1
|
Gu Y, Wang M, Gong Y, Li X, Wang Z, Wang Y, Jiang S, Zhang D, Li C. Unveiling breast cancer risk profiles: a survival clustering analysis empowered by an online web application. Future Oncol 2023; 19:2651-2667. [PMID: 38095059 DOI: 10.2217/fon-2023-0736] [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: 12/23/2023] Open
Abstract
Aim: To develop a shiny app for doctors to investigate breast cancer treatments through a new approach by incorporating unsupervised clustering and survival information. Materials & methods: Analysis is based on the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset, which contains 1726 subjects and 22 variables. Cox regression was used to identify survival risk factors for K-means clustering. Logrank tests and C-statistics were compared across different cluster numbers and Kaplan-Meier plots were presented. Results & conclusion: Our study fills an existing void by introducing a unique combination of unsupervised learning techniques and survival information on the clinician side, demonstrating the potential of survival clustering as a valuable tool in uncovering hidden structures based on distinct risk profiles.
Collapse
Affiliation(s)
- Yuan Gu
- Department of Statistics, The George Washington University, Washington, DC 20052, USA
| | - Mingyue Wang
- Department of Mathematics, Syracuse University, Syracuse, NY 13244, USA
| | - Yishu Gong
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, NY 02115, USA
| | - Xin Li
- Department of Statistics, The George Washington University, Washington, DC 20052, USA
| | - Ziyang Wang
- Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Yuli Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Song Jiang
- Department of Biochemistry, Huzhou Institute of Biological Products Co., Ltd., 313017, China
| | - Dan Zhang
- Department of Information Science and Engineering, Shandong University, Shan Dong, China
| | - Chen Li
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, 14195, Germany
| |
Collapse
|
2
|
Ottaiano A, Ianniello M, Santorsola M, Ruggiero R, Sirica R, Sabbatino F, Perri F, Cascella M, Di Marzo M, Berretta M, Caraglia M, Nasti G, Savarese G. From Chaos to Opportunity: Decoding Cancer Heterogeneity for Enhanced Treatment Strategies. BIOLOGY 2023; 12:1183. [PMID: 37759584 PMCID: PMC10525472 DOI: 10.3390/biology12091183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
Cancer manifests as a multifaceted disease, characterized by aberrant cellular proliferation, survival, migration, and invasion. Tumors exhibit variances across diverse dimensions, encompassing genetic, epigenetic, and transcriptional realms. This heterogeneity poses significant challenges in prognosis and treatment, affording tumors advantages through an increased propensity to accumulate mutations linked to immune system evasion and drug resistance. In this review, we offer insights into tumor heterogeneity as a crucial characteristic of cancer, exploring the difficulties associated with measuring and quantifying such heterogeneity from clinical and biological perspectives. By emphasizing the critical nature of understanding tumor heterogeneity, this work contributes to raising awareness about the importance of developing effective cancer therapies that target this distinct and elusive trait of cancer.
Collapse
Affiliation(s)
- Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Monica Ianniello
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| | - Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Raffaella Ruggiero
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| | - Roberto Sirica
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| | - Francesco Sabbatino
- Oncology Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Baronissi, Italy;
| | - Francesco Perri
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Marco Cascella
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Massimiliano Di Marzo
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Massimiliano Berretta
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy;
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Via Luigi De Crecchio 7, 80138 Naples, Italy;
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| |
Collapse
|
3
|
Mukherjee S, Heng HH, Frenkel-Morgenstern M. Emerging Role of Chimeric RNAs in Cell Plasticity and Adaptive Evolution of Cancer Cells. Cancers (Basel) 2021; 13:4328. [PMID: 34503137 PMCID: PMC8431553 DOI: 10.3390/cancers13174328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Gene fusions can give rise to somatic alterations in cancers. Fusion genes have the potential to create chimeric RNAs, which can generate the phenotypic diversity of cancer cells, and could be associated with novel molecular functions related to cancer cell survival and proliferation. The expression of chimeric RNAs in cancer cells might impact diverse cancer-related functions, including loss of apoptosis and cancer cell plasticity, and promote oncogenesis. Due to their recurrence in cancers and functional association with oncogenic processes, chimeric RNAs are considered biomarkers for cancer diagnosis. Several recent studies demonstrated that chimeric RNAs could lead to the generation of new functionality for the resistance of cancer cells against drug therapy. Therefore, targeting chimeric RNAs in drug resistance cancer could be useful for developing precision medicine. So, understanding the functional impact of chimeric RNAs in cancer cells from an evolutionary perspective will be helpful to elucidate cancer evolution, which could provide a new insight to design more effective therapies for cancer patients in a personalized manner.
