1
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Beretta GL, Alampi D, Corno C, Carenini N, Corna E, Perego P. KiSS-1 Modulation by Epigenetic Agents Improves the Cisplatin Sensitivity of Lung Cancer Cells. Int J Mol Sci 2024; 25:5048. [PMID: 38732265 PMCID: PMC11084743 DOI: 10.3390/ijms25095048] [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: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024] Open
Abstract
Epigenetic alterations my play a role in the aggressive behavior of Non-Small Cell Lung Cancer (NSCLC). Treatment with the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA, vorinostat) has been reported to interfere with the proliferative and invasive potential of NSCLC cells. In addition, the DNA methyltransferase inhibitor azacytidine (AZA, vidaza) can modulate the levels of the metastasis suppressor KiSS-1. Thus, since cisplatin is still clinically available for NSCLC therapy, the aim of this study was to evaluate drug combinations between cisplatin and SAHA as well as AZA using cisplatin-sensitive H460 and -resistant H460/Pt NSCLC cells in relation to KiSS-1 modulation. An analysis of drug interaction according to the Combination-Index values indicated a more marked synergistic effect when the exposure to SAHA or AZA preceded cisplatin treatment with respect to a simultaneous schedule. A modulation of proteins involved in apoptosis (p53, Bax) was found in both sensitive and resistant cells, and compared to the treatment with epigenetic agents alone, the combination of cisplatin and SAHA or AZA increased apoptosis induction. The epigenetic treatments, both as single agents and in combination, increased the release of KiSS-1. Finally, the exposure of cisplatin-sensitive and -resistant cells to the kisspeptin KP10 enhanced cisplatin induced cell death. The efficacy of the combination of SAHA and cisplatin was tested in vivo after subcutaneous inoculum of parental and resistant cells in immunodeficient mice. A significant tumor volume inhibition was found when mice bearing advanced tumors were treated with the combination of SAHA and cisplatin according to the best schedule identified in cellular studies. These results, together with the available literature, support that epigenetic drugs are amenable for the combination treatment of NSCLC, including patients bearing cisplatin-resistant tumors.
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Affiliation(s)
- Giovanni Luca Beretta
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; (D.A.); (C.C.); (N.C.); (E.C.)
| | | | | | | | | | - Paola Perego
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; (D.A.); (C.C.); (N.C.); (E.C.)
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2
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Todesca LM, Gerke M, Bulk EE, Bachmann M, Rudersdorf A, Antonuzzo L, Pillozzi S, Düfer M, Szabo I, Schwab A. Targeting K Ca3.1 channels to overcome erlotinib resistance in non-small cell lung cancer cells. Cell Death Discov 2024; 10:2. [PMID: 38177097 PMCID: PMC10767088 DOI: 10.1038/s41420-023-01776-5] [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] [Received: 09/26/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024] Open
Abstract
Almost all non-small cell lung cancer (NSCLC) patients initially responding to EGFR tyrosine kinase inhibitors (TKIs) develop acquired resistance. Since KCa3.1 channels, expressed in mitochondria and plasma membrane, regulate similar behavioral traits of NSCLC cells as EGFR, we hypothesized that their blockade contributes to overcoming EGFR-TKI resistance. Meta-analysis of microarray data revealed that KCa3.1 channel expression in erlotinib-resistant NSCLC cells correlates with that of genes of integrin and apoptosis pathways. Using erlotinib-sensitive and -resistant NSCLC cells we monitored the role of mitochondrial KCa3.1 channels in integrin signaling by studying cell-matrix adhesion with single-cell force spectroscopy. Apoptosis was quantified with fluorescence-based assays. The function of mitochondrial KCa3.1 channels in these processes was assessed by measuring the mitochondrial membrane potential and by quantifying ROS production. Functional assays were supplemented by biochemical analyses. We show that KCa3.1 channel inhibition with senicapoc in erlotinib-resistant NSCLC cells increases cell adhesion by increasing β1-integrin expression, that in turn depends on mitochondrial ROS release. Increased adhesion impairs migration of NSCLC cells in a 3D matrix. At the same time, the senicapoc-dependent ROS production induces cytochrome C release and triggers apoptosis of erlotinib-resistant NSCLC cells. Thus, KCa3.1 channel blockade overcomes EGFR-TKI resistance by inhibiting NSCLC motility and inducing apoptosis.
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Affiliation(s)
| | - Matthias Gerke
- Institute of Physiology II, University of Münster, Münster, Germany
| | - Emma Etmar Bulk
- Institute of Physiology II, University of Münster, Münster, Germany
| | | | - Alisa Rudersdorf
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Lorenzo Antonuzzo
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Serena Pillozzi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Martina Düfer
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Ildiko Szabo
- Department of Biology, University of Padova, Padua, Italy
| | - Albrecht Schwab
- Institute of Physiology II, University of Münster, Münster, Germany
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3
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Deng Q, Du Y, Wang Z, Chen Y, Wang J, Liang H, Zhang D. Identification and validation of a DNA methylation-driven gene-based prognostic model for clear cell renal cell carcinoma. BMC Genomics 2023; 24:307. [PMID: 37286941 DOI: 10.1186/s12864-023-09416-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a malignant tumor with heterogeneous morphology and poor prognosis. This study aimed to establish a DNA methylation (DNAm)-driven gene-based prognostic model for ccRCC. METHODS Reduced representation bisulfite sequencing (RRBS) was performed on the DNA extracts from ccRCC patients. We analyzed the RRBS data from 10 pairs of patient samples to screen the candidate CpG sites, then trained and validated an 18-CpG site model, and integrated the clinical characters to establish a Nomogram model for the prognosis or risk evaluation of ccRCC. RESULTS We identified 2261 DMRs in the promoter region. After DMR selection, 578 candidates were screened, and was correspondence with 408 CpG dinucleotides in the 450 K array. We collected the DNAm profiles of 478 ccRCC samples from TCGA dataset. Using the training set with 319 samples, a prognostic panel of 18 CpGs was determined by univariate Cox regression, LASSO regression, and multivariate Cox proportional hazards regression analyses. We constructed a prognostic model by combining the clinical signatures. In the test set (159 samples) and whole set (478 samples), the Kaplan-Meier plot showed significant differences; and the ROC curve and survival analyses showed AUC greater than 0.7. The Nomogram integrated with clinicopathological characters and methylation risk score had better performance, and the decision curve analyses also showed a beneficial effect. CONCLUSIONS This work provides insight into the role of hypermethylation in ccRCC. The targets identified might serve as biomarkers for early ccRCC diagnosis and prognosis biomarkers for ccRCC. We believe our findings have implications for better risk stratification and personalized management of this disease.
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Affiliation(s)
- Qiong Deng
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, 518109, China
- College of Basic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Ye Du
- Central Laboratory, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, 518109, China
| | - Zhu Wang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, 518109, China
| | - Yeda Chen
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, 518109, China
| | - Jieyan Wang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, 518109, China
| | - Hui Liang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, 518109, China
| | - Du Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No 7, Pengfei Road, Dapeng New District, Shenzhen, 518120, China.
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4
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Thale I, Maskri S, Grey L, Todesca LM, Budde T, Maisuls I, Strassert CA, Koch O, Schwab A, Wünsch B. Imaging of K Ca 3.1 Channels in Tumor Cells with PET and Small-Molecule Fluorescent Probes. ChemMedChem 2023; 18:e202200551. [PMID: 36315933 PMCID: PMC10098740 DOI: 10.1002/cmdc.202200551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/31/2022] [Indexed: 01/20/2023]
Abstract
The Ca2+ activated K+ channel KCa 3.1 is overexpressed in several human tumor cell lines, e. g. clear cell renal carcinoma, prostate cancer, non-small cell lung cancer. Highly aggressive cancer cells use this ion channel for key processes of the metastatic cascade such as migration, extravasation and invasion. Therefore, small molecules, which are able to image this KCa 3.1 channel in vitro and in vivo represent valuable diagnostic and prognostic tool compounds. The [18 F]fluoroethyltriazolyl substituted senicapoc was used as positron emission tomography (PET) tracer and showed promising properties for imaging of KCa 3.1 channels in lung adenocarcinoma cells in mice. The novel senicapoc BODIPY conjugates with two F-atoms (9 a) and with a F-atom and a methoxy moiety (9 b) at the B-atom led to the characteristic punctate staining pattern resulting from labeling of single KCa 3.1 channels in A549-3R cells. This punctate pattern was completely removed by preincubation with an excess of senicapoc confirming the high specificity of KCa 3.1 labeling. Due to the methoxy moiety at the B-atom and the additional oxyethylene unit in the spacer, 9 b exhibits higher polarity, which improves solubility and handling without reduction of fluorescence quantum yield. Docking studies using a cryo-electron microscopy (EM) structure of the KCa 3.1 channel confirmed the interaction of 9 a and 9 b with a binding pocket in the channel pore.
