1
|
Pane K, Zanfardino M, Grimaldi AM, Leone I, Nuzzo S, Salvatore M, Franzese M. Feature Selection and Network-Driven Analyses to Unveil Common RNA Signatures in Colon and Pancreatic KRAS-Mutant Cancers. Cancer Med 2025; 14:e70468. [PMID: 40013338 DOI: 10.1002/cam4.70468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 11/12/2024] [Accepted: 11/22/2024] [Indexed: 02/28/2025] Open
Abstract
BACKGROUND Colon cancer and pancreatic ductal adenocarcinoma are among the most aggressive tumors for which therapeutic options are limited. Both cancers share common features, such as some KRAS pathogenic variants and common epidemiology. The integration of multidimensional datasets by combining machine learning and bioinformatics approaches could provide deeper insights into the intricate KRAS-related networks underlying cancer progression and unveil novel biomarkers and potential therapeutic targets. This study aimed to uncover colon and pancreatic cancers that shared transcriptional changes closely related to KRAS missense mutations. METHODS Feature Selection (FS) technique and Qiagen's Ingenuity Pathway Analysis (IPA) were used to combine DNA-Seq and RNA-Seq data from mutant and wild-type (WT) KRAS colon and pancreatic tumor samples. RESULTS From the FS, we prioritized 70 genes (54 protein-coding genes and 16 ncRNA-coding genes) that were able to discriminate between WT and mutated KRAS patients. These genes were involved in KRAS signaling and other related processes, such as EMT signaling, glycolysis, apical junction, Wnt/beta-catenin signaling, and IL-2/STAT5 signaling. Using IPA, we identified a top-scoring network of 19 upregulated genes in both tumor types stratified into mutant KRAS and WT KRAS samples. For a set of genes, qRT-PCR performed on colon and pancreatic representative cancer cell lines showed concordant expression trends when comparing colon-dominant KRAS mutants versus WT KRAS and dominant pancreatic KRAS mutants versus WT KRAS, as expected according to in silico analyses. CONCLUSIONS Our findings may provide insight into the common transcriptional signatures potentially underlying colon and pancreatic KRAS-mutant cancers. However, further studies are needed to elucidate the diagnostic and prognostic value of targets identified as common features in our study.
Collapse
Affiliation(s)
- Katia Pane
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| | - Mario Zanfardino
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| | - Anna Maria Grimaldi
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| | - Ilaria Leone
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| | - Silvia Nuzzo
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| | - Marco Salvatore
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| | - Monica Franzese
- Bioinformatics And Biostatistics Laboratory, IRCCS SYNLAB SDN, Naples, Italy
| |
Collapse
|
2
|
Morau MV, Seguin CS, Visacri MB, Pincinato EDC, Moriel P. Genetic Variants in the ABCB1 and ABCG2 Gene Drug Transporters Involved in Gefitinib-Associated Adverse Reaction: A Systematic Review and Meta-Analysis. Genes (Basel) 2024; 15:591. [PMID: 38790220 PMCID: PMC11120674 DOI: 10.3390/genes15050591] [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: 04/09/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
This systematic review and meta-analysis aimed to verify the association between the genetic variants of adenosine triphosphate (ATP)-binding cassette subfamily B member 1 (ABCB1) and ATP-binding cassette subfamily G member 2 (ABCG2) genes and the presence and severity of gefitinib-associated adverse reactions. We systematically searched PubMed, Virtual Health Library/Bireme, Scopus, Embase, and Web of Science databases for relevant studies published up to February 2024. In total, five studies were included in the review. Additionally, eight genetic variants related to ABCB1 (rs1045642, rs1128503, rs2032582, and rs1025836) and ABCG2 (rs2231142, rs2231137, rs2622604, and 15622C>T) genes were analyzed. Meta-analysis showed a significant association between the ABCB1 gene rs1045642 TT genotype and presence of diarrhea (OR = 5.41, 95% CI: 1.38-21.14, I2 = 0%), the ABCB1 gene rs1128503 TT genotype and CT + TT group and the presence of skin rash (OR = 4.37, 95% CI: 1.51-12.61, I2 = 0% and OR = 6.99, 95%CI: 1.61-30.30, I2= 0%, respectively), and the ABCG2 gene rs2231142 CC genotype and presence of diarrhea (OR = 3.87, 95% CI: 1.53-9.84, I2 = 39%). No ABCB1 or ABCG2 genes were positively associated with the severity of adverse reactions associated with gefitinib. In conclusion, this study showed that ABCB1 and ABCG2 variants are likely to exhibit clinical implications in predicting the presence of adverse reactions to gefitinib.