Collapse
Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
| |
Collapse
|
4
|
Chaturvedi A, Cruz Corella J, Robbins C, Loha A, Menin L, Gasilova N, Masclaux FG, Lee SJ, Sanders IR. The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya. Commun Biol 2021; 4:901. [PMID: 34294866 PMCID: PMC8298701 DOI: 10.1038/s42003-021-02414-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis. Anurag Chaturvedi et al. use long-read PacBio sequencing and LC-MS to profile 5mC and 6mA DNA methylation in the model arbuscular mycorrhizal fungus, Rhizophagus irregularis. Their results suggest that R. irregularis shows methylation profiles distinct from other early-diverging fungi, and Dikarya and provide further insight into how these fungi may have adapted to form symbiotic relationships with important plant species.
Collapse
Affiliation(s)
- Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Environmental Genomics Group, School of Biosciences, The University of Birmingham, Birmingham, UK
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Chanz Robbins
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Anita Loha
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), SSMI, Batochime, Lausanne, Switzerland
| | - Natalia Gasilova
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), SSMI, Batochime, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
5
|
Aziz MNM, Rahim NFC, Hussin Y, Yeap SK, Masarudin MJ, Mohamad NE, Akhtar MN, Osman MA, Cheah YK, Alitheen NB. Anti-Metastatic and Anti-Angiogenic Effects of Curcumin Analog DK1 on Human Osteosarcoma Cells In Vitro. Pharmaceuticals (Basel) 2021; 14:ph14060532. [PMID: 34204873 PMCID: PMC8228595 DOI: 10.3390/ph14060532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 12/26/2022] Open
Abstract
Osteosarcoma (OS) is a life-threatening malignant bone tumor associated with poor prognosis among children. The survival rate of the patient is still arguably low even with intensive treatment provided, plus with the inherent side effects from the chemotherapy, which gives more unfavorable outcomes. Hence, the search for potent anti-osteosarcoma agent with promising safety profile is still on going. Natural occurring substance like curcumin has gained a lot of attention due to its splendid safety profile as well as it pharmacological advantages such as anti-metastasis and anti-angiogenesis. However, natural curcumin was widely known for its poor cellular uptake, which undermines all potential that it possesses. This prompted the development of synthetically synthesized curcuminoid analog, known as (Z)-3-hydroxy-1-(2-hydroxyphenyl)-3-phenylprop-2- en-1-one (DK1). In this present study, in vitro scratch assay, transwell migration/invasion assay, HUVEC tube formation assay, and ex vivo rat aortic ring assays were performed in order to investigate the anti-metastatic and anti-angiogenic potential of DK1. For further comprehension of DK1 mechanism on human osteosarcoma cell lines, microarray gene expression analysis, quantitative polymerase chain reaction (qPCR), and proteome profiler were adopted, providing valuable forecast from the expression of important genes and proteins related to metastasis and angiogenesis. Based on the data gathered from the bioassays, DK1 was able to inhibit the metastasis and angiogenesis of human osteosarcoma cell lines by significantly reducing the cell motility, number of migrated and invaded cells as well as the tube formation and micro-vessels sprouting. Additionally, DK1 also has significantly regulated several cancer pathways involved in OS proliferation, metastasis, and angiogenesis such as PI3K/Akt and NF-κB in both U-2 OS and MG-63. Regulation of PI3K/Akt caused up-regulation of genes related to metastasis inhibition, namely, PTEN, FOXO, PLK3, and GADD45A. Meanwhile, NF-κB pathway was regulated by mitigating the expression of NF-κB activator such as IKBKB and IKBKE in MG-63, whilst up-regulating the expression of NF-κB inhibitors such as NFKBIA and NFKBIE in U-2 OS. Finally, DK1 also has successfully hindered the metastatic and angiogenic capability of OS cell lines by down-regulating the expression of pro-metastatic genes and proteins like MMP3, COL11A1, FGF1, Endoglin, uPA, and IGFBP2 in U-2 OS. Whilst for MG-63, the significantly down-regulated oncogenes were Serpin E1, AKT2, VEGF, uPA, PD-ECGF, and Endoglin. These results suggest that curcumin analog DK1 may serve as a potential new anti-osteosarcoma agent due to its anti-metastatic and anti-angiogenic attributes.