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Affiliation(s)
- Insa Thale
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, Corrensstraße 48, 48149, Münster, Germany
| | - Sarah Maskri
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, Corrensstraße 48, 48149, Münster, Germany
| | - Lucie Grey
- Westfälische Wilhelms-Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, Corrensstraße 48, 48149, Münster, Germany
| | - Luca Matteo Todesca
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Universitätsklinikum Münster, Institute of Physiology II, Robert-Koch-Straße 27b, 48149, Münster, Germany
| | - Thomas Budde
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Universitätsklinikum Münster, Institute of Physiology I, Robert-Koch-Straße 27a, 48149, Münster, Germany
| | - Ivan Maisuls
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie CiMIC, SoN, Corrensstraße 28, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, CeNTech, Heisenbergstraße 11, 48149, Münster, Germany
| | - Cristian A Strassert
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie CiMIC, SoN, Corrensstraße 28, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, CeNTech, Heisenbergstraße 11, 48149, Münster, Germany
| | - Oliver Koch
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, Corrensstraße 48, 48149, Münster, Germany
| | - Albrecht Schwab
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Universitätsklinikum Münster, Institute of Physiology II, Robert-Koch-Straße 27b, 48149, Münster, Germany
| | - Bernhard Wünsch
- Westfälische Wilhelms-Universität Münster, GRK 2515, Chemical biology of ion channels (Chembion), Corrensstraße 48, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, Corrensstraße 48, 48149, Münster, Germany
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5
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Konken CP, Heßling K, Thale I, Schelhaas S, Dabel J, Maskri S, Bulk E, Budde T, Koch O, Schwab A, Schäfers M, Wünsch B. Imaging of the calcium activated potassium channel 3.1 (K Ca 3.1) in vivo using a senicapoc-derived positron emission tomography tracer. Arch Pharm (Weinheim) 2022; 355:e2200388. [PMID: 36161669 DOI: 10.1002/ardp.202200388] [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: 07/22/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022]
Abstract
The calcium-activated potassium channel 3.1 (KCa 3.1) is overexpressed in many tumor entities and has predictive power concerning disease progression and outcome. Imaging of the KCa 3.1 channel in vivo using a radiotracer for positron emission tomography (PET) could therefore establish a potentially powerful diagnostic tool. Senicapoc shows high affinity and excellent selectivity toward the KCa 3.1 channel. We have successfully pursued the synthesis of the 18 F-labeled derivative [18 F]3 of senicapoc using the prosthetic group approach with 1-azido-2-[18 F]fluoroethane ([18 F]6) in a "click" reaction. The biological activity of the new PET tracer was evaluated in vitro and in vivo. Inhibition of the KCa 3.1 channel by 3 was demonstrated by patch clamp experiments and the binding pose was analyzed by docking studies. In mouse and human serum, [18 F]3 was stable for at least one half-life of [18 F]fluorine. Biodistribution experiments in wild-type mice were promising, showing rapid and predominantly renal excretion. An in vivo study using A549-based tumor-bearing mice was performed. The tumor signal could be delineated and image analysis showed a tumor-to-muscle ratio of 1.47 ± 0.24. The approach using 1-azido-2-[18 F]fluoroethane seems to be a good general strategy to achieve triarylacetamide-based fluorinated PET tracers for imaging of the KCa 3.1 channel in vivo.
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Affiliation(s)
- Christian P Konken
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany
| | - Kathrin Heßling
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Münster, Germany
| | - Insa Thale
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sonja Schelhaas
- European Institute for Molecular Imaging (EIMI), Westphalian Wilhelms-University Münster, Münster, Germany.,Cells-in-Motion Interfaculty Center, Westphalian Wilhelms-University Münster, Münster, Germany
| | - Jennifer Dabel
- European Institute for Molecular Imaging (EIMI), Westphalian Wilhelms-University Münster, Münster, Germany
| | - Sarah Maskri
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Etmar Bulk
- Institute for Physiology II, University Hospital Münster, Münster, Germany
| | - Thomas Budde
- GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany.,Institute for Physiology I, University Hospital Münster, Münster, Germany
| | - Oliver Koch
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Albrecht Schwab
- GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany.,Institute for Physiology II, University Hospital Münster, Münster, Germany
| | - Michael Schäfers
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany.,European Institute for Molecular Imaging (EIMI), Westphalian Wilhelms-University Münster, Münster, Germany.,Cells-in-Motion Interfaculty Center, Westphalian Wilhelms-University Münster, Münster, Germany
| | - Bernhard Wünsch
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany.,Cells-in-Motion Interfaculty Center, Westphalian Wilhelms-University Münster, Münster, Germany
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6
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Bulk E, Todesca LM, Bachmann M, Szabo I, Rieke M, Schwab A. Functional expression of mitochondrial K Ca3.1 channels in non-small cell lung cancer cells. Pflugers Arch 2022; 474:1147-1157. [PMID: 36152073 PMCID: PMC9560933 DOI: 10.1007/s00424-022-02748-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/21/2022] [Accepted: 09/05/2022] [Indexed: 12/01/2022]
Abstract
Lung cancer is one of the leading causes of cancer-related deaths worldwide. The Ca2+-activated K+ channel KCa3.1 contributes to the progression of non-small cell lung cancer (NSCLC). Recently, KCa3.1 channels were found in the inner membrane of mitochondria in different cancer cells. Mitochondria are the main sources for the generation of reactive oxygen species (ROS) that affect the progression of cancer cells. Here, we combined Western blotting, immunofluorescence, and fluorescent live-cell imaging to investigate the expression and function of KCa3.1 channels in the mitochondria of NSCLC cells. Western blotting revealed KCa3.1 expression in mitochondrial lysates from different NSCLC cells. Using immunofluorescence, we demonstrate a co-localization of KCa3.1 channels with mitochondria of NSCLC cells. Measurements of the mitochondrial membrane potential with TMRM reveal a hyperpolarization following the inhibition of KCa3.1 channels with the cell-permeable blocker senicapoc. This is not the case when cells are treated with the cell-impermeable peptidic toxin maurotoxin. The hyperpolarization of the mitochondrial membrane potential is accompanied by an increased generation of ROS in NSCLC cells. Collectively, our results provide firm evidence for the functional expression of KCa3.1 channels in the inner membrane of mitochondria of NSCLC cells.
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Affiliation(s)
- Etmar Bulk
- Institute of Physiology II, University of Münster, 48149, Münster, Germany.
| | | | | | - Ildiko Szabo
- Department of Biology, University of Padova, Padua, Italy
| | - Marius Rieke
- Institute of Physiology II, University of Münster, 48149, Münster, Germany
| | - Albrecht Schwab
- Institute of Physiology II, University of Münster, 48149, Münster, Germany
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7
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Yu Q, Chen J, Fu W, Muhammad KG, Li Y, Liu W, Xu L, Dong H, Wang D, Liu J, Lu Y, Chen X. Smartphone-Based Platforms for Clinical Detections in Lung-Cancer-Related Exhaled Breath Biomarkers: A Review. BIOSENSORS 2022; 12:bios12040223. [PMID: 35448283 PMCID: PMC9028493 DOI: 10.3390/bios12040223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 12/24/2022]
Abstract
Lung cancer has been studied for decades because of its high morbidity and high mortality. Traditional methods involving bronchoscopy and needle biopsy are invasive and expensive, which makes patients suffer more risks and costs. Various noninvasive lung cancer markers, such as medical imaging indices, volatile organic compounds (VOCs), and exhaled breath condensates (EBCs), have been discovered for application in screening, diagnosis, and prognosis. However, the detection of markers still relies on bulky and professional instruments, which are limited to training personnel or laboratories. This seriously hinders population screening for early diagnosis of lung cancer. Advanced smartphones integrated with powerful applications can provide easy operation and real-time monitoring for healthcare, which demonstrates tremendous application scenarios in the biomedical analysis region from medical institutions or laboratories to personalized medicine. In this review, we propose an overview of lung-cancer-related noninvasive markers from exhaled breath, focusing on the novel development of smartphone-based platforms for the detection of these biomarkers. Lastly, we discuss the current limitations and potential solutions.
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Affiliation(s)
- Qiwen Yu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Jing Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310051, China;
| | - Wei Fu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Kanhar Ghulam Muhammad
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Yi Li
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Wenxin Liu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Linxin Xu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Hao Dong
- Research Center for Sensing Materials and Devices, Zhejiang Lab, Hangzhou 311100, China; (H.D.); (D.W.)
| | - Di Wang
- Research Center for Sensing Materials and Devices, Zhejiang Lab, Hangzhou 311100, China; (H.D.); (D.W.)
| | - Jun Liu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
| | - Yanli Lu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
- Correspondence: (Y.L.); (X.C.)
| | - Xing Chen
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China; (Q.Y.); (W.F.); (K.G.M.); (Y.L.); (W.L.); (L.X.); (J.L.)
- Correspondence: (Y.L.); (X.C.)