Collapse
Affiliation(s)
- Mariana Vieira Morau
- Department of Pharmacology, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas 13083-888, SP, Brazil; (M.V.M.); (C.S.S.)
| | - Cecília Souto Seguin
- Department of Pharmacology, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas 13083-888, SP, Brazil; (M.V.M.); (C.S.S.)
| | - Marília Berlofa Visacri
- Department of Pharmacy, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Eder de Carvalho Pincinato
- Department of Clinical Pathology, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas 13083-888, SP, Brazil;
| | - Patricia Moriel
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas 13083-859, SP, Brazil
| |
Collapse
|
3
|
Aryal S, Park S, Park H, Park C, Kim WC, Thakur D, Won YJ, Key J. Clinical Trials for Oral, Inhaled and Intravenous Drug Delivery System for Lung Cancer and Emerging Nanomedicine-Based Approaches. Int J Nanomedicine 2023; 18:7865-7888. [PMID: 38146467 PMCID: PMC10749572 DOI: 10.2147/ijn.s432839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/19/2023] [Indexed: 12/27/2023] Open
Abstract
Lung cancer is one of the most common malignant tumors worldwide and is characterized by high morbidity and mortality rates and a poor prognosis. It is the leading cause of cancer-related death in the United States and worldwide. Most patients with lung cancer are treated with chemotherapy, radiotherapy, or surgery; however, effective treatment options remain limited. In this review, we aim to provide an overview of clinical trials, ranging from Phase I to III, conducted on drug delivery systems for lung cancer treatment. The trials included oral, inhaled, and intravenous administration of therapeutics. Furthermore, the study also talks about the evolving paradigm of targeted therapy and immunotherapy providing promising directions for personalized treatment. In addition, we summarize the best results and limitations of these drug delivery systems and discuss the potential capacity of nanomedicine.
Collapse
Affiliation(s)
- Susmita Aryal
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| | - Sanghyo Park
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| | - Hyungkyu Park
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| | - Chaewon Park
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| | - Woo Cheol Kim
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| | - Deepika Thakur
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| | - Young-Joo Won
- Division of Health Administration, College of Software Digital Healthcare Convergence, Yonsei University, Wonju, Gangwon State, 26493, Korea
| | - Jaehong Key
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon Province, 26493, Korea
| |
Collapse
|
4
|
Joshua JM, KD S, K P, Vijayan M. Crizotinib, an Effective Agent in ROS1-Rearranged Adenocarcinoma of Lungs: A Case Report. CLINICAL MEDICINE INSIGHTS-CASE REPORTS 2018; 11:1179547617749615. [PMID: 29371790 PMCID: PMC5772496 DOI: 10.1177/1179547617749615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/29/2017] [Indexed: 12/22/2022]
Abstract
Introduction: ROS1 rearrangement has recently emerged as a new molecular subtype in non–small-cell lung cancer (NSCLC) and is predominantly found in lung adenocarcinoma compared with other oncogenes such as EGFR, KRAS, or ALK. It has been identified in only 1% to 2% of NSCLC cases. Case Report: We report a case of 52-year-old man (nonsmoker) with a medical history of allergic rhinitis and bronchial asthma. Histopathologic examination of bronchoscopic-guided biopsy showed adenocarcinoma histology on September 2015. After 2 months, he developed left-sided pneumonia for which he was treated with multiple intravenous antibiotics. In the meantime, fiberoptic bronchoscopy was done which revealed purulent secretion from right upper lobe and narrowed opening of right middle lobe. His cancer symptoms got worsened and bronchial biopsy showed EGFR mutation negative. For further diagnosis, fluorescent in situ hybridization test was done which showed ROS1 mutation positive. By then, the patient was started with crizotinib 250 mg twice daily for ROS1 mutation in July 2016. Later, patient appears to benefit from treatment with crizotinib. X-ray report and positron emission tomographic-computed tomographic scan revealed that the patient was overall better with clear chest and well tolerated with the therapy. Crizotinib was approved on March 11, 2016 by Food and Drug Administration for the treatment of patients with ROS1-positive NSCLC. Conclusions: In this report, crizotinib showed marked antitumor activity in patients with advanced ROS1 rearrangement, a third molecular subgroup of NSCLC.