Collapse
Affiliation(s)
- Muhammad Nazirul Mubin Aziz
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
| | - Nurul Fattin Che Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
| | - Yazmin Hussin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang 43900, Selangor, Malaysia;
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nurul Elyani Mohamad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | | | - Mohd Azuraidi Osman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
| | - Yoke Kqueen Cheah
- Department of Biomedical Science, Faculty of Medicine and Health Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (M.N.M.A.); (N.F.C.R.); (Y.H.); (M.J.M.); (N.E.M.); (M.A.O.)
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-3-9769-7471
| |
Collapse
|
6
|
Wu T, Jiang X, Zhang X, Wu B, Xu B, Liu X, Zheng L, Wang Y. Intrahepatic Cholangiocarcinoma: State of the Art of FGFR Inhibitors. Cancer Control 2021; 28:1073274821989314. [PMID: 33618536 PMCID: PMC8482710 DOI: 10.1177/1073274821989314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/11/2020] [Accepted: 12/30/2020] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Intrahepatic cholangiocarcinoma (iCCA), the second most common type of primary liver tumor, has an increasing incidence in the past few decades. iCCA is highly malignant, with a 5-year survival rate of approximately 5-10%. Surgical resection is usually the prescribed treatment for patients with early stage iCCA; however, patients are usually in an advanced stage iCCA upon diagnosis. Currently, targeted therapy combined with chemotherapy and other comprehensive treatment measures have been mainly adopted as palliative treatment measures. As a common candidate of targeted therapy, FGFR inhibitors have demonstrated their unique advantages in clinical trials. At present, the prospect of FGFR targeted therapy is encouraging. The landscape of FGFR inhibitors in iCCA is needed to be showed urgently. METHODS We searched relative reports of clinical trials on FGFR inhibitors in PubMed as well as Web of Science. We also concluded other available clinical trials of FGFR inhibitors (Data were collected from clinicaltrials.gov). RESULTS Several relatively effective targeted drugs are being used in clinical trials. Some preliminary results indicate the outlook of targeted therapy such as BGJ398, TAS120, and HSP90 inhibitors. CONCLUSIONS In summary, FGFR targeted therapy has broad prospects for the treatment of iCCA.