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8
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Feng H, Conneely K, Wu H. Differential Methylation Analysis for Bisulfite Sequencing (BS-Seq) Data. Methods Mol Biol 2022; 2432:211-226. [PMID: 35505218 DOI: 10.1007/978-1-0716-1994-0_16] [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: 06/14/2023]
Abstract
Bisulfite sequencing (BS-seq) technology has enabled the detection and measurement of DNA methylation at the single-nucleotide level. A fundamental question in functional epigenomics research is whether DNA methylation varies under different biological contexts. Thus, identifying differentially methylated loci/regions (DML/DMRs) is a key task in BS-seq data analysis. Here we describe detailed procedures to perform differential methylation analyses for BS-seq using the Bioconductor package DSS. The analysis scheme in this chapter will guide researchers through differential methylation analyses by providing step-by-step instructions for analytical tools.
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Affiliation(s)
- Hao Feng
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Karen Conneely
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA
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9
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Stefanello ST, Luchtefeld I, Liashkovich I, Pethö Z, Azzam I, Bulk E, Rosso G, Döhlinger L, Hesse B, Oeckinghaus A, Shahin V. Impact of the Nuclear Envelope on Malignant Transformation, Motility, and Survival of Lung Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102757. [PMID: 34658143 PMCID: PMC8596107 DOI: 10.1002/advs.202102757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Indexed: 05/08/2023]
Abstract
Nuclear pore complexes (NPCs) selectively mediate all nucleocytoplasmic transport and engage in fundamental cell-physiological processes. It is hypothesized that NPCs are critical for malignant transformation and survival of lung cancer cells, and test the hypothesis in lowly and highly metastatic non-small human lung cancer cells (NSCLCs). It is shown that malignant transformation is paralleled by an increased NPCs density, and a balanced pathological weakening of the physiological stringency of the NPC barrier. Pharmacological interference using barrier-breaking compounds collapses the stringency. Concomitantly, it induces drastic overall structural changes of NSCLCs, terminating their migration. Moreover, the degree of malignancy is found to be paralleled by substantially decreased lamin A/C levels. The latter provides crucial structural and mechanical stability to the nucleus, and interacts with NPCs, cytoskeleton, and nucleoskeleton for cell maintenance, survival, and motility. The recent study reveals the physiological importance of the NPC barrier stringency for mechanical and structural resilience of normal cell nuclei. Hence, reduced lamin A/C levels in conjunction with controlled pathological weakening of the NPC barrier stringency may facilitate deformability of NSCLCs during the metastasis steps. Modulation of the NPC barrier presents a potential strategy for suppressing the malignant phenotype or enhancing the effectiveness of currently existing chemotherapeutics.
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Affiliation(s)
- Sílvio Terra Stefanello
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Isabelle Luchtefeld
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Ivan Liashkovich
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Zoltan Pethö
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Ihab Azzam
- Institute of Immunology, University of Münster, Röntgen-Str. 21, Münster, 48149, Germany
| | - Etmar Bulk
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Gonzalo Rosso
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Lilly Döhlinger
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Bettina Hesse
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Andrea Oeckinghaus
- Institute of Molecular Tumor Biology, University of Münster, Robert-Koch-Str. 43, Münster, 48149, Germany
| | - Victor Shahin
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
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10
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K Ca channel blockers increase effectiveness of the EGF receptor TK inhibitor erlotinib in non-small cell lung cancer cells (A549). Sci Rep 2021; 11:18330. [PMID: 34526525 PMCID: PMC8443639 DOI: 10.1038/s41598-021-97406-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/18/2021] [Indexed: 11/08/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) has a poor prognosis with a 5 year survival rate of only ~ 10%. Important driver mutations underlying NSCLC affect the epidermal growth factor receptor (EGFR) causing the constitutive activation of its tyrosine kinase domain. There are efficient EGFR tyrosine kinase inhibitors (TKIs), but patients develop inevitably a resistance against these drugs. On the other hand, KCa3.1 channels contribute to NSCLC progression so that elevated KCa3.1 expression is a strong predictor of poor NSCLC patient prognosis. The present study tests whether blocking KCa3.1 channels increases the sensitivity of NSCLC cells towards the EGFR TKI erlotinib and overcomes drug resistance. mRNA expression of KCa3.1 channels in erlotinib-sensitive and -resistant NSCLC cells was analysed in datasets from Gene expression omnibus (GEO) and ArrayExpress. We assessed proliferation and migration of NSCLC cells. These (live cell-imaging) experiments were complemented by patch clamp experiments and Western blot analyses. We identified three out of four datasets comparing erlotinib-sensitive and -resistant NSCLC cells which revealed an altered expression of KCa3.1 mRNA in erlotinib-resistant NSCLC cells. Therefore, we evaluated the combined effect of erlotinib and the KCa3.1 channel inhibition with sencapoc. Erlotinib elicits a dose-dependent inhibition of migration and proliferation of NSCLC cells. The simultaneous application of the KCa3.1 channel blocker senicapoc increases the sensitivity towards a low dose of erlotinib (300 nmol/L) which by itself has no effect on migration and proliferation. Partial erlotinib resistance can be overcome by KCa3.1 channel blockade. The sensitivity towards erlotinib as well as the potentiating effect of KCa3.1 blockade is further increased by mimicking hypoxia. Our results suggest that KCa3.1 channel blockade may constitute a therapeutic concept for treating NSCLC and overcome EGFR TKI resistance. We propose that this is due to complementary mechanisms of action of both blockers.
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11
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Deep enzymology studies on DNA methyltransferases reveal novel connections between flanking sequences and enzyme activity. J Mol Biol 2021; 433:167186. [PMID: 34375615 DOI: 10.1016/j.jmb.2021.167186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
DNA interacting enzymes recognize their target sequences embedded in variable flanking sequence context. The influence of flanking sequences on enzymatic activities of DNA methyltransferases (DNMTs) can be systematically studied with "deep enzymology" approaches using pools of double-stranded DNA substrates, which contain target sites in random flanking sequence context. After incubation with DNMTs and bisulfite conversion, the methylation states and flanking sequences of individual DNA molecules are determined by NGS. Deep enzymology studies with different human and mouse DNMTs revealed strong influences of flanking sequences on the CpG and non-CpG methylation activity and structure of DNMT-DNA complexes. Differences in flanking sequence preferences of DNMT3A and DNMT3B were shown to be related to the prominent role of DNMT3B in the methylation of human SATII repeat elements. Mutational studies in DNMT3B discovered alternative interaction networks between the enzyme and the DNA leading to a partial equalization of the effects of different flanking sequences. Structural studies in DNMT1 revealed striking correlations between enzymatic activities and flanking sequence dependent conformational changes upon DNA binding. Correlation of the biochemical data with cellular methylation patterns demonstrated that flanking sequence preferences are an important parameter that influences genomic DNA methylation patterns together with other mechanisms targeting DNMTs to genomic sites.
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12
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Liang Y, Lei Y, Du M, Liang M, Liu Z, Li X, Gao Y. The increased expression and aberrant methylation of SHC1 in non-small cell lung cancer: Integrative analysis of clinical and bioinformatics databases. J Cell Mol Med 2021; 25:7039-7051. [PMID: 34117717 PMCID: PMC8278126 DOI: 10.1111/jcmm.16717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Despite the previous evidence showing that SHC adaptor protein 1 (SHC1) could encode three distinct isoforms (p46SHC, p52SHC and p66SHC) that function in different activities such as regulating life span and Ras activation, the precise underlying role of SHC1 in lung cancer also remains obscure. In this study, we firstly found that SHC1 expression was up‐regulated both in lung adenocarcinoma (LUAD) and in lung squamous cell carcinoma (LUSC) tissues. Furthermore, compared to patients with lower SHC1 expression, LUAD patients with higher expression of SHC1 had poorer overall survival (OS). Moreover, higher expression of SHC1 was also associated with worse OS in patients with stages 1 and 2 but not stage 3 lung cancer. Significantly, the analysis showed that SHC1 methylation level was associated with OS in lung cancer patients. It seemed that the methylation level at specific probes within SHC1 showed negative correlations with SHC1 expression both in LUAD and in LUSC tissues. The LUAD and LUSC patients with hypermethylated SHC1 at cg12473916 and cg19356022 probes had a longer OS. Therefore, it is reasonable to conclude that SHC1 has a potential clinical significance in LUAD and LUSC patients.
