group 3. A total of 285 tumors (211 [74%] peripheral and 74 [26%] central) were treated. The most common dose was 25 Gy in 1 fraction (158 tumors). The median (range) follow-up period was 33 (2-109) months, and the median overall survival was 59 (95% CI, 49-82) months. Freedom from local recurrence at 1 year was 97% (90% CI, 91%-99%) for group 1, 94% (90% CI, 87%-97%) for group 2, and 96% (90% CI, 89%-98%) for group 3. Freedom from local recurrence at 5 years ranged from 83% to 93% in the 3 groups. The proportion of patients with grade 3 to 5 toxic effects was low, at 5% (including a single patient [1%] with grade 5 toxic effects). Conclusions and Relevance The results of this nonrandomized controlled trial suggest that individualized SABR (iSABR) used to treat lung tumors may allow minimization of treatment dose and is associated with excellent local control. Individualized dosing should be considered for use in future trials. Trial Registration ClinicalTrials.gov Identifier: NCT01463423.
Collapse
Affiliation(s)
- Michael F. Gensheimer
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Harriet Gee
- Sydney West Radiation Oncology Network, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Hiroki Shirato
- Department of Radiation Oncology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroshi Taguchi
- Department of Radiation Oncology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - John M. Snyder
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Alexander L. Chin
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Lucas K. Vitzthum
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Peter G. Maxim
- Department of Radiation Oncology, University of California Irvine, Irvine, California
| | - Heather A. Wakelee
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Joel Neal
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Millie Das
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Daniel T. Chang
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Elizabeth Kidd
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Steven L. Hancock
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - David B. Shultz
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Kathleen C. Horst
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Samantha Wong
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Eleanor Brown
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Ngan Nguyen
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Rachel Liang
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Billy W. Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California
| |
Collapse
|
70
|
Mäkinen N, Meyerson M. Genomic insights into the mechanisms of FGFR1 dependency in squamous cell lung cancer. J Clin Invest 2023; 133:e174171. [PMID: 37909331 PMCID: PMC10617760 DOI: 10.1172/jci174171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Although subsets of patients with lung squamous cell carcinoma (LSCC) benefit from immunotherapy, there are few effective molecularly targeted treatments for LSCC. Fibroblast growth factor receptor (FGFR) inhibitors provide a therapeutic option for patients with LSCC harboring FGFR aberrations, but their therapeutic efficacy has been limited to date. In this issue of the JCI, Malchers et al. identified tail-to-tail rearrangements, either within or near FGFR1, that are associated with FGFR1 dependency and sensitivity to FGFR inhibition in LSCC. These results may help improve the selection of patients with LSCC who are most likely to benefit from treatment with FGFR inhibitors.
Collapse
MESH Headings
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Genomics
- Epithelial Cells/metabolism
Collapse
Affiliation(s)
- Netta Mäkinen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Departments of Genetics and Medicine, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
71
|
Tuna M, Mills GB, Amos CI. Common and distinct patterns of acquired uniparental disomy and homozygous deletions between lung squamous cell carcinomas and lung adenocarcinoma. Neoplasia 2023; 45:100932. [PMID: 37801862 PMCID: PMC10562662 DOI: 10.1016/j.neo.2023.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 08/19/2023] [Accepted: 08/31/2023] [Indexed: 10/08/2023]
Abstract
Acquired uniparental disomy (aUPD) is a chromosomal alteration that can lead to homozygosity of existing aberrations. We used data from The Cancer Genome Atlas SNP-based arrays to identify distinct and common aUPD profiles in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Moreover, we tested relevance of aUPD for homozygous deletion (HMD), overall survival (OS), and recurrence-free survival (RFS). Overall, we found significantly higher aUPD (q = 5.34E-09) in LUSC than in LUAD. A significant portion of HMD was associated with aUPD in LUSC (24.9%) and LUAD (19.7%). We identified segmental, whole-chromosome arm and whole-chromosome aUPD, in which whole 7p arm aUPD was restricted to LUSC, while whole-chromosome 3 aUPD was observed only in LUAD, and whole-chromosome 21 aUPD was common to both LUSC and LUAD. The most frequent aUPD and HMD were observed at CDKN2A/B region in both LUAD and LUSC. In LUAD, aUPD and HMD at CDKN2A/B region were associated with shorter OS (q < 0.021 and q < 0.005), and RFS (q < 0.005 and q < 0.005), while heterozygous deletion was not associated with OS and RFS. In contrast, no association was found between aUPD at CDKN2A/B region and survival in LUSC. In LUAD, CTLA expression was significantly lower in samples with aUPD at CDKN2A/B regions than in samples without copy number and allele-based changes. Immune infiltration correlated with aUPD or HMD at CDKN2A/B, gain at HLA class I region, and aUPD at whole-chromosome q-arm or whole chromosome in LUAD, but not in LUSC. Both LUSC and LUAD have common and distinct patterns of aUPD regions with differing frequencies of occurrence and associations with outcome.
Collapse
Affiliation(s)
- Musaffe Tuna
- Department of Medicine, Institute of Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
| | - Gordon B Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health Science University, Portland, OR 97239, USA
| | - Christopher I Amos
- Department of Medicine, Institute of Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| |
Collapse
|
72
|
Lapouge M, Meloche S. A renaissance for YES in cancer. Oncogene 2023; 42:3385-3393. [PMID: 37848624 DOI: 10.1038/s41388-023-02860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
Most of our understanding regarding the involvement of SRC-family tyrosine kinases in cancer has stemmed from studies focused on the prototypical SRC oncogene. However, emerging research has shed light on the important role of YES signaling in oncogenic transformation, tumor growth, metastatic progression, and resistance to various cancer therapies. Clinical evidence indicates that dysregulated expression or activity of YES is a frequent occurrence in human cancers and is associated with unfavorable outcomes. These findings provide a compelling rationale for specifically targeting YES in certain cancer subtypes. Here, we review the crucial role of YES in cancer and discuss the challenges associated with translating preclinical observations into effective YES-targeted therapies.
Collapse
Affiliation(s)
- Marjorie Lapouge
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada.
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
| |
Collapse
|
73
|
Kozłowska E, Swierniak A. Mathematical Model of Intrinsic Drug Resistance in Lung Cancer. Int J Mol Sci 2023; 24:15801. [PMID: 37958784 PMCID: PMC10650033 DOI: 10.3390/ijms242115801] [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: 09/05/2023] [Revised: 09/25/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Drug resistance is a bottleneck in cancer treatment. Commonly, a molecular treatment for cancer leads to the emergence of drug resistance in the long term. Thus, some drugs, despite their initial excellent response, are withdrawn from the market. Lung cancer is one of the most mutated cancers, leading to dozens of targeted therapeutics available against it. Here, we have developed a mechanistic mathematical model describing sensitization to nine groups of targeted therapeutics and the emergence of intrinsic drug resistance. As we focus only on intrinsic drug resistance, we perform the computer simulations of the model only until clinical diagnosis. We have utilized, for model calibration, the whole-exome sequencing data combined with clinical information from over 1000 non-small-cell lung cancer patients. Next, the model has been applied to find an answer to the following questions: When does intrinsic drug resistance emerge? And how long does it take for early-stage lung cancer to grow to an advanced stage? The results show that drug resistance is inevitable at diagnosis but not always detectable and that the time interval between early and advanced-stage tumors depends on the selection advantage of cancer cells.