Collapse
Affiliation(s)
- Tianyu Wu
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Xiaoqing Jiang
- Surgical Intensive Care Unit, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Xin Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Bodeng Wu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Bin Xu
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Xiaoliu Liu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yu Wang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| |
Collapse
|
7
|
Krook MA, Lenyo A, Wilberding M, Barker H, Dantuono M, Bailey KM, Chen HZ, Reeser JW, Wing MR, Miya J, Samorodnitsky E, Smith AM, Dao T, Martin DM, Ciombor KK, Hays J, Freud AG, Roychowdhury S. Efficacy of FGFR Inhibitors and Combination Therapies for Acquired Resistance in FGFR2-Fusion Cholangiocarcinoma. Mol Cancer Ther 2020; 19:847-857. [PMID: 31911531 PMCID: PMC7359896 DOI: 10.1158/1535-7163.mct-19-0631] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/15/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022]
Abstract
The fibroblast growth factor receptor (FGFR) signaling pathway is aberrantly activated in approximately 15% to 20% of patients with intrahepatic cholangiocarcinoma. Currently, several FGFR kinase inhibitors are being assessed in clinical trials for patients with FGFR-altered cholangiocarcinoma. Despite evidence of initial responses and disease control, virtually all patients eventually develop acquired resistance. Thus, there is a critical need for the development of innovative therapeutic strategies to overcome acquired drug resistance. Here, we present findings from a patient with FGFR2-altered metastatic cholangiocarcinoma who enrolled in a phase II clinical trial of the FGFR inhibitor, infigratinib (BGJ398). Treatment was initially effective as demonstrated by imaging and tumor marker response; however, after 8 months on trial, the patient exhibited tumor regrowth and disease progression. Targeted sequencing of tumor DNA after disease progression revealed the FGFR2 kinase domain p.E565A and p.L617M single-nucleotide variants (SNV) hypothesized to drive acquired resistance to infigratinib. The sensitivities of these FGFR2 SNVs, which were detected post-infigratinib therapy, were extended to include clinically relevant FGFR inhibitors, including AZD4547, erdafitinib (JNJ-42756493), dovitinib, ponatinib, and TAS120, and were evaluated in vitro Through a proteomics approach, we identified upregulation of the PI3K/AKT/mTOR signaling pathway in cells harboring the FGFR2 p.E565A mutation and demonstrated that combination therapy strategies with FGFR and mTOR inhibitors may be used to overcome resistance to FGFR inhibition, specific to infigratinib. Collectively, these studies support the development of novel combination therapeutic strategies in addition to the next generation of FGFR inhibitors to overcome acquired resistance in patients.
Collapse
MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Apoptosis
- Bile Duct Neoplasms/drug therapy
- Bile Duct Neoplasms/genetics
- Bile Duct Neoplasms/metabolism
- Bile Duct Neoplasms/pathology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Proliferation
- Cholangiocarcinoma/drug therapy
- Cholangiocarcinoma/genetics
- Cholangiocarcinoma/metabolism
- Cholangiocarcinoma/pathology
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Middle Aged
- Mutation
- Oncogene Proteins, Fusion/genetics
- Phenylurea Compounds/therapeutic use
- Prognosis
- Protein Kinase Inhibitors/therapeutic use
- Pyrimidines/therapeutic use
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Signal Transduction
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Melanie A Krook
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Alexandria Lenyo
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Max Wilberding
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Hannah Barker
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Mikayla Dantuono
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Kelly M Bailey
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Hui-Zi Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Department of Internal Medicine, Hematology and Oncology Fellowship Program, The Ohio State University, Columbus, Ohio
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Jharna Miya
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | | | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Thuy Dao
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Dorrelyn M Martin
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Kristen K Ciombor
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John Hays
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Aharon G Freud
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| |
Collapse
|
8
|
Krook MA, Bonneville R, Chen HZ, Reeser JW, Wing MR, Martin DM, Smith AM, Dao T, Samorodnitsky E, Paruchuri A, Miya J, Baker KR, Yu L, Timmers C, Dittmar K, Freud AG, Allenby P, Roychowdhury S. Tumor heterogeneity and acquired drug resistance in FGFR2-fusion-positive cholangiocarcinoma through rapid research autopsy. Cold Spring Harb Mol Case Stud 2019; 5:a004002. [PMID: 31371345 PMCID: PMC6672025 DOI: 10.1101/mcs.a004002] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
Cholangiocarcinoma is a highly aggressive and lethal malignancy, with limited treatment options available. Recently, FGFR inhibitors have been developed and utilized in FGFR-mutant cholangiocarcinoma; however, resistance often develops and the genomic determinants of resistance are not fully characterized. We completed whole-exome sequencing (WES) of 11 unique tumor samples obtained from a rapid research autopsy on a patient with FGFR-fusion-positive cholangiocarcinoma who initially responded to the pan-FGFR inhibitor, INCB054828. In vitro studies were carried out to characterize the novel FGFR alteration and secondary FGFR2 mutation identified. Multisite WES and analysis of tumor heterogeneity through subclonal inference identified four genetically distinct cancer cell populations, two of which were only observed after treatment. Additionally, WES revealed an FGFR2 N549H mutation hypothesized to confer resistance to the FGFR inhibitor INCB054828 in a single tumor sample. This hypothesis was corroborated with in vitro cell-based studies in which cells expressing FGFR2-CLIP1 fusion were sensitive to INCB054828 (IC50 value of 10.16 nM), whereas cells with the addition of the N549H mutation were resistant to INCB054828 (IC50 value of 1527.57 nM). Furthermore, the FGFR2 N549H secondary mutation displayed cross-resistance to other selective FGFR inhibitors, but remained sensitive to the nonselective inhibitor, ponatinib. Rapid research autopsy has the potential to provide unprecedented insights into the clonal evolution of cancer throughout the course of the disease. In this study, we demonstrate the emergence of a drug resistance mutation and characterize the evolution of tumor subclones within a cholangiocarcinoma disease course.