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Affiliation(s)
- Yicheng Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangyang Lei
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minjun Du
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zixu Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingkai Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yushun Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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13
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Brömmel K, Maskri S, Bulk E, Pethő Z, Rieke M, Budde T, Koch O, Schwab A, Wünsch B. Co-staining of K Ca 3.1 Channels in NSCLC Cells with a Small-Molecule Fluorescent Probe and Antibody-Based Indirect Immunofluorescence. ChemMedChem 2020; 15:2462-2469. [PMID: 33043595 PMCID: PMC7756743 DOI: 10.1002/cmdc.202000652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/21/2020] [Indexed: 01/01/2023]
Abstract
The Ca2+ activated potassium channel 3.1 (KCa 3.1) is involved in critical steps of the metastatic cascade, such as proliferation, migration, invasion and extravasation. Therefore, a fast and efficient protocol for imaging of KCa 3.1 channels was envisaged. The novel fluorescently labeled small molecule imaging probes 1 and 2 were synthesized by connecting a dimethylpyrrole-based BODIPY dye with a derivative of the KCa 3.1 channel inhibitor senicapoc via linkers of different length. Patch-clamp experiments revealed the inhibition of KCa 3.1 channels by the probes confirming interaction with the channel. Both probes 1 and 2 were able to stain KCa 3.1 channels in non-small-cell lung cancer (NSCLC) cells following a simple, fast and efficient protocol. Pre-incubation with unlabeled senicapoc removed the punctate staining pattern showing the specificity of the new probes 1 and 2. Staining of the channel with the fluorescently labeled senicapoc derivatives 1 or 2 or with antibody-based indirect immunofluorescence yielded identical or very similar densities of stained KCa 3.1 channels. However, co-staining using both methods did not lead to the expected overlapping punctate staining pattern. This observation was explained by docking studies showing that the antibody used for indirect immunofluorescence and the probes 1 and 2 label different channel populations. Whereas the antibody binds at the closed channel conformation, the probes 1 and 2 bind within the open channel.
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Affiliation(s)
- Kathrin Brömmel
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University MünsterCorrensstraße 4848149MünsterGermany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University MünsterWaldeyerstraße 1584149MünsterGermany
| | - Sarah Maskri
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University MünsterCorrensstraße 4848149MünsterGermany
| | - Etmar Bulk
- Institute for Physiology IIUniversity Hospital MünsterRobert-Koch-Straße 27b48149MünsterGermany
| | - Zoltan Pethő
- Institute for Physiology IIUniversity Hospital MünsterRobert-Koch-Straße 27b48149MünsterGermany
| | - Marius Rieke
- Institute for Physiology IIUniversity Hospital MünsterRobert-Koch-Straße 27b48149MünsterGermany
| | - Thomas Budde
- Institute for Physiology IUniversity Hospital MünsterRobert-Koch-Straße 27a48149MünsterGermany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University MünsterWaldeyerstraße 1584149MünsterGermany
| | - Oliver Koch
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University MünsterCorrensstraße 4848149MünsterGermany
| | - Albrecht Schwab
- Institute for Physiology IIUniversity Hospital MünsterRobert-Koch-Straße 27b48149MünsterGermany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University MünsterWaldeyerstraße 1584149MünsterGermany
| | - Bernhard Wünsch
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University MünsterCorrensstraße 4848149MünsterGermany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University MünsterWaldeyerstraße 1584149MünsterGermany
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14
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Halla-Aho V, Lähdesmäki H. LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation. Bioinformatics 2020; 36:4535-4543. [PMID: 32484876 PMCID: PMC7750928 DOI: 10.1093/bioinformatics/btaa539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 11/19/2022] Open
Abstract
Motivation DNA methylation is an important epigenetic modification, which has multiple functions. DNA methylation and its connections to diseases have been extensively studied in recent years. It is known that DNA methylation levels of neighboring cytosines are correlated and that differential DNA methylation typically occurs rather as regions instead of individual cytosine level. Results We have developed a generalized linear mixed model, LuxUS, that makes use of the correlation between neighboring cytosines to facilitate analysis of differential methylation. LuxUS implements a likelihood model for bisulfite sequencing data that accounts for experimental variation in underlying biochemistry. LuxUS can model both binary and continuous covariates, and mixed model formulation enables including replicate and cytosine random effects. Spatial correlation is included to the model through a cytosine random effect correlation structure. We show with simulation experiments that using the spatial correlation, we gain more power to the statistical testing of differential DNA methylation. Results with real bisulfite sequencing dataset show that LuxUS is able to detect biologically significant differentially methylated cytosines. Availability and implementation The tool is available at https://github.com/hallav/LuxUS. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Viivi Halla-Aho
- Department of Computer Science, Aalto University, FI-00076 Aalto, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, FI-00076 Aalto, Finland
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15
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DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation. Nat Commun 2020; 11:3723. [PMID: 32709850 PMCID: PMC7381644 DOI: 10.1038/s41467-020-17531-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023] Open
Abstract
DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.
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16
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Brömmel K, Maskri S, Maisuls I, Konken CP, Rieke M, Pethő Z, Strassert CA, Koch O, Schwab A, Wünsch B. Synthesis of Small‐Molecule Fluorescent Probes for the In Vitro Imaging of Calcium‐Activated Potassium Channel K
Ca
3.1. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kathrin Brömmel
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University Münster Corrensstraße 48 48149 Münster Germany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University Münster Waldeyerstraße 15 84149 Münster Germany
| | - Sarah Maskri
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University Münster Corrensstraße 48 48149 Münster Germany
| | - Ivan Maisuls
- Center for NanotechnologyCenter for Soft NanoscienceInstitute for Inorganic and Analytical ChemistryWestphalian Wilhelms-University Münster Heisenbergstraße 11 48149 Münster Germany
| | - Christian Paul Konken
- Department of Nuclear MedicineUniversity Hospital Münster Albert-Schweitzer-Campus 1, Building A1 48149 Münster Germany
| | - Marius Rieke
- Institute for Physiology IIUniversity Hospital Münster Robert-Koch-Straße 27b 48149 Münster Germany
| | - Zoltan Pethő
- Institute for Physiology IIUniversity Hospital Münster Robert-Koch-Straße 27b 48149 Münster Germany
| | - Cristian A. Strassert
- Center for NanotechnologyCenter for Soft NanoscienceInstitute for Inorganic and Analytical ChemistryWestphalian Wilhelms-University Münster Heisenbergstraße 11 48149 Münster Germany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University Münster Waldeyerstraße 15 84149 Münster Germany
| | - Oliver Koch
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University Münster Corrensstraße 48 48149 Münster Germany
| | - Albrecht Schwab
- Institute for Physiology IIUniversity Hospital Münster Robert-Koch-Straße 27b 48149 Münster Germany
| | - Bernhard Wünsch
- Institute for Pharmaceutical and Medicinal ChemistryWestphalian Wilhelms-University Münster Corrensstraße 48 48149 Münster Germany
- Cells-in-Motion Interfaculty CenterWestphalian Wilhelms-University Münster Waldeyerstraße 15 84149 Münster Germany
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17
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Brömmel K, Maskri S, Maisuls I, Konken CP, Rieke M, Pethő Z, Strassert CA, Koch O, Schwab A, Wünsch B. Synthesis of Small-Molecule Fluorescent Probes for the In Vitro Imaging of Calcium-Activated Potassium Channel K Ca 3.1. Angew Chem Int Ed Engl 2020; 59:8277-8284. [PMID: 32097518 PMCID: PMC7318252 DOI: 10.1002/anie.202001201] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/19/2020] [Indexed: 01/15/2023]
Abstract
Small-molecule probes for the in vitro imaging of KCa 3.1 channel-expressing cells were developed. Senicapoc, showing high affinity and selectivity for the KCa 3.1 channels, was chosen as the targeting component. BODIPY dyes 15-20 were synthesized and connected by a CuI -catalyzed azide-alkyne [3+2]cycloaddition with propargyl ether senicapoc derivative 8, yielding fluorescently labeled ligands 21-26. The dimethylpyrrole-based imaging probes 25 and 26 allow staining of KCa 3.1 channels in NSCLC cells. The specificity was shown by removing the punctate staining pattern by pre-incubation with senicapoc. The density of KCa 3.1 channels detected with 25 and by immunostaining was identical. The punctate structure of the labeled channels could also be observed in living cells. Molecular modeling showed binding of the senicapoc-targeting component towards the binding site within the ion channel and orientation of the linker with the dye along the inner surface of the ion channel.
