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Morshed RA, Cummins DD, Nguyen MP, Saggi S, Vasudevan HN, Braunstein SE, Goldschmidt E, Chang EF, McDermott MW, Berger MS, Theodosopoulos PV, Daras M, Hervey-Jumper SL, Aghi MK. Genomic alterations associated with postoperative nodular leptomeningeal disease after resection of brain metastases. J Neurosurg 2024; 140:328-337. [PMID: 37548547 PMCID: PMC11175692 DOI: 10.3171/2023.5.jns23460] [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: 02/25/2023] [Accepted: 05/30/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVE The relationship between brain metastasis resection and risk of nodular leptomeningeal disease (nLMD) is unclear. This study examined genomic alterations found in brain metastases with the aim of identifying alterations associated with postoperative nLMD in the context of clinical and treatment factors. METHODS A retrospective, single-center study was conducted on patients who underwent resection of brain metastases between 2014 and 2022 and had clinical and genomic data available. Postoperative nLMD was the primary endpoint of interest. Targeted next-generation sequencing of > 500 oncogenes was performed in brain metastases. Cox proportional hazards analyses were performed to identify clinical features and genomic alterations associated with nLMD. RESULTS The cohort comprised 101 patients with tumors originating from multiple cancer types. There were 15 patients with nLMD (14.9% of the cohort) with a median time from surgery to nLMD diagnosis of 8.2 months. Two supervised machine learning algorithms consistently identified CDKN2A/B codeletion and ERBB2 amplification as the top predictors associated with postoperative nLMD across all cancer types. In a multivariate Cox proportional hazards analysis including clinical factors and genomic alterations observed in the cohort, tumor volume (× 10 cm3; HR 1.2, 95% CI 1.01-1.5; p = 0.04), CDKN2A/B codeletion (HR 5.3, 95% CI 1.7-16.9; p = 0.004), and ERBB2 amplification (HR 3.9, 95% CI 1.1-14.4; p = 0.04) were associated with a decreased time to postoperative nLMD. CONCLUSIONS In addition to increased resected tumor volume, ERBB2 amplification and CDKN2A/B deletion were independently associated with an increased risk of postoperative nLMD across multiple cancer types. Additional work is needed to determine if targeted therapy decreases this risk in the postoperative setting.
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Affiliation(s)
- Ramin A. Morshed
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Daniel D. Cummins
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Minh P. Nguyen
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Satvir Saggi
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Harish N. Vasudevan
- Department of Neurological Surgery, University of California, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Steve E. Braunstein
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Ezequiel Goldschmidt
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Edward F. Chang
- Department of Neurological Surgery, University of California, San Francisco, California
| | | | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, California
| | | | - Mariza Daras
- Department of Neurological Surgery, University of California, San Francisco, California
| | | | - Manish K. Aghi
- Department of Neurological Surgery, University of California, San Francisco, California
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Han T, Liu Y, Zhou J, Guo J, Xing Y, Xie J, Bai Y, Wu J, Hu D. Development of an invasion score based on metastasis-related pathway activity profiles for identifying invasive molecular subtypes of lung adenocarcinoma. Sci Rep 2024; 14:1692. [PMID: 38243040 PMCID: PMC10799059 DOI: 10.1038/s41598-024-51681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
The invasive capacity of lung adenocarcinoma (LUAD) is an important factor influencing patients' metastatic status and survival outcomes. However, there is still a lack of suitable biomarkers to evaluate tumor invasiveness. LUAD molecular subtypes were identified by unsupervised consistent clustering of LUAD. The differences in prognosis, tumor microenvironment (TME), and mutation were assessed among different subtypes. After that, the invasion-related gene score (IRGS) was constructed by genetic differential analysis, WGCNA analysis, and LASSO analysis, then we evaluated the relationship between IRGS and invasive characteristics, TME, and prognosis. The predictive ability of the IRGS was verified by in vitro experiments. Next, the "oncoPredict" R package and CMap were used to assess the potential value of IRGS in drug therapy. The results showed that LUAD was clustered into two molecular subtypes. And the C1 subtype exhibited a worse prognosis, higher stemness enrichment activity, less immune infiltration, and higher mutation frequency. Subsequently, IRGS developed based on molecular subtypes demonstrated a strong association with malignant characteristics such as invasive features, higher stemness scores, less immune infiltration, and worse survival. In vitro experiments showed that the higher IRGS LUAD cell had a stronger invasive capacity than the lower IRGS LUAD cell. Predictive analysis based on the "oncoPredict" R package showed that the high IRGS group was more sensitive to docetaxel, erlotinib, paclitaxel, and gefitinib. Among them, in vitro experiments verified the greater killing effect of paclitaxel on high IRGS cell lines. In addition, CMap showed that purvalanol-a, angiogenesis-inhibitor, and masitinib have potential therapeutic effects in the high IRGS group. In summary we identified and analyzed the molecular subtypes associated with the invasiveness of LUAD and developed IRGS that can efficiently predict the prognosis and invasive ability of the tumor. IRGS may be able to facilitate the precision treatment of LUAD to some extent.