Collapse
Affiliation(s)
- Melanie A Krook
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Russell Bonneville
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hui-Zi Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Dorrelyn M Martin
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Thuy Dao
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Eric Samorodnitsky
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anoosha Paruchuri
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jharna Miya
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kaitlin R Baker
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Cynthia Timmers
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kristin Dittmar
- Department of Radiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Aharon G Freud
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Patricia Allenby
- Department of Pathology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
9
|
Bioenergetics of life, disease and death phenomena. Theory Biosci 2018; 137:155-168. [PMID: 29992378 PMCID: PMC6208829 DOI: 10.1007/s12064-018-0266-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
In this article, some new aspects of unified cell bioenergetics are presented. From the perspective of unified cell bioenergetics certain subsequent stages of cancer development, from initiation stage, through transformation to metastasis, are analyzed. Here we show that after transformation, cancer cells are permanently exposed to reactive oxygen species, that causes continual random DNA mutations and as a result genome and chromosomal destabilizations. The modern cancer attractor hypothesis has been extended in explaining cancer development. Discussion is conducted in light of current cancerogenesis research, including bioenergetic cancer initiation, the somatic mutation theory and the tissue organization field theory. In the article reasons complicating the discovery of patterns of cancer genome changes and cancer evolution are presented. In addition certain cancer therapeutic aspects are given attention to.
Collapse
|
10
|
Chiang YS, Huang YF, Midha MK, Chen TH, Shiau HC, Chiu KP. Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions. PLoS One 2018; 13:e0199471. [PMID: 29920548 PMCID: PMC6007910 DOI: 10.1371/journal.pone.0199471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/07/2018] [Indexed: 12/22/2022] Open
Abstract
Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively. High consistency in HKG expression levels across all four SCTs, along with transcriptional silencing of LDHB, was observed, suggesting a high sensitivity and reproducibility of the SCT analysis. Cross-library comparison on expression levels by scatter plotting revealed a linear correlation and an 83–94% overlap in transcript isoforms and expressed genes were also observed. To gain insight of transcriptional diversity among the SCTs, expressed genes were split into consistently expressed (CE) (expressed in all SCTs) and inconsistently expressed (IE) (expressed in some but not all SCTs) genes for further characterization, along with the 142 expressed HKGs as a reference. Distinct transcriptional strengths were found among these groups, with averages of 1,612.0, 88.0 and 1.2 FPKM for HKGs, CE and IE, respectively. Comparison between CE and IE groups further indicated that expressions of CE genes vary more significantly than that of IE genes. Gene Ontology analysis indicated that proteins encoded by CE genes are mainly involved in fundamental intracellular activities, while proteins encoded by IE genes are mainly for extracellular activities, especially acting as receptors or ion channels. The diversified gene expressions, especially for those encoded by IE genes, may contribute to cancer drug resistance.