Collapse
Affiliation(s)
| | - Andrzej Swierniak
- Department of Systems Biology and Engineering, Silesian University of Technology, 44100 Gliwie, Poland;
| |
Collapse
|
74
|
Dai S, Li F, Xu S, Hu J, Gao L. The important role of miR-1-3p in cancers. J Transl Med 2023; 21:769. [PMID: 37907984 PMCID: PMC10617136 DOI: 10.1186/s12967-023-04649-8] [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: 07/12/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023] Open
Abstract
Cancer is a malignant tumor that seriously threatens human life and health. At present, the main treatment methods include surgical resection, chemotherapy, radiotherapy, and immunotherapy. However, the mechanism of tumor occurrence and development is complex, and it produces resistance to some traditional treatment methods, leading to treatment failure and a high mortality rate for patients. Therefore, exploring the molecular mechanisms of tumor occurrence, development, and drug resistance is a very important task. MiRNAs are a type of non-coding small RNA that regulate a series of biological effects by binding to the 3'-UTR of the target mRNA, degrading the mRNA, or inhibiting its translation. MiR-1-3p is an important member of them, which is abnormally expressed in various tumors and closely related to the occurrence and development of tumors. This article introduces miR-1-3p from multiple aspects, including its production and regulation, role in tumor occurrence and development, clinical significance, role in drug resistance, and approaches for targeting miR-1-3p. Intended to provide readers with a comprehensive understanding of the important role of miR-1-3p in tumors.
Collapse
Affiliation(s)
- Shangming Dai
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Fengjiao Li
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Shuoguo Xu
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Jinda Hu
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Lichen Gao
- Department of Pharmacy, School of Pharmacy, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China.
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China.
| |
Collapse
|
75
|
Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
Collapse
Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
| |
Collapse
|
76
|
Cui Y, Wu Y, Zhang M, Zhu Y, Su X, Kong W, Zheng X, Sun G. Identification of prognosis-related lncRNAs and cell validation in lung squamous cell carcinoma based on TCGA data. Front Oncol 2023; 13:1240868. [PMID: 37965447 PMCID: PMC10642190 DOI: 10.3389/fonc.2023.1240868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
Objective To discern long non-coding RNAs (lncRNAs) with prognostic relevance in the context of lung squamous cell carcinoma (LUSC), we intend to predict target genes by leveraging The Cancer Genome Atlas (TCGA) repository. Subsequently, we aim to investigate the proliferative potential of critical lncRNAs within the LUSC milieu. Methods DESeq2 was employed to identify differentially expressed genes within the TCGA database. Following this, we utilized both univariate and multivariate Cox regression analyses to identify lncRNAs with prognostic relevance. Noteworthy lncRNAs were selected for validation in cell lines. The intracellular localization of these lncRNAs was ascertained through nucleocytoplasmic isolation experiments. Additionally, the impact of these lncRNAs on cellular proliferation, invasion, and migration capabilities was investigated using an Antisense oligonucleotides (ASO) knockdown system. Results Multivariate Cox regression identified a total of 12 candidate genes, consisting of seven downregulated lncRNAs (BRE-AS1, CCL15-CCL14, DNMBP-AS1, LINC00482, LOC100129034, MIR22HG, PRR26) and five upregulated lncRNAs (FAM83A-AS1, LINC00628, LINC00923, LINC01341, LOC100130691). The target genes associated with these lncRNAs exhibit significant enrichment within diverse biological pathways, including metabolic processes, cancer pathways, MAPK signaling, PI3K-Akt signaling, protein binding, cellular components, cellular transformation, and other functional categories. Furthermore, nucleocytoplasmic fractionation experiments demonstrated that LINC00923 and LINC01341 are predominantly localized within the cellular nucleus. Subsequent investigations utilizing CCK-8 assays and colony formation assays revealed that the knockdown of LINC00923 and LINC01341 effectively suppressed the proliferation of H226 and H1703 cells. Additionally, transwell assays showed that knockdown of LINC00923 and LINC01341 significantly attenuated the invasive and migratory capacities of H226 and H1703 cells. Conclusion This study has identified 12 candidate lncRNA associated with prognostic implications, among which LINC00923 and LINC01341 exhibit potential as markers for the prediction of LUSC outcomes.
Collapse
Affiliation(s)
- Yishuang Cui
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Yanan Wu
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Mengshi Zhang
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Yingze Zhu
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Xin Su
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Wenyue Kong
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Xuan Zheng
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Guogui Sun
- Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| |
Collapse
|
77
|
Han R, Guan Y, Tang M, Li M, Zhang B, Fei G, Zhou S, Wang R. High Expression of PSRC1 Predicts Poor Prognosis in Lung Adenocarcinoma. J Cancer 2023; 14:3321-3334. [PMID: 37928428 PMCID: PMC10622992 DOI: 10.7150/jca.88635] [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: 07/29/2023] [Accepted: 09/06/2023] [Indexed: 11/07/2023] Open
Abstract
Background: The incidence of lung cancer is increasing annually, but the mechanism of its occurrence and development requires further study. This study aimed to investigate the biological function and prognostic value of proline- and serine-rich coiled-coil 1 (PSRC1) in lung cancer. Methods: We used data from The Cancer Genome Atlas (TCGA) to analyze the association between clinical features and PSRC1 expression in non-small cell carcinoma. The relationship between PSRC1 expression and prognosis in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) was analyzed using Kaplan-Meier curves. The function of PSRC1 was identified using enrichment analysis, and the relationship between PSRC1 expression and immune cell infiltration was studied. In addition, the expression of PSRC1 in 150 patients with non-small cell carcinoma was detected using immunohistochemistry, and its clinical significance was analyzed. Results: It was found that the expression level of PSRC1 was higher in LUAD and LUSC tumor tissues than in normal tissues, and the results were confirmed by immunohistochemistry in 150 patients. TCGA data showed that high PSRC1 expression in LUAD was associated with poorer overall survival (p = 0.003) and progression-free interval (p = 0.012). Multivariable analysis showed that PSRC1 was an independent risk factor for LUAD. Functional enrichment analysis showed that PSRC1 is related to tumor development. Conclusion: High PSRC1 expression is significantly associated with LUAD survival and may be a promising prognostic biomarker.