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Affiliation(s)
- Kathrin Brömmel
- Institute for Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Corrensstraße 48, 48149, Münster, Germany
- Cells-in-Motion Interfaculty Center, Westphalian Wilhelms-University Münster, Waldeyerstraße 15, 84149, Münster, Germany
| | - Sarah Maskri
- Institute for Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Ivan Maisuls
- Center for Nanotechnology, Center for Soft Nanoscience, Institute for Inorganic and Analytical Chemistry, Westphalian Wilhelms-University Münster, Heisenbergstraße 11, 48149, Münster, Germany
| | - Christian Paul Konken
- Department of Nuclear Medicine, University Hospital Münster, Albert-Schweitzer-Campus 1, Building A1, 48149, Münster, Germany
| | - Marius Rieke
- Institute for Physiology II, University Hospital Münster, Robert-Koch-Straße 27b, 48149, Münster, Germany
| | - Zoltan Pethő
- Institute for Physiology II, University Hospital Münster, Robert-Koch-Straße 27b, 48149, Münster, Germany
| | - Cristian A Strassert
- Center for Nanotechnology, Center for Soft Nanoscience, Institute for Inorganic and Analytical Chemistry, Westphalian Wilhelms-University Münster, Heisenbergstraße 11, 48149, Münster, Germany
- Cells-in-Motion Interfaculty Center, Westphalian Wilhelms-University Münster, Waldeyerstraße 15, 84149, Münster, Germany
| | - Oliver Koch
- Institute for Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Albrecht Schwab
- Institute for Physiology II, University Hospital Münster, Robert-Koch-Straße 27b, 48149, Münster, Germany
| | - Bernhard Wünsch
- Institute for Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University Münster, Corrensstraße 48, 48149, Münster, Germany
- Cells-in-Motion Interfaculty Center, Westphalian Wilhelms-University Münster, Waldeyerstraße 15, 84149, Münster, Germany
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18
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Abstract
Bisulfite sequencing (BS-seq) technology measures DNA methylation at single nucleotide resolution. A key task in BS-seq data analysis is to identify differentially methylation (DM) under different conditions. Here we provide a tutorial for BS-seq DM analysis using Bioconductor package DSS. DSS uses a beta-binomial model to characterize the sequence counts from BS-seq, and implements rigorous statistical method for hypothesis testing. It provides flexible functionalities for a variety of DM analyses.
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19
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Quintanal-Villalonga Á, Molina-Pinelo S. Epigenetics of lung cancer: a translational perspective. Cell Oncol (Dordr) 2019; 42:739-756. [PMID: 31396859 DOI: 10.1007/s13402-019-00465-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lung cancer remains the most common cause of cancer-related death, with a 5-year survival rate of only 18%. In recent years, the development of targeted pharmacological agents and immunotherapies has substantially increased the survival of a subset of patients. However, most patients lack such efficacious therapy and are, thus, treated with classical chemotherapy with poor clinical outcomes. Therefore, novel therapeutic strategies are urgently needed. In recent years, the development of epigenetic assays and their application to cancer research have highlighted the relevance of epigenetic regulation in the initiation, development, progression and treatment of lung cancer. CONCLUSIONS A variety of epigenetic modifications do occur at different steps of lung cancer development, some of which are key to tumor progression. The rise of cutting-edge technologies such as single cell epigenomics is, and will continue to be, crucial for uncovering epigenetic events at a single cell resolution, leading to a better understanding of the biology underlying lung cancer development and to the design of novel therapeutic options. This approach has already led to the development of strategies involving single agents or combined agents targeting epigenetic modifiers, currently in clinical trials. Here, we will discuss the epigenetics of every step of lung cancer development, as well as the translation of these findings into clinical applications.
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Affiliation(s)
| | - Sonia Molina-Pinelo
- Unidad Clínica de Oncología Médica, Radioterapia y Radiofísica, Instituto de Biomedicina de Sevilla (IBIS) (HUVR, CSIC, Universidad de Sevilla), Avda. Manuel Siurot s/n, 41013, Seville, Spain. .,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.
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20
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Epigenetic Suppression of the T-box Subfamily 2 ( TBX2) in Human Non-Small Cell Lung Cancer. Int J Mol Sci 2019; 20:ijms20051159. [PMID: 30866410 PMCID: PMC6429281 DOI: 10.3390/ijms20051159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022] Open
Abstract
(1) The TBX2 subfamily of transcription factors (TBXs 2, 3, 4 and 5) are markedly down-regulated in human non-small cell lung cancer (NSCLC) and exert tumor suppressor effects in lung malignancy. Yet, mechanisms underlying suppressed expression of the TBX2 subfamily in NSCLC are elusive. Here, we interrogated probable epigenetic mechanisms in suppressed expression of the TBX2 subfamily in human NSCLC. (2) TBX2 subfamily gene expression and methylation levels in NSCLC and normal lung tissues were surveyed using publicly available RNA-sequence and genome-wide methylation datasets. Methylation β-values of the four genes were statistically compared between NSCLCs and normal lung tissues, correlated with gene expression levels, and interrogated with clinicopathological variables. Expression and methylation levels of TBXs were quantified in NSCLC cells using real-time PCR and methylation-specific PCR assays, respectively. Effects of the DNA methyltransferase inhibitor 5-azacytidine (Aza) on TBX2 subfamily expression were assessed in NSCLC cells. Impact of TBX2 subfamily expression on Aza-treated cells was evaluated by RNA interference. (3) All four TBXs were significantly hypermethylated in NSCLCs relative to normal lung tissues (p < 0.05). Methylation β-values of the genes, with exception of TBX2, were significantly inversely correlated with corresponding mRNA expression levels (p < 0.05). We found no statistically significant differences in hypermethylation levels of the TBX2 subfamily by clinicopathological features including stage and tobacco history. Expression levels of the TBX genes were overall suppressed in NSCLC cells relative to normal alveolar cells. Members of the subfamily were significantly hypermethylated in all tested NSCLC cell lines relative to normal alveolar cells. Treatment with Aza induced the expression of the TBX2 subfamily concomitant with NSCLC cell growth inhibition. Further, simultaneous knockdown of the four TBX genes markedly reduced anti-growth effects of Aza in NSCLC cells. (4) Our study sheds light on new epigenetic profiles in the molecular pathogenesis of human NSCLC.
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21
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Shahabi S, Kumaran V, Castillo J, Cong Z, Nandagopal G, Mullen DJ, Alvarado A, Correa MR, Saizan A, Goel R, Bhat A, Lynch SK, Zhou B, Borok Z, Marconett CN. LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response. Cancer Res 2019; 79:3050-3062. [PMID: 30796052 DOI: 10.1158/0008-5472.can-18-2034] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
Lung cancer is the leading cause of cancer-related death in the United States. Long noncoding RNAs (lncRNA) are a class of regulatory molecules whose role in lung carcinogenesis is poorly understood. In this study, we profiled lncRNA expression in lung adenocarcinoma (LUAD) cell lines, compared their expression with that of purified alveolar epithelial type II cells (the purported cell of origin for LUAD), cross-referenced these with lncRNAs altered in the primary human tumors, and interrogated for lncRNAs whose expression correlated with patient survival. We identified LINC00261, a lncRNA with unknown function in LUAD, adjacent to the pioneering transcription factor FOXA2. Loss of LINC00261 was observed in multiple tumor types, including liver, breast, and gastric cancer. Reintroduction of LINC00261 into human LUAD cell lines inhibited cell migration and slowed proliferation by inducing G2-M cell-cycle arrest, while upregulating DNA damage pathway genes and inducing phosphorylation-mediated activation of components of the DNA damage pathway. FOXA2 was able to induce LINC00261 expression, and the entire locus underwent hypermethylation in LUAD, leading to loss of expression. We have thus identified an epigenetically deregulated lncRNA, whose loss of expression in LUAD promotes the malignant phenotype and blocks activation of the DNA damage machinery, predisposing lung cells to cancer development. SIGNIFICANCE: These findings identify LINC00261 as a tumor suppressor that blocks cellular proliferation by activating the DNA damage response and suggest that epigenetic therapy to inhibit DNA methylation may enhance treatment of LUAD. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/12/3050/F1.large.jpg.See related commentary by Davalos and Esteller, p. 3028.
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Affiliation(s)
- Shandy Shahabi
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Vishaly Kumaran
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jonathan Castillo
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zhengmin Cong
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gopika Nandagopal
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Daniel J Mullen
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander Alvarado
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Michele Ramos Correa
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Autumn Saizan
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Riya Goel
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Amrita Bhat
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Sean K Lynch
- Department of Product Engineering, Division of Manufacturing Operations, MAXIM Integrated Products, Sunnyvale, California
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zea Borok
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Crystal N Marconett
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. .,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
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22
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Sarne V, Braunmueller S, Rakob L, Seeboeck R. The Relevance of Gender in Tumor-Influencing Epigenetic Traits. EPIGENOMES 2019; 3:epigenomes3010006. [PMID: 34991275 PMCID: PMC8594720 DOI: 10.3390/epigenomes3010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/20/2019] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
Tumorigenesis as well as the molecular orchestration of cancer progression are very complex mechanisms that comprise numerous elements of influence and regulation. Today, many of the major concepts are well described and a basic understanding of a tumor's fine-tuning is given. Throughout the last decade epigenetics has been featured in cancer research and it is now clear that the underlying mechanisms, especially DNA and histone modifications, are important regulators of carcinogenesis and tumor progression. Another key regulator, which is well known but has been neglected in scientific approaches as well as molecular diagnostics and, consequently, treatment conceptualization for a long time, is the subtle influence patient gender has on molecular processes. Naturally, this is greatly based on hormonal differences, but from an epigenetic point of view, the diverse susceptibility to stress and environmental influences is of prime interest. In this review we present the current view on which and how epigenetic modifications, emphasizing DNA methylation, regulate various tumor diseases. It is our aim to elucidate gender and epigenetics and their interconnectedness, which will contribute to understanding of the prospect molecular orchestration of cancer in individual tumors.