Collapse
Affiliation(s)
| | - Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Mohit K. Midha
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- College of Life Science, National Taiwan University, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
11
|
Zhu S, Beaulaurier J, Deikus G, Wu TP, Strahl M, Hao Z, Luo G, Gregory JA, Chess A, He C, Xiao A, Sebra R, Schadt EE, Fang G. Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing. Genome Res 2018; 28:1067-1078. [PMID: 29764913 PMCID: PMC6028124 DOI: 10.1101/gr.231068.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 05/01/2018] [Indexed: 01/31/2023]
Abstract
N6-Methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes; however, methods for high-resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes. Based on these differences, we describe the first approach for mapping m6dA events using SMRT sequencing specifically designed for the study of eukaryotic genomes and provide appropriate strategies for designing experiments and carrying out sequencing in future studies. We apply the novel approach to study two eukaryotic genomes. For green algae, we construct the first complete genome-wide map of m6dA at single-nucleotide and single-molecule resolution. For human lymphoblastoid cells (hLCLs), it was necessary to integrate SMRT sequencing data with independent sequencing data. The joint analyses suggest putative m6dA events are enriched in the promoters of young full-length LINE-1 elements (L1s), but call for validation by additional methods. These analyses demonstrate a general method for rigorous mapping and characterization of m6dA events in eukaryotic genomes.
Collapse
Affiliation(s)
- Shijia Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Tao P Wu
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Maya Strahl
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ziyang Hao
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Guanzheng Luo
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - James A Gregory
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, New York 10013, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrew Xiao
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
12
|
Ye CJ, Regan S, Liu G, Alemara S, Heng HH. Understanding aneuploidy in cancer through the lens of system inheritance, fuzzy inheritance and emergence of new genome systems. Mol Cytogenet 2018; 11:31. [PMID: 29760781 PMCID: PMC5946397 DOI: 10.1186/s13039-018-0376-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In the past 15 years, impressive progress has been made to understand the molecular mechanism behind aneuploidy, largely due to the effort of using various -omics approaches to study model systems (e.g. yeast and mouse models) and patient samples, as well as the new realization that chromosome alteration-mediated genome instability plays the key role in cancer. As the molecular characterization of the causes and effects of aneuploidy progresses, the search for the general mechanism of how aneuploidy contributes to cancer becomes increasingly challenging: since aneuploidy can be linked to diverse molecular pathways (in regards to both cause and effect), the chances of it being cancerous is highly context-dependent, making it more difficult to study than individual molecular mechanisms. When so many genomic and environmental factors can be linked to aneuploidy, and most of them not commonly shared among patients, the practical value of characterizing additional genetic/epigenetic factors contributing to aneuploidy decreases. RESULTS Based on the fact that cancer typically represents a complex adaptive system, where there is no linear relationship between lower-level agents (such as each individual gene mutation) and emergent properties (such as cancer phenotypes), we call for a new strategy based on the evolutionary mechanism of aneuploidy in cancer, rather than continuous analysis of various individual molecular mechanisms. To illustrate our viewpoint, we have briefly reviewed both the progress and challenges in this field, suggesting the incorporation of an evolutionary-based mechanism to unify diverse molecular mechanisms. To further clarify this rationale, we will discuss some key concepts of the genome theory of cancer evolution, including system inheritance, fuzzy inheritance, and cancer as a newly emergent cellular system. CONCLUSION Illustrating how aneuploidy impacts system inheritance, fuzzy inheritance and the emergence of new systems is of great importance. Such synthesis encourages efforts to apply the principles/approaches of complex adaptive systems to ultimately understand aneuploidy in cancer.