Collapse
Affiliation(s)
- Rui Han
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Youhong Guan
- Department of infectious disease, Hefei second people's hospital, Hefei 230001, China
| | - Min Tang
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Min Li
- Department of oncology, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Binbin Zhang
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Guanghe Fei
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Sijing Zhou
- Department of Occupational Disease, Hefei third clinical college of Anhui Medical University, Hefei 230022, China
| | - Ran Wang
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| |
Collapse
|
78
|
Yan S, Ma C, Zhou F, Zheng H, Yang L, Xiao Z, Zhu J, Zhao H, Zhao C, Xu X. Cinobufagin exerts an antitumor effect in non-small-cell lung cancer by blocking STAT3 signaling. J Cancer 2023; 14:3309-3320. [PMID: 37928418 PMCID: PMC10622998 DOI: 10.7150/jca.86544] [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: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 11/07/2023] Open
Abstract
Background: Non-small-cell lung cancer (NSCLC) is the most common histological subtype of lung cancer with significant morbidity and mortality rates worldwide. Cinobufagin, the primary component of Chansu and the major active ingredient of cinobufacini, has attracted widespread attention for its excellent anticancer effects, but its activity remains poorly characterized in NSCLC. Methods: The functions of cinobufagin treatment in anti-tumor was evaluated using various in vitro and in vivo assays. The change of STAT3 signaling by cinobufagin was analyzed using molecular docking, immunofluorescence technic and western blotting. Results: In vitro, we confirmed the inhibitory effect of cinobufagin on cell viability, proliferation, migration, epithelial-mesenchymal transition (EMT), as well as an apoptosis-inducing effect. The antitumor effects of cinobufagin were confirmed in vivo by measuring tumor growth in a mouse xenograft model. Cinobufagin was found to significantly inhibit the phosphorylation of signal transducer and activator of transcription 3 (STAT3) at tyrosine 705 (Y705) in a time- and concentration-dependent manner. Moreover, cinobufagin reversed IL-6-induced nuclear translocation of STAT3. Conclusions: Our study has demonstrated that cinobufagin exerts an antitumor effect in non-small-cell lung cancer by blocking STAT3 signaling, and cinobufagin is a promising candidate agent for NSCLC therapy.
Collapse
Affiliation(s)
- Sunshun Yan
- Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, China
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Chunbo Ma
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
- The Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, China
- Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Feng Zhou
- The Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, China
- Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Hailun Zheng
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Lehe Yang
- Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Zhongxiang Xiao
- Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Jiandong Zhu
- Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Haiyang Zhao
- The Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Chengguang Zhao
- Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Xiaoling Xu
- Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| |
Collapse
|
79
|
Formanti Alonso L, Atienza Cuevas L, Romero García R, Mohigefer Barrera J, Del Río Ignacio JJ, Santisteban Espejo A, Bernal Florindo I, Catalina Fernández I, García Rojo M. [Study of genetic variants in 169 non-small cell lung cancer patients]. REVISTA ESPANOLA DE PATOLOGIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ANATOMIA PATOLOGICA Y DE LA SOCIEDAD ESPANOLA DE CITOLOGIA 2023; 56:233-242. [PMID: 37879820 DOI: 10.1016/j.patol.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION Lung cancer is the leading cause of cancer death in our country. Non-small cell lung cancer (NSCLC) represents the paradigm of personalized medicine. The main objective of this study is analysing the distribution of the most frequently described clinically significant variants in NSCLC, in our environment. MATERIAL AND METHODS We studied the immunohistochemical expression of TTF1, p40 and PD-L1 and the genetic variants frequency using Next-Generation Sequencing (NGS) with a panel of 52 genes, in 174 NSCLC paraffin-embedded samples in 169 patients (111 men and 52 women) from the province of Cádiz. RESULTS The immunohistochemical expression of TTF1, p40 and PD-L1 was positive in 87%, 0% and 46% in adenocarcinoma, and 0%, 100% and 41% in squamous cell carcinoma. In NGS, the most common single nucleotide variants (SNVs) were KRAS (36%), EGFR (14%), BRAF (10%), PIK3CA (8%), and MET (3%). The most frequent copy number variants (CNVs) were amplifications in NF1 (30%), EGFR (18%), CCND1 (9%), MYC (9%) and KRAS (7%). In women, SNV in EGFR are more frequent than in men (P<.0001). Adenocarcinoma is the most frequent histological type with SNV in KRAS (P=.007361) or in EGFR (P<.0001). Gene fusions were detected in 16 patients (9.47%), in 9 cases in the MET gene. CONCLUSIONS We detected associations, not described so far, between immunohistochemical expression and specific gene variants, which could have an impact on the treatment of NSCLC patients.
Collapse
Affiliation(s)
- Lydia Formanti Alonso
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España.
| | - Lidia Atienza Cuevas
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Raquel Romero García
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Javier Mohigefer Barrera
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| | - Juan Jesús Del Río Ignacio
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| | - Antonio Santisteban Espejo
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Irene Bernal Florindo
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| | - Inmaculada Catalina Fernández
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España; Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario Puerta del Mar, Cádiz, España
| | - Marcial García Rojo
- Unidad de Gestión Clínica Anatomía Patológica, Hospital Universitario de Jerez de la Frontera, Jerez de la Frontera, Cádiz, España; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, España
| |
Collapse
|
80
|
Guo T, Wang Z, Wang S, Zhang Y, Pang J, Ying Y, Ou Q, Shen D, Li G. Predictive value of DOT1L mutations for clinical outcomes in non-small-cell lung cancer patients receiving immune checkpoint inhibitor therapy. Clin Transl Med 2023; 13:e1430. [PMID: 37784247 PMCID: PMC10545889 DOI: 10.1002/ctm2.1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/25/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Affiliation(s)
- Tianxing Guo
- Department of Thoracic SurgeryShengli Clinical Medical College of Fujian Medical UniversityFujian Provincial HospitalFuzhouChina
| | - Zhaofeng Wang
- Department of Respiratory MedicineAffiliated Jinling Hospital, Medical School of Nanjing UniversityNanjingChina
| | - Song Wang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Yaru Zhang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Jiaohui Pang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Yajun Ying
- Department of PathologyTaizhou Cancer Hospital, TaizhouZhejiangChina
| | - Qiuxiang Ou
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Dong Shen
- Department of OncologyThe Affiliated Jiangyin Hospital of Nantong University, JiangyinJiangsuChina
| | - Gang Li
- Department of Thoracic SurgerySichuan Provincial People's Hospital, University of Electronic Science and Technology of ChinaChengduChina
- Department of Thoracic SurgerySichuan Translational Medicine Research Hospital, Chinese Academy of SciencesChengduChina
| |
Collapse
|
81
|
Soulette CM, Hrabeta-Robinson E, Arevalo C, Felton C, Tang AD, Marin MG, Brooks AN. Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations. Life Sci Alliance 2023; 6:e202000641. [PMID: 37487637 PMCID: PMC10366530 DOI: 10.26508/lsa.202000641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA splicing alterations; however, the full-length altered mRNA isoforms associated with the mutation are largely unknown. To better understand the impact U2AF1 has on full-length isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without a U2AF1 S34F mutation. We identified 49,366 multi-exon transcript isoforms, more than half of which did not match GENCODE or short-read-assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes relative to WT, only 68% of which were assembled by short reads. Expression of isoforms from immune-related genes is largely down-regulated in mutant cells and without observed splicing changes. Finally, we reveal that isoforms likely targeted by nonsense-mediated decay are down-regulated in U2AF1 S34F cells, suggesting that isoform changes may alter the translational output of those affected genes. Altogether, our work provides a resource of full-length isoforms associated with U2AF1 S34F in lung cells.
