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Identification of Potential microRNA Panels for Male Non-Small Cell Lung Cancer Identification Using Microarray Datasets and Bioinformatics Methods. J Pers Med 2022; 12:jpm12122056. [PMID: 36556276 PMCID: PMC9780989 DOI: 10.3390/jpm12122056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Background: Non-small cell lung cancer (NSCLC) is still one of the types of cancer with the highest death rates. MicroRNAs (miRNAs) play essential roles in NSCLC development. This study evaluates miRNA expression patterns and specific mechanisms in male patients with NSCLC. Methods: We report an integrated microarray analysis of miRNAs for eight matched samples of males with NSCLC compared to the study of public datasets of males with NSCLC from TCGA, followed by qRT-PCR validation. Results: For the TCGA dataset, we identified 385 overexpressed and 75 underexpressed miRNAs. Our cohort identified 54 overexpressed and 77 underexpressed miRNAs, considering a fold-change (FC) of ±1.5 and p < 0.05 as the cutoff value. The common miRNA signature consisted of eight overexpressed and nine underexpressed miRNAs. Validation was performed using qRT-PCR on the tissue samples for miR-183-3p and miR-34c-5p and on plasma samples for miR-34c-5p. We also created mRNA-miRNA regulatory networks to identify critical molecules, revealing NSCLC signaling pathways related to underexpressed and overexpressed transcripts. The genes targeted by these transcripts were correlated with overall survival. Conclusions: miRNAs and some of their target genes could play essential roles in investigating the mechanisms involved in NSCLC evolution and provide opportunities to identify potential therapeutic targets.
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Mohan A, Ansari A, Masroor M, Saxena A, Pandey RM, Upadhyay A, Luthra K, Khilnani GC, Jain D, Kumar R, Guleria R. Measurement of Serum EGFR mRNA Expression is a Reliable Predictor of Treatment Response and Survival Outcomes in Non- Small Cell Lung Cancer. Asian Pac J Cancer Prev 2020; 21:3153-3163. [PMID: 33247670 PMCID: PMC8033130 DOI: 10.31557/apjcp.2020.21.11.3153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Indexed: 01/09/2023] Open
Abstract
Background: EGFR over-expression plays a key role in the development and progression of lung cancer. However, its status as a prognostic biomarker for survival outcomes is unclear. Objectives: To evaluate the prognostic utility of serum EGFR mRNA expression in Non-Small cell lung cancer (NSCLC) for treatment response and survival. Methods: EGFR mRNA levels were determined in serum using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Based on ROC curve, a cut off value of 16.0-fold increase was selected to categorize patients into low EGFR (≤ 16.0) and high EGFR (> 16.0) groups. Results: A total of 350 subjects were included (78.3% males), with mean (± SD) age of 57.1 (± 11.2) years, and including 247 (70.6%) adenocarcinoma (ADC). Majority (73.1%) had metastatic (stage IV) disease. Patients had higher pre-treatment serum EGFR mRNA levels than controls [median fold-increase (min, max), 16.2 (1.9, 66.7). Serum EGFR mRNA levels significantly reduced in those who achieved objective response and disease control. Significantly longer OS and PFS was observed in subjects having baseline EGFR mRNA expression ≤ 16.0 fold- increase compared to those with > 16.0 fold- increase [median (95% CI) OS: 25.0 (14.9, NR) versus 7.7 (6.3, 8.9) months; HR (95% CI) 2.9 (2.3, 4.0), p< 0.001; and PFS: 9.9 (7.1, 11.5) versus 6.0 (4.1, 7.5) months; HR (95% CI) 1.8 (1.3, 2.4), p< 0.001]. Conclusion: Serum EGFR mRNA expression is a useful parameter for predicting treatment response and survival outcomes in NSCLC.
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Affiliation(s)
- Anant Mohan
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Ashraf Ansari
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Mirza Masroor
- Department of Biochemistry, Maulana Azad Medical College, New Delhi, India
| | - Alpana Saxena
- Department of Biochemistry, Maulana Azad Medical College, New Delhi, India
| | - R M Pandey
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi
| | - Ashish Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi
| | - Kalpana Luthra
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi
| | - G C Khilnani
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Department of Nuclear Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
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Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients. Sci Rep 2020; 10:2070. [PMID: 32034196 PMCID: PMC7005734 DOI: 10.1038/s41598-020-58819-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/29/2019] [Indexed: 02/05/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) ≥ 5% at >500 × coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.
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Misra P, Singh S. Role of cytokines in combinatorial immunotherapeutics of non-small cell lung cancer through systems perspective. Cancer Med 2019; 8:1976-1995. [PMID: 30997737 PMCID: PMC6536974 DOI: 10.1002/cam4.2112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the leading cause of deaths related to cancer and accounts for more than a million deaths per year. Various new strategies have been developed and adapted for treatment; still the survival for 5 years is just 16% in patients with non‐small cell lung cancer (NSCLC). Most of these strategies to combat NSCLC whether it is a drug molecule or immunotherapy/vaccine candidate require a big cost and time. Integration of computational modeling with systems biology has opened new avenues for understanding complex cancer biology. Resolving the complex interactions of various pathways and their crosstalk leading to oncogenic changes could identify new therapeutic targets with lesser cost and time. Herein, this review provides an overview of various aspects of NSCLC along with available strategies for its cure concluding with our insight into how systems approach could serve as a therapeutic intervention dissecting the immunologic parameters and cross talk between various pathways involved.