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Affiliation(s)
- Tao Han
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
| | - Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, 232035, China
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China
| | - Yingru Xing
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China
- Department of Clinical Laboratory, Anhui Zhongke Gengjiu Hospital, Hefei, China
| | - Jun Xie
- Affiliated Cancer Hospital, Anhui University of Science and Technology, Huainan, 232035, China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China.
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Anhui University of Science and Technology, Huainan, 232001, China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Anhui University of Science and Technology, Huainan, 232001, China.
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Ma M, Guo B, Lu H, Hong L. SCN4B inhibits the progression of lung adenocarcinoma and is associated with better prognosis. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:1233-1245. [PMID: 37826914 PMCID: PMC10730470 DOI: 10.1111/crj.13709] [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: 06/13/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023]
Abstract
INTRODUCTION Lung adenocarcinoma (LUAD) is the major type of non-small cell lung cancer with low a survival rate caused by metastasis. SCN4B encoding voltage-gated sodium channel β subunit is regarded as a metastasis-suppressor gene. We aim to explore how SCN4B influences the progression and prognosis of LUAD. METHODS The gene expression profiles of 585 LUAD samples in TCGA and GSE31210, GSE116959, and GSE72094 datasets from the GEO database were downloaded for analysis. Differentially expressed genes were obtained through the "limma" package. The "clusterProfiler" package was used to conduct GSEA. Survival analysis was conducted via "survival" and "survminer" packages. Transcription factors regulating SCN4B expression were screened by correlation analysis and further predicted by FIMO. Infiltration of immune cells was analyzed by CIBERSORT. ESTIMATE algorithm was used to evaluate the immune-related scores. RESULTS SCN4B expressed higher in normal samples than in LUAD samples and higher in female samples than male samples. One hundred and twenty-six pathways were significantly enriched between high and low SCN4B expression groups. Six transcription factors' expressions were positively related to SCN4B expression, and ChIP-seq data from "Cistrome" verified that TAL1 and ERG might bind to the upstream sequence of SCN4B. SCN4B expression was significantly correlated with activated memory CD4 T cells, resting mast cells, and monocytes. TMB status, three scores based on ESTIMATE algorithm, and expression of three immune checkpoints showed significant differences between SCN4B high- and low-expression groups. SCN4B could be considered as an independent prognostic signature of LUAD patients that higher expression represents a better prognosis. CONCLUSION SCN4B expresses higher in normal samples, and SCN4B is able to be an independent prognostic signature for LUAD patients. TAL1 and ERG may regulate the expression of SCN4B by binding its upstream sequences. Our research is valuable in improving the effectiveness of treatment in LUAD.
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Affiliation(s)
- Minting Ma
- Department of OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebei ProvinceChina
| | - Bin Guo
- Department of Thoracic SurgeryThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebei ProvinceChina
| | - Hongwei Lu
- Department of OphthalmologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebei ProvinceChina
| | - Lei Hong
- Department of OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebei ProvinceChina
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Yu H, Zhang W, Xu XR, Chen S. Drug resistance related genes in lung adenocarcinoma predict patient prognosis and influence the tumor microenvironment. Sci Rep 2023; 13:9682. [PMID: 37322027 PMCID: PMC10272185 DOI: 10.1038/s41598-023-35743-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the predominant type of non-small lung cancer (NSCLC) with strong invasive ability and poor prognosis. The drug resistance related genes are potentially associated with prognosis of LUAD. Our research aimed to identify the drug resistance related genes and explore their potential prognostic value in LUAD patients. The data used in this study were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Firstly, we screened drug resistance related genes in LUAD by differential gene analysis, univariate Cox regression and drug sensitivity analyses. Subsequently, we constructed a risk score model using LASSO Cox regression analysis, and verified whether the risk score can predict the survival of LUAD patients independent of other factors. Moreover, we explored the immune infiltration of 22 immune cells between high-risk and low-risk patients. Totally 10 drug-resistance positively related genes (PLEK2, TFAP2A, KIF20A, S100P, GDF15, HSPB8, SASH1, WASF3, LAMA3 and TCN1) were identified in LUAD. The risk score model of LUAD constructed with these 10 genes could reliably predict the prognosis of LUAD patients. 18 pathways were significantly activated in high-risk group compared with low-risk group. In addition, the infiltration proportion of multiple immune cells was significantly different between high-risk and low-risk groups, and the proportion of M1 phagocytes was significantly higher in the high-risk group compared with the low-risk group. The drug resistance related genes (PLEK2, TFAP2A, KIF20A, S100P, GDF15, HSPB8, SASH1, WASF3, LAMA3 and TCN1) could predict the prognosis of LUAD patients. Clarifying the roles and mechanisms of these 10 genes in regulating drug resistance in LUAD will help to improve individualized clinical treatment protocols and predict patient sensitivity to treatment.