Collapse
Affiliation(s)
- Cameron M Soulette
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Carlos Arevalo
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Maximillian G Marin
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| |
Collapse
|
82
|
Desai A, Dimou A. Toxicity From Sotorasib After Immune Checkpoint Inhibitors: A Note of Caution and Reflections of Future Advancements in the Field. J Thorac Oncol 2023; 18:1265-1267. [PMID: 37758343 DOI: 10.1016/j.jtho.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Aakash Desai
- Division of Medical Oncology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Anastasios Dimou
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
83
|
Watkins TBK, Colliver EC, Huska MR, Kaufmann TL, Lim EL, Duncan CB, Haase K, Van Loo P, Swanton C, McGranahan N, Schwarz RF. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity. PLoS Comput Biol 2023; 19:e1011379. [PMID: 37871126 PMCID: PMC10621967 DOI: 10.1371/journal.pcbi.1011379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 11/02/2023] [Accepted: 07/22/2023] [Indexed: 10/25/2023] Open
Abstract
Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
Collapse
Affiliation(s)
- Thomas B. K. Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Matthew R. Huska
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Tom L. Kaufmann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Emilia L. Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Cody B. Duncan
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kerstin Haase
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| |
Collapse
|
84
|
Joon HK, Thalor A, Gupta D. Machine learning analysis of lung squamous cell carcinoma gene expression datasets reveals novel prognostic signatures. Comput Biol Med 2023; 165:107430. [PMID: 37703712 DOI: 10.1016/j.compbiomed.2023.107430] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) patients are often diagnosed at an advanced stage and have poor prognoses. Thus, identifying novel biomarkers for the LUSC is of utmost importance. METHODS Multiple datasets from the NCBI-GEO repository were obtained and merged to construct the complete dataset. We also constructed a subset from this complete dataset with only known cancer driver genes. Further, machine learning classifiers were employed to obtain the best features from both datasets. Simultaneously, we perform differential gene expression analysis. Furthermore, survival and enrichment analyses were performed. RESULTS The kNN classifier performed comparatively better on the complete and driver datasets' top 40 and 50 gene features, respectively. Out of these 90 gene features, 35 were found to be differentially regulated. Lasso-penalized Cox regression further reduced the number of genes to eight. The median risk score of these eight genes significantly stratified the patients, and low-risk patients have significantly better overall survival. We validated the robust performance of these eight genes on the TCGA dataset. Pathway enrichment analysis identified that these genes are associated with cell cycle, cell proliferation, and migration. CONCLUSION This study demonstrates that an integrated approach involving machine learning and system biology may effectively identify novel biomarkers for LUSC.
Collapse
Affiliation(s)
- Hemant Kumar Joon
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Anamika Thalor
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
85
|
Karlow JA, Pehrsson EC, Xing X, Watson M, Devarakonda S, Govindan R, Wang T. Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:991-1013. [PMID: 37742993 PMCID: PMC10928376 DOI: 10.1016/j.gpb.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 02/11/2023] [Accepted: 03/14/2023] [Indexed: 09/26/2023]
Abstract
Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment outcome. To determine the potential contribution of DNAmethylation alterations to tumor phenotype in non-small cell lung cancer (NSCLC) in both smoker and never-smoker patients, we performed genome-wide profiling of DNA methylation in 17 primary NSCLC tumors and 10 matched normal lung samples using the complementary assays, methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation sensitive restriction enzyme sequencing (MRE-seq). We reported recurrent methylation changes in the promoters of several genes, many previously implicated in cancer, including FAM83A and SEPT9 (hypomethylation), as well as PCDH7, NKX2-1, and SOX17 (hypermethylation). Although many methylation changes between tumors and their paired normal samples were shared across patients, several were specific to a particular smoking status. For example, never-smokers displayed a greater proportion of hypomethylated differentially methylated regions (hypoDMRs) and a greater number of recurrently hypomethylated promoters, including those of ASPSCR1, TOP2A, DPP9, and USP39, all previously linked to cancer. Changes outside of promoters were also widespread and often recurrent, particularly methylation loss over repetitive elements, highly enriched for ERV1 subfamilies. Recurrent hypoDMRs were enriched for several transcription factor binding motifs, often for genes involved in signaling and cell proliferation. For example, 71% of recurrent promoter hypoDMRs contained a motif for NKX2-1. Finally, the majority of DMRs were located within an active chromatin state in tissues profiled using the Roadmap Epigenomics data, suggesting that methylation changes may contribute to altered regulatory programs through the adaptation of cell type-specific expression programs.
Collapse
Affiliation(s)
- Jennifer A Karlow
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mark Watson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Siddhartha Devarakonda
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
| |
Collapse
|
86
|
Mukherjee A, Yadav PH, Mukunthan KS. Unveiling Potential Targeted Therapeutic Opportunities for Co-Overexpressed Targeting Protein for Xklp2 and Aurora-A Kinase in Lung Adenocarcinoma. Mol Biotechnol 2023:10.1007/s12033-023-00879-9. [PMID: 37768502 DOI: 10.1007/s12033-023-00879-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Lung adenocarcinoma (LUAD) is one of the most prevalent and leading causes of cancer deaths globally, with limited diagnostic and clinically significant therapeutic targets. Identifying the genes and processes involved in developing and progressing LUAD is crucial for developing effective targeted therapeutics and improving patient outcomes. Therefore, the study aimed to explore the RNA sequencing data of LUAD from The Cancer Genome Atlas (TCGA) and gene expression profile datasets involving GSE10072, GSE31210, and GSE32863 from the Gene Expression Omnibus (GEO) databases. The differential gene expression and the downstream analysis determined clinically significant biomarkers using a network-based approach. These therapeutic targets predominantly enriched the dysregulation of mitotic cell cycle regulation and revealed the co-overexpression of Aurora-A Kinase (AURKA) and Targeting Protein for Xklp2 (TPX2) with high survival risk in LUAD patients. The hydrophobic residues of the AURKA-TPX2 interaction were considered as the target site to block the autophosphorylation of AURKA during the mitotic cell cycle. The tyrosine kinase inhibitor (TKI) dacomitinib demonstrated the strong binding potential to hinder TPX2, shielding the AURKA destabilization. This in silico study lays the foundation for repurposing targeted therapeutic options to impede the Protein-Protein Interactions (PPIs) in LUAD progression and aid in future translational investigations.