Collapse
Affiliation(s)
- Julie Mariam Joshua
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Salima KD
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Pavithran K
- Department of Medical Oncology and Hematology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Meenu Vijayan
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, India
- Meenu Vijayan, Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi 682041, India.
| |
Collapse
|
5
|
Kwon T, Rho JK, Lee JC, Park YH, Shin HJ, Cho S, Kang YK, Kim BY, Yoon DY, Yu DY. An important role for peroxiredoxin II in survival of A549 lung cancer cells resistant to gefitinib. Exp Mol Med 2015; 47:e165. [PMID: 26021759 PMCID: PMC4454996 DOI: 10.1038/emm.2015.24] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/22/2014] [Accepted: 01/19/2015] [Indexed: 12/27/2022] Open
Abstract
Redox adaptation is an important concept that explains the mechanisms by which cancer cells survive under persistent endogenous oxidative stress and become resistant to certain anticancer agents. To investigate this concept, we determined the expression levels of peroxiredoxins (Prxs), antioxidant enzymes in drug-resistant non-small cell lung carcinoma cells. Prx II was remarkably increased only in A549/GR (gefitinib-resistant) cells compared with A549 cells, consistent with methylation/demethylation. Prx II was highly methylated in the A549 cells but was demethylated in the A549/GR cells. The elevated expression of Prx II resulted in the downregulation of reactive oxygen species (ROS) and cell death and upregulation of cell cycle progression in the A549/GR cells. When Prx II mRNA in the A549/GR cells was knocked down, the levels of ROS and apoptosis were significantly recovered to the levels of the controls. In addition, signaling molecules involved in apoptosis were increased in the A549/GR-shPrx II cells. There was no difference in the expression of MAPK/ERK between the A549/GR cells and A549/GR-shPrx II cells, but the phosphorylation of JNK was increased in the A549/GR cells and was markedly decreased in the A549/GR-shPrx II cells. Colony number and tumor growth were significantly decreased in the A549/GR-shPrx II cells compared with the A549/GR cells. Our findings suggest that Prx II has an important role in cancer cell survival via the modulation of signaling molecules involved in apoptosis and the phosphorylation of JNK by the downregulation of ROS levels in A549/GR cells.
Collapse
Affiliation(s)
- Taeho Kwon
- 1] Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea [2] Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| | - Jin Kyung Rho
- Asan Institute for Life Sciences, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea
| | - Jae Cheol Lee
- Asan Institute for Life Sciences, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Korea
| | - Young-Ho Park
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Hye-Jun Shin
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Sunwha Cho
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Bo-Yeon Kim
- World Class Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Chungbuk, Korea
| | - Do-Young Yoon
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| | - Dae-Yeul Yu
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| |
Collapse
|
6
|
Wang SY, Tsai CM, Lin CC. Relationship of Cytokines to Symptom Distress and Symptom Clusters Among Non-small-cell Lung Cancer Patients Receiving Gefitinib Treatment: A Pilot Study. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.jecm.2014.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
7
|
Wang SY, Tsai CM, Lin CC. Changes in symptom severity in Taiwanese lung cancer patients after gefitinib treatment: a pilot study. Int J Palliat Nurs 2014; 20:135-42. [PMID: 24675540 DOI: 10.12968/ijpn.2014.20.3.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIM The purpose of this study was to investigate symptom severity in advanced non-small cell lung cancer patients prior to gefitinib treatment and at 1-, 3- and 6-month intervals after starting treatment. METHODOLOGY Fifty seven patients completed the Taiwanese version of the M.D. Anderson Symptom Inventory. The data were analysed using descriptive statistics, the Friedman non-parametric test, and Pearson correlation coefficients. RESULTS Symptoms of nausea, difficulty remembering, lack of appetite, sadness, and vomiting increased at 1 month after treatment started, pain and shortness of breath increased at 3 months, and disturbed sleep, drowsiness, and numbness increased after 6 months. Fatigue and dry mouth increased at 3 months after treatment started and then decreased. Only distress decreased throughout the course of treatment. CONCLUSION The findings may lead to the development of better clinical guidelines and improved information for patients on when to expect the greatest impact from their symptoms during the course of treatment.
Collapse
Affiliation(s)
- Shu-Yi Wang
- Associate Professor, Regis University, Colorado, USA
| | - Chun-Ming Tsai
- Medical Doctor, Chest Department, Taipei Veterans General Hospital and School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Chin Lin
- Professor and Dean, College of Nursing, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|