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Affiliation(s)
- Hui Yu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438 Jiefang Road, Zhenjiang, 212001, Jiangsu, People's Republic of China.
| | - Wenting Zhang
- Department of Galactophore, Danyang Maternal and Child Health Hospital, Danyang, 212300, Jiangsu, People's Republic of China
| | - Xian Rong Xu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438 Jiefang Road, Zhenjiang, 212001, Jiangsu, People's Republic of China
| | - Shengjie Chen
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438 Jiefang Road, Zhenjiang, 212001, Jiangsu, People's Republic of China
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Morshed RA, Nguyen MP, Cummins DD, Saggi S, Young JS, Haddad AF, Goldschmidt E, Chang EF, McDermott MW, Berger MS, Theodosopoulos PV, Hervey-Jumper SL, Daras M, Aghi MK. CDKN2A/B co-deletion is associated with increased risk of local and distant intracranial recurrence after surgical resection of brain metastases. Neurooncol Adv 2023; 5:vdad007. [PMID: 36915611 PMCID: PMC10007908 DOI: 10.1093/noajnl/vdad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background While genetic alterations in brain metastases (BMs) have been previously explored, there are limited data examining their association with recurrence after surgical resection. This study aimed to identify genetic alterations within BMs associated with CNS recurrence after surgery across multiple cancer types. Methods A retrospective, single-center study was conducted with patients who underwent resection of a BM with available clinical and gene sequencing data available. Local and remote CNS recurrence were the primary study outcomes. Next-generation sequencing of the coding regions in over 500 oncogenes was performed in brain metastasis specimens. Cox proportional hazards analyses were performed to identify clinical features and genomic alterations associated with CNS recurrence. Results A total of 90 patients undergoing resection of 91 BMs composed the cohort. Genes most frequently mutated in the cohort included TP53 (64%), CDKN2A (37%), TERT (29%), CDKN2B (23%), NF1 (14%), KRAS (14%), and PTEN (13%), all of which occurred across multiple cancer types. CDKN2A/B co-deletion was seen in 21 (23.1%) brain metastases across multiple cancer types. In multivariate Cox proportional hazard analyses including patient, tumor, and treatment factors, CDKN2A/B co-deletion in the brain metastasis was associated with increased risk of local (HR 4.07, 95% CI 1.32-12.54, P = 0.014) and remote (HR 2.28, 95% CI 1.11-4.69, P = 0.025) CNS progression. Median survival and length of follow-up were not different based on CDKN2A/B mutation status. Conclusions CDKN2A/B co-deletion detected in BMs is associated with increased CNS recurrence after surgical resection. Additional work is needed to determine whether more aggressive treatment in patients with this mutation may improve outcomes.
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Affiliation(s)
- Ramin A Morshed
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Minh P Nguyen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel D Cummins
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Satvir Saggi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander F Haddad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ezequiel Goldschmidt
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | | | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Philip V Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mariza Daras
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
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The Metastatic Process through the Eyes of Epigenetic Regulation: A Promising Horizon for Cancer Therapy. Int J Mol Sci 2022; 23:ijms232415446. [PMID: 36555088 PMCID: PMC9778637 DOI: 10.3390/ijms232415446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Genetic aberrations, including chromosomal rearrangements, loss or amplification of DNA, and point mutations, are major elements of cancer development [...].
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