Collapse
Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | | | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
| |
Collapse
|
87
|
Sahu P, Donovan C, Paudel KR, Pickles S, Chimankar V, Kim RY, Horvart JC, Dua K, Ieni A, Nucera F, Bielefeldt-Ohmann H, Mazilli S, Caramori G, Lyons JG, Hansbro PM. Pre-clinical lung squamous cell carcinoma mouse models to identify novel biomarkers and therapeutic interventions. Front Oncol 2023; 13:1260411. [PMID: 37817767 PMCID: PMC10560855 DOI: 10.3389/fonc.2023.1260411] [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: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Primary lung carcinoma or lung cancer (LC) is classified into small-cell or non-small-cell (NSCLC) lung carcinoma. Lung squamous cell carcinoma (LSCC) is the second most common subtype of NSCLC responsible for 30% of all LCs, and its survival remains low with only 24% of patients living for five years or longer post-diagnosis primarily due to the advanced stage of tumors at the time of diagnosis. The pathogenesis of LSCC is still poorly understood and has hampered the development of effective diagnostics and therapies. This review highlights the known risk factors, genetic and epigenetic alterations, miRNA biomarkers linked to the development and diagnosis of LSCC and the lack of therapeutic strategies to target specifically LSCC. We will also discuss existing animal models of LSCC including carcinogen induced, transgenic and xenograft mouse models, and their advantages and limitations along with the chemopreventive studies and molecular studies conducted using them. The importance of developing new and improved mouse models will also be discussed that will provide further insights into the initiation and progression of LSCC, and enable the identification of new biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Priyanka Sahu
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Chantal Donovan
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Sophie Pickles
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Vrushali Chimankar
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Richard Y. Kim
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Jay C. Horvart
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Antonio Ieni
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Anatomic Pathology, University of Messina, Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Sarah Mazilli
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Messina, Italy
| | - J. Guy Lyons
- Department of Dermatology, The University of Sydney at Royal Prince Alfred Hospital, Sydney, Australia, and Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Philip M. Hansbro
- Immune Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| |
Collapse
|
88
|
Bai X, Shao J, Duan T, Liu X, Wang M, Li X, You Q, Zhang Z, Pan J. Exo-miR-1290-induced by COX-2 overexpression promotes cancer-associated fibroblasts activation and tumor progression by CUL3-Nrf2 pathway in lung adenocarcinoma. Cell Commun Signal 2023; 21:242. [PMID: 37723559 PMCID: PMC10506250 DOI: 10.1186/s12964-023-01268-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/12/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are critically involved in tumor progression by maintaining extracellular mesenchyma (ECM) production and improving tumor development. Cyclooxygenase-2 (COX-2) has been proved to promote ECM formation and tumor progression. However, the mechanisms of COX-2 mediated CAFs activation have not yet been elucidated. Therefore, we conducted this study to identify the effects and mechanisms of COX-2 underlying CAFs activation by tumor-derived exosomal miRNAs in lung adenocarcinoma (LUAD) progression. METHODS As measures of CAFs activation, the expressions of fibroblasts activated protein-1 (FAP-1) and α-smooth muscle actin (α-SMA), the main CAFs markers, were detected by Western blotting and Immunohistochemistry. And the expression of Fibronectin (FN1) was used to analyze ECM production by CAFs. The exosomes were extracted by ultracentrifugation and exo-miRNAs were detected by qRT-PCR. Herein, we further elucidated the implicated mechanisms using online prediction software, luciferase reporter assays, co-immunoprecipitation, and experimental animal models. RESULTS In vivo, a positive correlation was observed between the COX-2 expression levels in parenchyma and α-SMA/FN1 expression levels in mesenchyma in LUAD. However, PGE2, one of major product of COX-2, did not affect CAFs activation directly. COX-2 overexpression increased exo-miR-1290 expression, which promoted CAFs activation. Furthermore, Cullin3 (CUL3), a potential target of miR-1290, was found to suppress COX-2/exo-miR-1290-mediated CAFs activation and ECM production, consequently impeding tumor progression. CUL3 is identified to induce the Nuclear Factor Erythroid 2-Related Factor 2 (NFE2L2, Nrf2) ubiquitination and degradation, while exo-miR-1290 can prevent Nrf2 ubiquitination and increase its protein stability by targeting CUL3. Additionally, we identified that Nrf2 is direcctly bound with promoters of FAP-1 and FN1, which enhanced CAFs activation by promoting FAP-1 and FN1 transcription. CONCLUSIONS Our data identify a new CAFs activation mechanism by exosomes derived from cancer cells that overexpress COX-2. Specifically, COX-2/exo-miR-1290/CUL3 is suggested as a novel signaling pathway for mediating CAFs activation and tumor progression in LUAD. Consequently, this finding suggests a novel strategy for cancer treatment that may tackle tumor progression in the future. Video Abstract.
Collapse
Affiliation(s)
- Xiaoming Bai
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Jiaofang Shao
- Department of Bioinformatics, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Tinghong Duan
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Xue Liu
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Min Wang
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Xuanya Li
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China
| | - Qiang You
- Department of Biotherapy, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, P.R. China
| | - Zhiyuan Zhang
- Department of Pathology, Nanjing Medical University, 101Longmian Avenue, Jiangning District, Nanjing, 211166, P.R. China.
| | - Jinshun Pan
- Department of Biotherapy, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, P.R. China.
| |
Collapse
|
89
|
Shen J, Sun N, Wang J, Zens P, Kunzke T, Buck A, Prade VM, Wang Q, Feuchtinger A, Hu R, Berezowska S, Walch A. Patterns of Carbon-Bound Exogenous Compounds Impact Disease Pathophysiology in Lung Cancer Subtypes in Different Ways. ACS NANO 2023; 17:16396-16411. [PMID: 37639684 PMCID: PMC10510585 DOI: 10.1021/acsnano.2c11161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAHs), tobacco-specific nitrosamines, aromatic amines, and organohalogens, are known to affect both tumor characteristics and patient outcomes in lung squamous cell carcinoma (LUSC); however, the roles of these compounds in lung adenocarcinoma (LUAD) remain unclear. We analyzed 11 carbon-bound exogenous compounds in LUAD and LUSC samples using in situ high mass-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging and performed a cluster analysis to compare the patterns of carbon-bound exogenous compounds between these two lung cancer subtypes. Correlation analyses were conducted to investigate associations among exogenous compounds, endogenous metabolites, and clinical data, including patient survival outcomes and smoking behaviors. Additionally, we examined differences in exogenous compound patterns between normal and tumor tissues. Our analyses revealed that PAHs, aromatic amines, and organohalogens were more abundant in LUAD than in LUSC, whereas the tobacco-specific nitrosamine nicotine-derived nitrosamine ketone was more abundant in LUSC. Patients with LUAD and LUSC could be separated according to carbon-bound exogenous compound patterns detected in the tumor compartment. The same compounds had differential impacts on patient outcomes, depending on the cancer subtype. Correlation and network analyses indicated substantial differences between LUAD and LUSC metabolomes, associated with substantial differences in the patterns of the carbon-bound exogenous compounds. These data suggest that the contributions of these carcinogenic compounds to cancer biology may differ according to the cancer subtypes.
Collapse
Affiliation(s)
- Jian Shen
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
- Nanxishan
Hospital of Guangxi Zhuang Autonomous Region, Institute of Pathology, Guilin 541002, People’s Republic of China
| | - Na Sun
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Jun Wang
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Philipp Zens
- Institute
of Tissue Medicine and Pathology, University
of Bern, Murtenstrasse 31, Bern 3008, Switzerland
- Graduate
School for Health Sciences, University of
Bern, Mittelstrasse 43, Bern 3012, Switzerland
| | - Thomas Kunzke
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Achim Buck
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Verena M. Prade
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Qian Wang
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Annette Feuchtinger
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Ronggui Hu
- Center
for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200030, People’s
Republic of China
| | - Sabina Berezowska
- Institute
of Tissue Medicine and Pathology, University
of Bern, Murtenstrasse 31, Bern 3008, Switzerland
- Department
of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Axel Walch
- Research
Unit Analytical Pathology, Helmholtz Zentrum
München − German Research Center for Environmental Health, Neuherberg 85764, Germany
| |
Collapse
|
90
|
Luo Y, Yang Y, Yang C, Li C, Hu R, Geng W, Kang X, Lin H. UBE3A and MCM6 synergistically regulate the proliferation and migration of lung adenocarcinoma cells. FEBS Open Bio 2023; 13:1756-1771. [PMID: 37454373 PMCID: PMC10476561 DOI: 10.1002/2211-5463.13675] [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: 02/07/2023] [Revised: 05/16/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
Lung cancer is a leading cause of mortality worldwide and shows substantial clinical and biomolecular heterogeneity. Currently, specific therapeutic strategies are lacking, so effective drug targets are urgently needed. E6AP/UBE3A is a multifaceted ubiquitin ligase that controls various signaling pathways implicated in neurological diseases and various cancers; however, its role in lung cancer is incompletely understood. Here, MCM6 was identified as an interacting partner of E6AP using the yeast two-hybrid assay. MCM2 and MCM4 were then shown to interact with E6AP. E6AP knockout enhanced the ubiquitination of MCM2/4/6, suggesting that E6AP was not the E3 ubiquitin ligase for these three MCM proteins. Ablation of E6AP inhibited proliferation and migration, but had no significant effect on apoptosis in A549 and H1975 cells, and proliferation and migration inhibition was also observed in MCM6 knockdown cells. Furthermore, ablation of MCM6 and E6AP synergistically suppressed the proliferation and migration of A549 and H1975 cells. To verify the above findings in vivo, we established tumor models in nude mice and identified that the tumorigenicity of human lung adenocarcinoma (LUAD) cells was synergistically regulated by MCM6 and E6AP. Moreover, the expression levels of MCM6 and E6AP were higher in LUAD tissues than in adjacent tissues. Furthermore, the expression levels of MCM6 and E6AP were positively correlated in human LUAD samples. Thus, our study suggests that the interaction of E6AP and MCM proteins plays an important role in the progression of LUAD, which might offer potential therapeutic targets for cancer treatment.