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23
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Bulk E, Kramko N, Liashkovich I, Glaser F, Schillers H, Schnittler HJ, Oberleithner H, Schwab A. K Ca3.1 channel inhibition leads to an ICAM-1 dependent increase of cell-cell adhesion between A549 lung cancer and HMEC-1 endothelial cells. Oncotarget 2017; 8:112268-112282. [PMID: 29348824 PMCID: PMC5762509 DOI: 10.18632/oncotarget.22735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/14/2017] [Indexed: 12/14/2022] Open
Abstract
Early metastasis leads to poor prognosis of lung cancer patients, whose 5-year survival rate is only 15%. We could recently show that the Ca2+ sensitive K+ channel KCa3.1 promotes aggressive behavior of non-small cell lung cancer (NSCLC) cells and that it can serve as a prognostic marker in NSCLC. Since NSCLC patients die of metastases, we investigated whether KCa3.1 channels contribute to poor patient prognosis by regulating distinct steps of the metastatic cascade. We investigated the extravasation of NSCLC cells and focused on their adhesion to endothelial cells and on transendothelial migration. We quantified the adhesion forces between NSCLC cells and endothelial cells by applying single cell force spectroscopy, and we monitored transendothelial migration using live-cell imaging. Inhibition of KCa3.1 channels with senicapoc or KCa3.1 silencing increases the adhesion force of A549 lung cancer cells to human microvascular endothelial cells (HMEC-1). Western blotting, immunofluorescence staining and biotinylation assays indicate that the elevated adhesion force is due to increased expression of ICAM-1 in both cell lines when KCa3.1 channels are downregulated. Consistent with this interpretation, an anti-ICAM-1 blocking antibody abolishes the KCa3.1-dependent increase in adhesion. Senicapoc inhibits transendothelial migration of A549 cells by 50%. Selectively silencing KCa3.1 channels in either NSCLC or endothelial cells reveals that transendothelial migration depends predominantly on endothelial KCa3.1 channels. In conclusion, our findings disclose a novel function of KCa3.1 channels in cancer. KCa3.1 channels regulate ICAM-1 dependent cell-cell adhesion between endothelial and cancer cells that affects the transmigration step of the metastatic cascade.
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Affiliation(s)
- Etmar Bulk
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Nadzeya Kramko
- Institute of Anatomy and Vascular Biology, University of Muenster, Münster, Germany
| | - Ivan Liashkovich
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Felix Glaser
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Hermann Schillers
- Institute of Physiology II, University of Muenster, Münster, Germany
| | | | - Hans Oberleithner
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Albrecht Schwab
- Institute of Physiology II, University of Muenster, Münster, Germany
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24
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Duruisseaux M, Esteller M. Lung cancer epigenetics: From knowledge to applications. Semin Cancer Biol 2017; 51:116-128. [PMID: 28919484 DOI: 10.1016/j.semcancer.2017.09.005] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Advances in our understanding of the genomics of lung cancer have led to substantial progress in the treatment of specific molecular subsets. Immunotherapy also emerges as a major breakthrough in lung cancer treatment. However, challenges remain as a consensual approach for early lung cancer detection remains elusive while primary or secondary drug resistance eventually leads to treatment failure in all patients with advanced disease. Furthermore, a large portion of patients are still treated with conventional chemotherapy that is only modestly effective. The last two decades have seen exponential developments in the epigenetic understanding of lung cancer. Epigenetic alterations in DNA methylation, non-coding RNA expression, chromatin modeling and post transcriptional regulators are key events in each step of lung cancer pathogenesis. Here, we review the central role epigenetic disruptions play in lung cancer carcinogenesis and the acquisition of cancerous phenotype and aggressive behavior as well as in the resistance to therapy. Epigenetic disruptions could represent reliable biomarkers for lung cancer risk assessment, early diagnosis, prognosis stratification, molecular classification and prediction of treatment efficacy. The therapeutic potential of epigenetics targeted drugs in combination with chemotherapy, targeted therapy and/or immunotherapy is currently being intensively investigated. We suggest that integration of tissue-derived or circulating epigenetic biomarkers and epidrugs in clinical trial design will translate epigenetic knowledge of lung cancer into the clinic and improve lung cancer patient outcomes.
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Affiliation(s)
- Michaël Duruisseaux
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Department of Respiratory Medecine, Hôpital Louis-Pradel, Hospices civils de Lyon, 28 avenue du Doyen Lépine, 69677, Lyon cedex, France.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Instituciò Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036, Barcelona, Catalonia, Spain.
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25
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Hopkins MM, Meier KE. Free Fatty Acid Receptors and Cancer: From Nutrition to Pharmacology. Handb Exp Pharmacol 2017; 236:233-251. [PMID: 27757756 DOI: 10.1007/164_2016_48] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The effects of fatty acids on cancer cells have been studied for decades. The roles of dietary long-chain n-3 polyunsaturated fatty acids, and of microbiome-generated short-chain butyric acid, have been of particular interest over the years. However, the roles of free fatty acid receptors (FFARs) in mediating effects of fatty acids in tumor cells have only recently been examined. In reviewing the literature, the data obtained to date indicate that the long-chain FFARs (FFA1 and FFA4) play different roles than the short-chain FFARs (FFA2 and FFA3). Moreover, FFA1 and FFA4 can in some cases mediate opposing actions in the same cell type. Another conclusion is that different types of cancer cells respond differently to FFAR activation. Currently, the best-studied models are prostate, breast, and colon cancer. FFA1 and FFA4 agonists can inhibit proliferation and migration of prostate and breast cancer cells, but enhance growth of colon cancer cells. In contrast, FFA2 activation can in some cases inhibit proliferation of colon cancer cells. Although the available data are sometimes contradictory, there are several examples in which FFAR agonists inhibit proliferation of cancer cells. This is a unique response to GPCR activation that will benefit from a mechanistic explanation as the field progresses. The development of more selective FFAR agonists and antagonists, combined with gene knockout approaches, will be important for unraveling FFAR-mediated inhibitory effects. These inhibitory actions, mediated by druggable GPCRs, hold promise for cancer prevention and/or therapy.
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Affiliation(s)
- Mandi M Hopkins
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, 99210-1495, USA
| | - Kathryn E Meier
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, 99210-1495, USA.
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26
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Association of Smoking, Alcohol Use, and Betel Quid Chewing with Epigenetic Aberrations in Cancers. Int J Mol Sci 2017; 18:ijms18061210. [PMID: 28587272 PMCID: PMC5486033 DOI: 10.3390/ijms18061210] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022] Open
Abstract
Numerous environmental factors such as diet, alcohol use, stress, and environmental chemicals are known to elicit epigenetic changes, leading to increased rates of cancers and other diseases. The incidence of head and neck cancer, one of the most common cancers in Taiwanese males, is increasing: oral cancer and nasopharyngeal carcinoma are ranked fourth and tenth respectively, among the top ten cancers in this group, and a major cause of cancer-related deaths in Taiwanese males. Previous studies have identified smoking, alcohol use, and betel quid chewing as the three major causes of head and neck cancers; these three social habits are commonly observed in Taiwanese males, resulting in an increasing morbidity rate of head and neck cancers in this population. In this literature review, we discuss the association between specific components of betel quid, alcohol, and tobacco, and the occurrence of head and neck cancers, lung cancer, gastrointestinal cancers, and urethral cancer. We focus on regulatory mechanisms at the epigenetic level and their oncogenic effects. The review further discusses the application of FDA-approved epigenetic drugs as therapeutic strategies against cancer.
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27
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Tanas AS, Borisova ME, Kuznetsova EB, Rudenko VV, Karandasheva KO, Nemtsova MV, Izhevskaya VL, Simonova OA, Larin SS, Zaletaev DV, Strelnikov VV. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics 2017; 9:833-847. [DOI: 10.2217/epi-2017-0031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: To develop a reduced representation bisulfite sequencing (RRBS) approach for rapid and affordable genome-wide DNA methylation analysis. Methods: We have selected restriction endonuclease XmaI to produce RRBS library fragments. After digestion and partial fill-in DNA fragments were ligated to barcoded adapters, bisulfite converted, size-selected, and sequenced on the Ion Torrent Personal Genome Machine. XmaI-RRBS results were compared with the previously published RRBS data. Results: We have developed an XmaI-RRBS method for rapid and affordable genome-wide DNA methylation analysis, with library preparation taking only 4 days and sequencing possible within 4 h. We have also addressed several challenges in order to further improve the RRBS technology. XmaI-RRBS may be performed on degraded DNA samples and is compatible with the bench-top next-generation sequencing machines.