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Affiliation(s)
- Pragya Misra
- National Centre for Cell ScienceSP Pune University CampusPuneIndia
| | - Shailza Singh
- National Centre for Cell ScienceSP Pune University CampusPuneIndia
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Borlak J, Länger F, Chatterji B. Serum proteome mapping of EGF transgenic mice reveal mechanistic biomarkers of lung cancer precursor lesions with clinical significance for human adenocarcinomas. Biochim Biophys Acta Mol Basis Dis 2018; 1864:3122-3144. [PMID: 29960043 DOI: 10.1016/j.bbadis.2018.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/12/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022]
Abstract
Atypical adenomatous hyperplasia (AAH) of the lung is a pre-invasive lesion (PL) with high risk of progression to lung cancer (LC). However, the pathways involved are uncertain. We searched for novel mechanistic biomarkers of AAH in an EGF transgenic disease model of lung cancer. Disease regulated proteins were validated by Western immunoblotting and immunohistochemistry (IHC) of control and morphologically altered respiratory epithelium. Translational work involved clinical resection material. Collectively, 68 unique serum proteins were identified by 2DE-MALDI-TOF mass spectrometry and 13 reached statistical significance (p < 0.05). EGF, amphiregulin and the EGFR endosomal sorting protein VPS28 were induced up to 5-fold while IHC confirmed strong induction of these proteins. Furthermore, ApoA1, α-2-macroglobulin, and vitamin-D binding protein were nearly 6- and 2-fold upregulated in AAH; however, ApoA1 was oppositely regulated in LC to evidence disease stage dependent regulation of this tumour suppressor. Conversely, plasminogen and transthyretin were highly significantly repressed by 3- and 20-fold. IHC confirmed induced ApoA1, Fetuin-B and transthyretin expression to influence calcification, inflammation and tumour-infiltrating macrophages. Moreover, serum ApoA4, ApoH and ApoM were 2-, 2- and 6-fold repressed; however tissue ApoM and sphingosine-1-phosphate receptor expression was markedly induced to suggest a critical role of sphingosine-1-phosphate signalling in PL and malignant transformation. Finally, a comparison of three different LC models revealed common and unique serum biomarkers mechanistically linked to EGFR, cMyc and cRaf signalling. Their validation by IHC on clinical resection material established relevance for distinct human lung pathologies. In conclusion, we identified mechanistic biomarker candidates recommended for in-depth clinical evaluation.
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Affiliation(s)
- Jürgen Borlak
- Hannover Medical School, Centre for Pharmacology and Toxicology, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
| | - Florian Länger
- Hannover Medical School, Institute of Pathology, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Bijon Chatterji
- Hannover Medical School, Centre for Pharmacology and Toxicology, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Tan J, Chen B, He L, Yin G, Jiang Z, Yao K, Jiang X. Renal access through the inferior calyx is associated with higher risk of severe bleeding after percutaneous nephrolithotomy. Arch Med Sci 2015; 11:340-5. [PMID: 25995750 PMCID: PMC4424251 DOI: 10.5114/aoms.2015.50966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/22/2012] [Accepted: 04/28/2013] [Indexed: 01/20/2023] Open
Abstract
INTRODUCTION Hemorrhage is a major complication after percutaneous nephrolithotomy (PCNL). In the current study, we analyzed the risk factors for severe bleeding after PCNL. MATERIAL AND METHODS Medical records of 982 consecutive patients undergoing PCNL at the Department of Urology, the Third Xiangya Hospital, were reviewed. The type of stone included: solitary (n = 471), multiple (n = 192) and staghorn (n = 319). 139 patients had renal stones of solitary kidney or functional solitary kidney. The puncture site was the inferior calyx in 246 cases, the middle calyx in 651 cases, and the upper calyx in the remaining 85 cases. RESULTS The success rate (complete removal of the stone) was 92.8%, 73.4%, and 80.9% for solitary, multiple and staghorn stones, respectively. Severe bleeding occurred in 3.25% (8/246) of the cases with inferior calyx access, and 0.3% (2/651) in cases with middle calyx access. No severe bleeding occurred in patients with upper calyx access. The bleeding was controlled successfully with focal embolization under angiography in all 10 cases. CONCLUSIONS Severe postoperative bleeding after PCNL is associated with renal puncture via the inferior calyx, multiple renal stones and solitary kidney stones.
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Affiliation(s)
- Jing Tan
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Binghai Chen
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Leye He
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Guangming Yin
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Jiang
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Kun Yao
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Xianzheng Jiang
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
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Yu K, Zhang J, Li X, Xu L, Zhang Y, Xing J, Shao J, Zhu L, Liu J, Zhao L, Han B. Establishment and management of a lung cancer biobank in Eastern China. Thorac Cancer 2015; 6:58-63. [PMID: 26273336 PMCID: PMC4448472 DOI: 10.1111/1759-7714.12144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/20/2014] [Indexed: 12/02/2022] Open
Abstract
Background The prevalence of lung cancer, a highly complex neoplasm, increases annually. Thus, a lung cancer biobank, which stores lung cancer tissue and blood matched according to standard methods, is needed to advance lung cancer research and develop promising therapies. Methods To accomplish this aim, we implemented standardized procedures for tissue samples and patient information acquired from consenting donors. The banked tissue includes blood, pleural effusions, and surgical resection samples. An independent information management system was used to match samples and collect data, including clinical cancer manifestation, laboratory tests, and de-identified data about cancer patients. Results From 2009 to 2013, more than 2000 lung cancer cases were collected. At this time, we have more than 10 000 biological samples stored in our biobank. DNA, ribonucleic acid (RNA), and protein quality were confirmed to be appropriate for clinical and basic research. Conclusion Our standardized, large-scale lung cancer biobank offers high quality cancer research samples for China and the world.
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Affiliation(s)
- Keke Yu
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jie Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Xin Li
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Lei Xu
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Ye Zhang
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jie Xing
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jinguo Liu
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Lanxiang Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Baohui Han
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pulmonary Medcine, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
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