Collapse
Affiliation(s)
- Yanyan Luo
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghaiChina
| | - Yun Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghaiChina
- School of MedicineGuizhou UniversityGuiyangChina
| | - Cong Yang
- Cancer Center, School of Medicine, Shanghai Tenth People's HospitalfTongji UniversityShanghaiChina
| | - Chuanyin Li
- Cancer Center, School of Medicine, Shanghai Tenth People's HospitalfTongji UniversityShanghaiChina
| | - Ronggui Hu
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell Science, Chinese Academy of SciencesShanghaiChina
| | - Wujun Geng
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
| | - Xianhui Kang
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
- Department of Anesthesiology, The First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Hai Lin
- Department of Pain, Wenzhou Key Laboratory of Perioperative MedicineThe First Affiliated Hospital of Wenzhou Medical UniversityChina
| |
Collapse
|
91
|
Mu D, Tang H, Teng G, Li X, Zhang Y, Gao G, Wang D, Bai L, Lian X, Wen M, Jiang L, Wu S, Jiang H, Zhu C. Differences of genomic alterations and heavy metals in non-small cell lung cancer with different histological subtypes. J Cancer Res Clin Oncol 2023; 149:9999-10013. [PMID: 37256381 PMCID: PMC10423170 DOI: 10.1007/s00432-023-04929-2] [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: 04/02/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
PURPOSE This study aimed to explore the correlations among heavy metals concentration, histologic subtypes and molecular characteristics in patients with non-small cell lung cancer (NSCLC). METHODS In this study, an NGS panel of 82 tumor-associated genes was used to identify genomic alternations in 180 newly diagnosed patients with NSCLC. The concentrations of 18 heavy metals in the serum samples were detected by inductively coupled plasma emission spectrometry (ICP-MS). RESULTS A total of 243 somatic mutations of 25 mutant genes were identified in 115 of 148 patients with LUAD and 45 somatic mutations of 15 mutant genes were found in 24 of 32 patients with LUSC. The genomic alternations, somatic interactions, traditional serum biomarkers, and heavy metals were markedly different between patients with LUAD and LUSC. Moreover, patients with LUSC were significantly positively correlated with Ba, but not LUAD. Lastly, patients with EGFR mutations presented significant negative correlations with Cd and Sr, whereas patients with TP53 mutations showed a significant positive correlation with Pb. CONCLUSION The genomic alternations, somatic interactions, traditional serum biomarkers, and heavy metals were different between patients with LUAC and LUSC, and heavy metals (e.g., Ba, Pb, and Cd) may contribute to the tumorigenesis of NSCLC with different histological and molecular subtypes.
Collapse
Affiliation(s)
- Die Mu
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Hui Tang
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
- Department of Interventional and Vascular Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Gen Teng
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Xinyang Li
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Yarui Zhang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Ge Gao
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Dongjuan Wang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Lu Bai
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Xiangyao Lian
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China
| | - Ming Wen
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
| | - Lisha Jiang
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
| | - Shouxin Wu
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China
| | - Huihui Jiang
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, 200135, China.
| | - Cuimin Zhu
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, 067000, China.
| |
Collapse
|
92
|
Cai R, Zhu H, Liu Y, Sha H, Peng W, Yin R, Zhou G, Fang Y. To be, or not to be: the dilemma of immunotherapy for non-small cell lung cancer harboring various driver mutations. J Cancer Res Clin Oncol 2023; 149:10027-10040. [PMID: 37261523 PMCID: PMC10423141 DOI: 10.1007/s00432-023-04919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Lung cancer is one of primary cancer type with high incidence and mortality, non-small cell lung cancer (NSCLC) is the most common type of lung cncer. For advanced lung cancer, traditional chemotherapy and targeted therapy become difficult to solve the dilemma of further progress. In recent years, with the clinical application of immunotherapy, the therapeutic strategy of lung cancer has changed dramatically. At present, immunotherapy has shown conspicuous efficacy in NSCLC patients with high expression of programmed death-ligand 1 (PD-L1) and high tumor mutational burden (TMB). The discovery of driver mutations brings delightful hope for targeted cancer therapy. However, it remains controversial whether immunotherapy can be used in NSCLC patients with these specific driver mutations. METHOD This article summarized the latest research progresses of immunotherapy in advanced NSCLC. We paid close attention to the relevance of various driver mutations and immunotherapy in NSCLC patients, and summarized the predictive effects of several driver mutations and immunotherapy. RESULTS The mutations of KRAS, KRAS+TP53, EPHA (especially EPHA5), ZFHX3, ZFHX3+TP53, NOTCH, BRAF and LRP1B+FAT3 have potential to be used as biomarkers to predict the positive effectiveness of immunotherapy. ZFHX3, ZFHX3+TP53, STKII/LKB1+KEAP1+SMARCA4+PBRM1 mutations in LUAD patients get more positive effect in immunotherapy. While the mutations of EGFR, KEAP1, STKII/LKB1+KRAS, EML4-ALK, MET exon 14 skipping mutation, PBRM1, STKII/LKB1+KEAP1+SMARCA4+PBRM1, ERBB2, PIK3CA and RET often indicate poor benefit from immunotherapy. CONCLUSION Many gene mutations have been shown to be associated with immunotherapy efficacy. Gene mutations should be combined with PD-L1, TMB, etc. to predict the effect of immunotherapy.