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Affiliation(s)
- Alexander S Tanas
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
- Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Marina E Borisova
- Chromatin Biology and Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Ekaterina B Kuznetsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
- Human Molecular Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Viktoria V Rudenko
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
| | - Kristina O Karandasheva
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
- Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Marina V Nemtsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
- Medical Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Vera L Izhevskaya
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
| | - Olga A Simonova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
| | - Sergey S Larin
- Molecular Immunology Laboratory, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology & Immunology, Moscow, Russia
- Gene Therapy Laboratory, Institute of Gene Biology, Moscow, Russia
| | - Dmitry V Zaletaev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
- Human Molecular Genetics Laboratory, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow 115478, Russia
- Molecular and Cell Genetics Chair, Pirogov Russian National Research Medical University, Moscow, Russia
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28
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Qi Y, Wang D, Wang D, Jin T, Yang L, Wu H, Li Y, Zhao J, Du F, Song M, Wang R. HEDD: the human epigenetic drug database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw159. [PMID: 28025347 PMCID: PMC5199199 DOI: 10.1093/database/baw159] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/06/2016] [Accepted: 11/06/2016] [Indexed: 01/08/2023]
Abstract
Epigenetic drugs are chemical compounds that target disordered post-translational modification of histone proteins and DNA through enzymes, and the recognition of these changes by adaptor proteins. Epigenetic drug-related experimental data such as gene expression probed by high-throughput sequencing, co-crystal structure probed by X-RAY diffraction and binding constants probed by bio-assay have become widely available. The mining and integration of multiple kinds of data can be beneficial to drug discovery and drug repurposing. HEMD and other epigenetic databases store comprehensively epigenetic data where users can acquire segmental information of epigenetic drugs. However, some data types such as high-throughput datasets are not provide by these databases and they do not support flexible queries for epigenetic drug-related experimental data. Therefore, in reference to HEMD and other epigenetic databases, we developed a relatively comprehensive database for human epigenetic drugs. The human epigenetic drug database (HEDD) focuses on the storage and integration of epigenetic drug datasets obtained from laboratory experiments and manually curated information. The latest release of HEDD incorporates five kinds of datasets: (i) drug, (ii) target, (iii) disease, (vi) high-throughput and (v) complex. In order to facilitate data extraction, flexible search options were built in HEDD, which allowed an unlimited condition query for specific kinds of datasets using drug names, diseases and experiment types. Database URL:http://hedds.org/
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Affiliation(s)
- Yunfeng Qi
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Dadong Wang
- Department of Computer Science and Technology, Computer College, Jilin Normal University, Siping, China
| | - Daying Wang
- Department of Social Physical Education, Physical Education College, Jilin Normal University, Siping, China
| | - Taicheng Jin
- Department of Biotechnology, School of Life Science, Jilin Normal University, Siping, China
| | - Liping Yang
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Hui Wu
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Yaoyao Li
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Jing Zhao
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Fengping Du
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Mingxia Song
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Renjun Wang
- Department of Biotechnology, School of Life Science, Jilin Normal University, Siping, China
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29
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Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B, Chen C, Zhu J, Wang Y, Liu H, Zhang Y. DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res 2016; 45:D888-D895. [PMID: 27899673 PMCID: PMC5210584 DOI: 10.1093/nar/gkw1123] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 01/11/2023] Open
Abstract
The human disease methylation database (DiseaseMeth, http://bioinfo.hrbmu.edu.cn/diseasemeth/) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease–gene associations from 216 201 to 679 602. DiseaseMeth version 2.0 provides an expanded comprehensive list of disease–gene associations based on manual curation from experimental studies and computational identification from high-throughput methylome data. Besides the data expansion, we also updated the search engine and visualization tools. In particular, we enhanced the differential analysis tools, which now enable online automated identification of DNA methylation abnormalities in human disease in a case-control or disease–disease manner. To facilitate further mining of the disease methylome, three new web tools were developed for cluster analysis, functional annotation and survival analysis. DiseaseMeth version 2.0 should be a useful resource platform for further understanding the molecular mechanisms of human diseases.
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Affiliation(s)
- Yichun Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yue Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jie Lyu
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Chuangeng Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jiang Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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30
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Dąbrowski JM, Pucelik B, Regiel-Futyra A, Brindell M, Mazuryk O, Kyzioł A, Stochel G, Macyk W, Arnaut LG. Engineering of relevant photodynamic processes through structural modifications of metallotetrapyrrolic photosensitizers. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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ANGPTL2/LILRB2 signaling promotes the propagation of lung cancer cells. Oncotarget 2016; 6:21004-15. [PMID: 26056041 PMCID: PMC4673246 DOI: 10.18632/oncotarget.4217] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/10/2015] [Indexed: 12/29/2022] Open
Abstract
Immune inhibitory receptors expressed on various types of immune cells deliver inhibitory signals that maintain the homeostasis of the immune system. Recently we demonstrated that leukocyte immunoglobulin-like receptor subfamily B member 2 (LILRB2) and its murine homolog, paired immunoglobulin-like receptor B (PIRB), are expressed on hematopoietic stem cells and acute myeloid leukemia stem cells and function in maintenance of stemness. Herein, we determined that both LILRB2 and its soluble ligand ANGPTL2 are highly expressed in non-small cell lung cancer (NSCLC) samples, and levels are adversely related to patient prognosis. Inhibition of LILRB2 expression in NSCLC cell lines, such as A549 cells, resulted in a dramatic decrease in proliferation, colony formation, and migration. Mechanistic analyses indicated that ANGPTL2 binds LILRB2 to support the growth of lung cancer cells and that the SHP2/CaMK1/CREB axis controls the proliferation of lung cancer cell lines. Our results suggest that signaling involving ANGPTL2 and LILRB2 is important for lung cancer development and represents a novel target for treatment of this type of cancer.
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32
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Park Y, Wu H. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics 2016; 32:1446-53. [PMID: 26819470 DOI: 10.1093/bioinformatics/btw026] [Citation(s) in RCA: 262] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/13/2016] [Indexed: 12/28/2022] Open
Abstract
MOTIVATION DNA methylation is an epigenetic modification with important roles in many biological processes and diseases. Bisulfite sequencing (BS-seq) has emerged recently as the technology of choice to profile DNA methylation because of its accuracy, genome coverage and higher resolution. Current statistical methods to identify differential methylation mainly focus on comparing two treatment groups. With an increasing number of experiments performed under a general and multiple-factor design, particularly in reduced representation bisulfite sequencing, there is a need to develop more flexible, powerful and computationally efficient methods. RESULTS We present a novel statistical model to detect differentially methylated loci from BS-seq data under general experimental design, based on a beta-binomial regression model with 'arcsine' link function. Parameter estimation is based on transformed data with generalized least square approach without relying on iterative algorithm. Simulation and real data analyses demonstrate that our method is accurate, powerful, robust and computationally efficient. AVAILABILITY AND IMPLEMENTATION It is available as Bioconductor package DSS. CONTACT yongpark@pitt.edu or hao.wu@emory.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yongseok Park
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA and
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
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33
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Anzengruber F, Avci P, de Freitas LF, Hamblin MR. T-cell mediated anti-tumor immunity after photodynamic therapy: why does it not always work and how can we improve it? Photochem Photobiol Sci 2015; 14:1492-1509. [PMID: 26062987 PMCID: PMC4547550 DOI: 10.1039/c4pp00455h] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodynamic therapy (PDT) uses the combination of non-toxic photosensitizers and harmless light to generate reactive oxygen species that destroy tumors by a combination of direct tumor cell killing, vascular shutdown, and activation of the immune system. It has been shown in some animal models that mice that have been cured of cancer by PDT, may exhibit resistance to rechallenge. The cured mice can also possess tumor specific T-cells that recognize defined tumor antigens, destroy tumor cells in vitro, and can be adoptively transferred to protect naïve mice from cancer. However, these beneficial outcomes are the exception rather than the rule. The reasons for this lack of consistency lie in the ability of many tumors to suppress the host immune system and to actively evade immune attack. The presence of an appropriate tumor rejection antigen in the particular tumor cell line is a requisite for T-cell mediated immunity. Regulatory T-cells (CD25+, Foxp3+) are potent inhibitors of anti-tumor immunity, and their removal by low dose cyclophosphamide can potentiate the PDT-induced immune response. Treatments that stimulate dendritic cells (DC) such as CpG oligonucleotide can overcome tumor-induced DC dysfunction and improve PDT outcome. Epigenetic reversal agents can increase tumor expression of MHC class I and also simultaneously increase expression of tumor antigens. A few clinical reports have shown that anti-tumor immunity can be generated by PDT in patients, and it is hoped that these combination approaches may increase tumor cures in patients.
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Affiliation(s)
- Florian Anzengruber
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, USA
| | - Pinar Avci
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, USA
- Department of Dermatology, Dermatooncology and Venerology, Semmelweis University School of Medicine, Budapest, 1085, Hungary
| | - Lucas Freitas de Freitas
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, USA
- Programa de Pos Graduacao Interunidades Bioengenharia – USP – Sao Carlos, Brazil
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA
- Correspondence to: Michael R Hamblin, PhD, Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA.