Collapse
Affiliation(s)
- Ruoxue Cai
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China
| | - Hongyu Zhu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, 210009, People's Republic of China
| | - Ying Liu
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China
| | - Huanhuan Sha
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Weiwei Peng
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, 210009, People's Republic of China
| | - Guoren Zhou
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China.
| | - Ying Fang
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| |
Collapse
|
93
|
Konda P, Garinet S, Van Allen EM, Viswanathan SR. Genome-guided discovery of cancer therapeutic targets. Cell Rep 2023; 42:112978. [PMID: 37572322 DOI: 10.1016/j.celrep.2023.112978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
The success of precision oncology-which aims to match the right therapies to the right patients based on molecular status-is predicated on a robust pipeline of molecular targets against which therapies can be developed. Recent advances in genomics and functional genetics have enabled the unbiased discovery of novel molecular targets at scale. We summarize the promise and challenges in integrating genomic and functional genetic landscapes of cancer to establish the next generation of cancer targets.
Collapse
Affiliation(s)
- Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon Garinet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
94
|
Buscà R, Onesto C, Egensperger M, Pouysségur J, Pagès G, Lenormand P. N-terminal alanine-rich (NTAR) sequences drive precise start codon selection resulting in elevated translation of multiple proteins including ERK1/2. Nucleic Acids Res 2023; 51:7714-7735. [PMID: 37414542 PMCID: PMC10450180 DOI: 10.1093/nar/gkad528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
We report the discovery of N-terminal alanine-rich sequences, which we term NTARs, that act in concert with their native 5'-untranslated regions to promote selection of the proper start codon. NTARs also facilitate efficient translation initiation while limiting the production of non-functional polypeptides through leaky scanning. We first identified NTARs in the ERK1/2 kinases, which are among the most important signaling molecules in mammals. Analysis of the human proteome reveals that hundreds of proteins possess NTARs, with housekeeping proteins showing a particularly high prevalence. Our data indicate that several of these NTARs act in a manner similar to those found in the ERKs and suggest a mechanism involving some or all of the following features: alanine richness, codon rarity, a repeated amino acid stretch and a nearby second AUG. These features may help slow down the leading ribosome, causing trailing pre-initiation complexes (PICs) to pause near the native AUG, thereby facilitating accurate translation initiation. Amplification of erk genes is frequently observed in cancer, and we show that NTAR-dependent ERK protein levels are a rate-limiting step for signal output. Thus, NTAR-mediated control of translation may reflect a cellular need to precisely control translation of key transcripts such as potential oncogenes. By preventing translation in alternative reading frames, NTAR sequences may be useful in synthetic biology applications, e.g. translation from RNA vaccines.
Collapse
Affiliation(s)
- Roser Buscà
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| | - Cercina Onesto
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Polytech’Nice Sophia, Bioengineering Department, Sophia-Antipolis, France
| | - Mylène Egensperger
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| | - Jacques Pouysségur
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco
| | - Gilles Pagès
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco
| | - Philippe Lenormand
- Université Côte d’Azur (UCA), CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging Nice (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
- Centre Antoine Lacassagne, Nice, France
| |
Collapse
|
95
|
Al-Hawary SIS, Alsalamy A, Gupta R, Alsaab HO, Hjazi A, Edilboyev U, Ramadan MF, Hussien BM, Ahmed M, Hosseini-Fard SR. VAV3 in human cancers: Mechanism and clinical implication. Pathol Res Pract 2023; 248:154681. [PMID: 37467637 DOI: 10.1016/j.prp.2023.154681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Guanine nucleotide exchange factors (GEFs) are primarily involved in signal transmission between cell membrane receptors and intracellular mediators. Upon replacing GDP with GTP, GEFs can alter their conformation, resulting in their binding to downstream effectors, such as GTPases like Ras homologous (Rho). VAV GEF family are versatile proteins working as an adaptor mediator and GEF for Rho GTPase. They act as a phosphorylation-dependent molecular switcher, fluctuating between active (tyrosine phosphorylated) and inactive (non-phosphorylated) conformation in cell signaling. Accumulating data showed that VAV3 is implicated in cancer progression. The higher levels of VAV3 in human cancers proposed that it may have an oncogenic role in cancer progression. Available studies demonstrated that VAV3 promoted cell proliferation, epithelial-mesenchymal transition (EMT), colony formation, cell cycle, survival, migration and invasion, and suppressed cell apoptosis. In addition, other studies indicated that VAV3 may have a prognostic value in cancer as well as it may act as a mediator in cancer chemoresistance. Here, we aimed to investigate the underlying molecular mechanism of VAV3 in cancer progression as well as to review its value as a prognostic biomarker and chemoresistance mediator in human cancers.
Collapse
Affiliation(s)
| | - Ali Alsalamy
- College of Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Reena Gupta
- Institute of Pharmaceutical Research, GLA University, District-Mathura, U.P., 281406, India
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif 21944, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Unarbek Edilboyev
- Department of Engineering Graphics and Design Theory, Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, National Research University, Tashkent, Uzbekistan
| | | | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Muhja Ahmed
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Seyed Reza Hosseini-Fard
- Biochemistry Department, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
96
|
Timilsina M, Fey D, Buosi S, Janik A, Costabello L, Carcereny E, Abreu DR, Cobo M, Castro RL, Bernabé R, Minervini P, Torrente M, Provencio M, Nováček V. Synergy between imputed genetic pathway and clinical information for predicting recurrence in early stage non-small cell lung cancer. J Biomed Inform 2023; 144:104424. [PMID: 37352900 DOI: 10.1016/j.jbi.2023.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023]
Abstract
OBJECTIVE Lung cancer exhibits unpredictable recurrence in low-stage tumors and variable responses to different therapeutic interventions. Predicting relapse in early-stage lung cancer can facilitate precision medicine and improve patient survivability. While existing machine learning models rely on clinical data, incorporating genomic information could enhance their efficiency. This study aims to impute and integrate specific types of genomic data with clinical data to improve the accuracy of machine learning models for predicting relapse in early-stage, non-small cell lung cancer patients. METHODS The study utilized a publicly available TCGA lung cancer cohort and imputed genetic pathway scores into the Spanish Lung Cancer Group (SLCG) data, specifically in 1348 early-stage patients. Initially, tumor recurrence was predicted without imputed pathway scores. Subsequently, the SLCG data were augmented with pathway scores imputed from TCGA. The integrative approach aimed to enhance relapse risk prediction performance. RESULTS The integrative approach achieved improved relapse risk prediction with the following evaluation metrics: an area under the precision-recall curve (PR-AUC) score of 0.75, an area under the ROC (ROC-AUC) score of 0.80, an F1 score of 0.61, and a Precision of 0.80. The prediction explanation model SHAP (SHapley Additive exPlanations) was employed to explain the machine learning model's predictions. CONCLUSION We conclude that our explainable predictive model is a promising tool for oncologists that addresses an unmet clinical need of post-treatment patient stratification based on the relapse risk while also improving the predictive power by incorporating proxy genomic data not available for specific patients.
Collapse
Affiliation(s)
- Mohan Timilsina
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland.
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Ireland.
| | - Samuele Buosi
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland.
| | | | | | - Enric Carcereny
- Catalan Institute of Oncology, Hospital Universitari Germans Trias i Pujol, B-ARGO, IGTP, Badalona, Spain.
| | | | - Manuel Cobo
- Medical Oncology Intercenter Unit. Regional and Virgen de la Victoria University Hospitals. IBIMA. Málaga., Spain.
| | | | - Reyes Bernabé
- Hospital Universitario Virgen del Rocio, Sevilla, Spain.
| | | | - Maria Torrente
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain.
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain.
| | - Vít Nováček
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland; Faculty of Informatics, Masaryk University Brno, Czech Republic; Masaryk Memorial Cancer Institute, Brno, Czech Republic.
| |
Collapse
|
97
|
Hu F, Chen B, Wang Q, Yang Z, Chu M. Multi-omics data analysis reveals the biological implications of alternative splicing events in lung adenocarcinoma. J Bioinform Comput Biol 2023; 21:2350020. [PMID: 37694487 DOI: 10.1142/s0219720023500208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cancer is characterized by the dysregulation of alternative splicing (AS). However, the comprehensive regulatory mechanisms of AS in lung adenocarcinoma (LUAD) are poorly understood. Here, we displayed the AS landscape in LUAD based on the integrated analyses of LUAD's multi-omics data. We identified 13,995 AS events in 6309 genes as differentially expressed alternative splicing events (DEASEs) mainly covering protein-coding genes. These DEASEs were strongly linked to "cancer hallmarks", such as apoptosis, DNA repair, cell cycle, cell proliferation, angiogenesis, immune response, generation of precursor metabolites and energy, p53 signaling pathway and PI3K-AKT signaling pathway. We further built a regulatory network connecting splicing factors (SFs) and DEASEs. In addition, RNA-binding protein (RBP) mutations that can affect DEASEs were investigated to find some potential cancer drivers. Further association analysis demonstrated that DNA methylation levels were highly correlated with DEASEs. In summary, our results can bring new insight into understanding the mechanism of AS and provide novel biomarkers for personalized medicine of LUAD.
Collapse
Affiliation(s)
- Fuyan Hu
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, Hubei 430070, P. R. China
| | - Bifeng Chen
- Department of Biological Science and Technology, School of Chemistry Chemical Engineering and Life Sciences, Wuhan University of Technology Wuhan, Hubei, P. R. China
| | - Qing Wang
- Department of Traditional Chinese Medicine of Wuhan Puren Hospital, Affiliated Hospital of Wuhan University of Science and Technology, 1# Benxi Street, Qingshan District, Wuhan, Hubei, P. R. China
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, P. R. China
| | - Man Chu
- The Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, P. R. China
| |
Collapse
|
98
|
DuCote TJ, Naughton KJ, Skaggs EM, Bocklage TJ, Allison DB, Brainson CF. Using Artificial Intelligence to Identify Tumor Microenvironment Heterogeneity in Non-Small Cell Lung Cancers. J Transl Med 2023; 103:100176. [PMID: 37182840 PMCID: PMC10527157 DOI: 10.1016/j.labinv.2023.100176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/16/2023] Open
Abstract
Lung cancer heterogeneity is a major barrier to effective treatments and encompasses not only the malignant epithelial cell phenotypes and genetics but also the diverse tumor-associated cell types. Current techniques used to investigate the tumor microenvironment can be time-consuming, expensive, complicated to interpret, and often involves destruction of the sample. Here we use standard hematoxylin and eosin-stained tumor sections and the HALO AI nuclear phenotyping software to characterize 6 distinct cell types (epithelial, mesenchymal, macrophage, neutrophil, lymphocyte, and plasma cells) in both murine lung cancer models and human lung cancer samples. CD3 immunohistochemistry and lymph node sections were used to validate lymphocyte calls, while F4/80 immunohistochemistry was used for macrophage validation. Consistent with numerous prior studies, we demonstrated that macrophages predominate the adenocarcinomas, whereas neutrophils predominate the squamous cell carcinomas in murine samples. In human samples, we showed a strong negative correlation between neutrophils and lymphocytes as well as between mesenchymal cells and lymphocytes and that higher percentages of mesenchymal cells correlate with poor prognosis. Taken together, we demonstrate the utility of this AI software to identify, quantify, and compare distributions of cell types on standard hematoxylin and eosin-stained slides. Given the simplicity and cost-effectiveness of this technique, it may be widely beneficial for researchers designing new therapies and clinicians working to select favorable treatments for their patients.
Collapse
Affiliation(s)
- Tanner J DuCote
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Kassandra J Naughton
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Erika M Skaggs
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Therese J Bocklage
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky; Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Derek B Allison
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky; Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Christine F Brainson
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky; Markey Cancer Center, University of Kentucky, Lexington, Kentucky.
| |
Collapse
|
99
|
Hong CS, Alanya H, DiStasio M, Boulware SD, Rimmer RA, Omay SB, Erson-Omay EZ. Sporadic pituitary adenoma with somatic double-hit loss of MEN1. Pituitary 2023; 26:488-494. [PMID: 37438451 DOI: 10.1007/s11102-023-01336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE Pituitary adenomas commonly arise in patients with MEN1 syndrome, an autosomal dominant condition predisposing to neuroendocrine tumor formation, and typically diagnosed in patients with a relevant family cancer history. In these patients with existing germline loss of MEN1 on one allele, somatic loss of the second MEN1 allele leads to complete loss of the MEN1 protein, menin, and subsequent tumor formation. METHODS Whole exome sequencing was performed on the tumor and matching blood under an institutional board approved protocol. DNA extraction and analysis was conducted according to previously described methods. RESULTS We describe a 23 year-old patient with no significant past medical history or relevant family history who underwent surgical resection of a symptomatic and medically resistant prolactinoma. Whole exome sequencing of tumor and blood samples revealed somatic loss of MEN1 at both alleles, suggesting a double hit mechanism, with no underlying germline MEN1 mutation. CONCLUSION To our knowledge, this is the first case of pituitary adenoma to arise from somatic loss of MEN1 and in the absence of an underlying germline MEN1 mutation.
Collapse
Affiliation(s)
- Christopher S Hong
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Hasan Alanya
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Susan D Boulware
- Department of Pediatrics, Section of Endocrinology and Diabetes, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Ryan A Rimmer
- Department of Surgery, Division of Otolaryngology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Sacit Bulent Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, 06510, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, 300 Cedar Street, TAC S327, New Haven, CT, 06511, USA.
| |
Collapse
|
100
|
Tang P, Sun D, Xu W, Li H, Chen L. Long non‑coding RNAs as potential therapeutic targets in non‑small cell lung cancer (Review). Int J Mol Med 2023; 52:68. [PMID: 37350412 PMCID: PMC10413047 DOI: 10.3892/ijmm.2023.5271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Non‑small cell lung cancer (NSCLC) is one of the most common malignancies with a high morbidity and mortality rate. Long non‑coding RNAs (lncRNAs) have been reported to be closely associated with the occurrence and progression of NSCLC. In addition, lncRNAs have been documented to participate in the development of drug resistance and radiation sensitivity in patients with NSCLC. Due to their extensive functional characterization, high tissue specificity and sex specificity, lncRNAs have been proposed to be novel biomarkers and therapeutic targets for NSCLC. Therefore, in the current review, the functional classification of lncRNAs were presented, whilst the potential roles of lncRNAs in NSCLC were also summarized. Various physiological aspects, including proliferation, invasion and drug resistance, were all discussed. It is anticipated that the present review will provide a perspective on lncRNAs as potential diagnostic molecular biomarkers and therapeutic targets for NSCLC.
Collapse
Affiliation(s)
- Peiyu Tang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| | - Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| | - Wei Xu
- Institute of Structural Pharmacology and TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
- Institute of Structural Pharmacology and TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016
| |
Collapse
|