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Bulk E, Ay AS, Hammadi M, Ouadid-Ahidouch H, Schelhaas S, Hascher A, Rohde C, Thoennissen NH, Wiewrodt R, Schmidt E, Marra A, Hillejan L, Jacobs AH, Klein HU, Dugas M, Berdel WE, Müller-Tidow C, Schwab A. Epigenetic dysregulation of KCa 3.1 channels induces poor prognosis in lung cancer. Int J Cancer 2015; 137:1306-17. [PMID: 25704182 DOI: 10.1002/ijc.29490] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 01/31/2023]
Abstract
Epigenomic changes are an important feature of malignant tumors. How tumor aggressiveness is affected by DNA methylation of specific loci is largely unexplored. In genome-wide DNA methylation analyses, we identified the KCa 3.1 channel gene (KCNN4) promoter to be hypomethylated in an aggressive non-small-cell lung carcinoma (NSCLC) cell line and in patient samples. Accordingly, KCa 3.1 expression was increased in more aggressive NSCLC cells. Both findings were strong predictors for poor prognosis in lung adenocarcinoma. Increased KCa 3.1 expression was associated with aggressive features of NSCLC cells. Proliferation and migration of pro-metastatic NSCLC cells depended on KCa 3.1 activity. Mechanistically, elevated KCa 3.1 expression hyperpolarized the membrane potential, thereby augmenting the driving force for Ca(2+) influx. KCa 3.1 blockade strongly reduced the growth of xenografted NSCLC cells in mice as measured by positron emission tomography-computed tomography. Thus, loss of DNA methylation of the KCNN4 promoter and increased KCa 3.1 channel expression and function are mechanistically linked to poor survival of NSCLC patients.
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Affiliation(s)
- Etmar Bulk
- Institute of Physiology II, University of Münster, Münster, Germany
| | - Anne-Sophie Ay
- Laboratory of Cellular Physiology, EA 4667, SFR CAP-SANTE (FED4231), UFR Sciences, University of Picardie Jules Verne, Amiens, 80039, France
| | - Mehdi Hammadi
- Laboratory of Cellular Physiology, EA 4667, SFR CAP-SANTE (FED4231), UFR Sciences, University of Picardie Jules Verne, Amiens, 80039, France.,Inserm U916, Institut Bergonié, Bordeaux, 33076, France
| | - Halima Ouadid-Ahidouch
- Laboratory of Cellular Physiology, EA 4667, SFR CAP-SANTE (FED4231), UFR Sciences, University of Picardie Jules Verne, Amiens, 80039, France
| | - Sonja Schelhaas
- European Institute for Molecular Imaging (EIMI), University of Münster, Münster, Germany
| | - Antje Hascher
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Christian Rohde
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany.,Department of Medicine, Hematology and Oncology, University Hospital of Halle (Saale), Halle (Saale), Germany
| | - Nils H Thoennissen
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany.,Department of Internal Medicine II and Clinic (Oncology Center), University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Rainer Wiewrodt
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Eva Schmidt
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Alessandro Marra
- Department of Thoracic Surgery, Niels-Stensen Clinics, Ostercappeln, Germany
| | - Ludger Hillejan
- Department of Thoracic Surgery, Niels-Stensen Clinics, Ostercappeln, Germany
| | - Andreas H Jacobs
- European Institute for Molecular Imaging (EIMI), University of Münster, Münster, Germany.,Department of Geriatric Medicine, Johanniter Hospital, Bonn, Germany
| | - Hans-Ulrich Klein
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Carsten Müller-Tidow
- Department of Medicine, Hematology, Oncology and Pneumology, University of Münster, Münster, Germany.,Department of Medicine, Hematology and Oncology, University Hospital of Halle (Saale), Halle (Saale), Germany
| | - Albrecht Schwab
- Institute of Physiology II, University of Münster, Münster, Germany
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Schamberger AC, Mise N, Meiners S, Eickelberg O. Epigenetic mechanisms in COPD: implications for pathogenesis and drug discovery. Expert Opin Drug Discov 2015; 9:609-28. [PMID: 24850530 DOI: 10.1517/17460441.2014.913020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death worldwide. The growing burden of COPD is due to continuous tobacco use, which is the most important risk factor of the disease, indoor fumes, occupational exposures and also aging of the world's population. Epigenetic mechanisms significantly contribute to COPD pathophysiology. AREAS COVERED This review focuses on disease-relevant changes in DNA modification, histone modification and non-coding RNA expression in COPD, and provides insight into novel therapeutic approaches modulating epigenetic mechanisms. Recent findings revealed, among others, globally changed DNA methylation patterns, decreased levels of histone deacetylases and reduced microRNAs levels in COPD. The authors also discuss a potential role of the chromatin silencing Polycomb group of proteins in COPD. EXPERT OPINION COPD is a highly complex disease and therapy development is complicated by the fact that many smokers develop both COPD and lung cancer. Of interest, combination therapies involving DNA methyltransferase inhibitors and anti-inflammatory drugs provide a promising approach, as they might be therapeutic for both COPD and cancer. Although the field of epigenetic research has virtually exploded over the last 10 years, particular efforts are required to enhance our knowledge of the COPD epigenome in order to successfully establish epigenetic-based therapies for this widespread disease.
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Affiliation(s)
- Andrea C Schamberger
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, University Hospital and Ludwig-Maximilians-University, Member of the German Center for Lung Research (DZL) , Max-Lebsche-Platz 31, 81377 Munich , Germany
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Abstract
Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high-throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.
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Füller M, Klein M, Schmidt E, Rohde C, Göllner S, Schulze I, Qianli J, Berdel WE, Edemir B, Müller-Tidow C, Tschanter P. 5-azacytidine enhances efficacy of multiple chemotherapy drugs in AML and lung cancer with modulation of CpG methylation. Int J Oncol 2014; 46:1192-204. [PMID: 25501798 DOI: 10.3892/ijo.2014.2792] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/12/2014] [Indexed: 11/06/2022] Open
Abstract
The DNA methyltransferase (DNMT) inhibitory drugs such as 5-azacytidine induce DNA hypomethylation by inhibiting DNA methyltransferases. While clinically effective, DNMT inhibitors are not curative. A combination with cytotoxic drugs might be beneficial, but this is largely unexplored. In the present study, we analyzed potential synergisms between cytotoxic drugs and 5-azacytidine in acute myeloid leukemia (AML) and non-small cell lung cancer (NSCLC) cells. Lung cancer and leukemia cell lines were exposed to low doses of 5-azacytidine with varying doses of cytarabine or etoposide for AML cells (U937 and HL60) as well as cisplatin or gemcitabine for NSCLC cells (A549 and HTB56) for 48 h. Drug interaction and potential synergism was analyzed according to the Chou-Talalay algorithm. Further analyses were based on soft agar colony formation assays, active caspase-3 staining and BrdU incorporation flow cytometry. To identify effects on DNA methylation patterns, we performed genome wide DNA methylation analysis using 450K bead arrays. Azacytidine at low doses was synergistic with cytotoxic drugs in NSCLC and in AML cell lines. Simultaneous exposure to 5-azacytidine with cytotoxic drugs showed strong synergistic activity. In colony formation assays these synergisms were repeatedly verified for 5-azacytidine (25 nM) with low doses of anticancer agents. 5-azacytidine neither affected the cell cycle nor increased apoptosis. 450K methylation bead arrays revealed 1,046 CpG sites in AML and 1,778 CpG sites in NSCLC cells with significant DNA hypomethylation (24-h exposure) to 5-azacytidine combined with the cytotoxic drugs. These CpG-sites were observed in the candidate tumor-suppressor genes MGMT and THRB. Additional incubation time after 24-h treatment led to a 4.1-fold increase of significant hypomethylated CpG-sites in NSCLC cells. These results suggest that the addition of DNA demethylating agents to cytotoxic anticancer drugs exhibits synergistic activity in AML and NSCLC. Dysregulation of an equilibrium of DNA methylation in cancer cells might increase the susceptibility for cytotoxic drugs.
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Affiliation(s)
- Mathias Füller
- Department of Medicine A, Hematology and Oncology, University of Münster, Münster, Germany
| | - Miriam Klein
- Department of Medicine A, Hematology and Oncology, University of Münster, Münster, Germany
| | - Eva Schmidt
- Department of Medicine A, Hematology and Oncology, University of Münster, Münster, Germany
| | - Christian Rohde
- Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany
| | - Stefanie Göllner
- Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany
| | - Isabell Schulze
- Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany
| | - Jiang Qianli
- Department of Medicine A, Hematology and Oncology, University of Münster, Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, Hematology and Oncology, University of Münster, Münster, Germany
| | - Bayram Edemir
- Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany
| | - Carsten Müller-Tidow
- Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany
| | - Petra Tschanter
- Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany
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