Collapse
Affiliation(s)
- Christine J. Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Sarah Regan
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Sarah Alemara
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Henry H. Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201 USA
| |
Collapse
|
13
|
A subset of microRNAs defining the side population of a human malignant mesothelioma cell line. Oncotarget 2018; 8:42847-42856. [PMID: 28467812 PMCID: PMC5522110 DOI: 10.18632/oncotarget.17086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/22/2017] [Indexed: 01/04/2023] Open
Abstract
This study was performed to investigate the global expression profile of microRNAs in distinct subpopulations of a human malignant mesothelioma cell line. Total RNAs were isolated from the sorted side population and non-side population of MS1. The RNAs were subjected to analysis using Affymetrix GeneChip microRNA Arrays. After data extraction and normalization, a subset of microRNAs defining cell subpopulations was identified using bioinformatics softwares. Based on the criteria of 2-fold difference and the p-value of < 0.05, a total of 95 microRNAs were differentially expressed in the side population compared to the non-side population. Functional ontology revealed that target genes of the miRNAs were categorized into various gene ontology terms, such as stem cell maintenance, cell proliferation, programmed cell death, cell migration, and cellular response to stress. The Kyoto Encyclopedia of Genes and Genomes analysis showed that ErbB-2 receptor tyrosine kinases signaling pathway was the most represented. Integrated analysis of MiRTarBase and RNA-seq identified 12 target genes of microRNAs defining side population, including DDIT4 and ROCK2. The present study indicates that a distinct set of microRNAs may be critically involved in the generation and maintenance of heterogeneous subpopulations of cancer cells. They could be a plausible target for the eradication of more aggressive cancer cell subpopulations.
Collapse
|
14
|
Heng HH, Horne SD, Chaudhry S, Regan SM, Liu G, Abdallah BY, Ye CJ. A Postgenomic Perspective on Molecular Cytogenetics. Curr Genomics 2018; 19:227-239. [PMID: 29606910 PMCID: PMC5850511 DOI: 10.2174/1389202918666170717145716] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/29/2017] [Accepted: 02/03/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The postgenomic era is featured by massive data collection and analyses from various large scale-omics studies. Despite the promising capability of systems biology and bioinformatics to handle large data sets, data interpretation, especially the translation of -omics data into clinical implications, has been challenging. DISCUSSION In this perspective, some important conceptual and technological limitations of current systems biology are discussed in the context of the ultimate importance of the genome beyond the collection of all genes. Following a brief summary of the contributions of molecular cytogenetics/cytogenomics in the pre- and post-genomic eras, new challenges for postgenomic research are discussed. Such discussion leads to a call to search for a new conceptual framework and holistic methodologies. CONCLUSION Throughout this synthesis, the genome theory of somatic cell evolution is highlighted in contrast to gene theory, which ignores the karyotype-mediated higher level of genetic information. Since "system inheritance" is defined by the genome context (gene content and genomic topology) while "parts inheritance" is defined by genes/epigenes, molecular cytogenetics and cytogenomics (which directly study genome structure, function, alteration and evolution) will play important roles in this postgenomic era.
Collapse
Affiliation(s)
- Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Steven D. Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sophia Chaudhry
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sarah M. Regan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Batoul Y. Abdallah
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Christine J. Ye
- The Division of Hematology/Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
| |
Collapse
|
15
|
Maßberg D, Jovancevic N, Offermann A, Simon A, Baniahmad A, Perner S, Pungsrinont T, Luko K, Philippou S, Ubrig B, Heiland M, Weber L, Altmüller J, Becker C, Gisselmann G, Gelis L, Hatt H. The activation of OR51E1 causes growth suppression of human prostate cancer cells. Oncotarget 2018; 7:48231-48249. [PMID: 27374083 PMCID: PMC5217014 DOI: 10.18632/oncotarget.10197] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/06/2016] [Indexed: 01/23/2023] Open
Abstract
The development of prostate cancer (PCa) is regulated by the androgen-dependent activity of the androgen receptor (AR). Androgen-deprivation therapy (ADT) is therefore the gold standard treatment to suppress malignant progression of PCa. Nevertheless, due to the development of castration resistance, recurrence of disease after initial response to ADT is a major obstacle to successful treatment. As G-protein coupled receptors play a fundamental role in PCa physiology, they might represent promising alternative or combinatorial targets for advanced diseases. Here, we verified gene expression of the olfactory receptors (ORs) OR51E1 [prostate-specific G-protein coupled receptor 2 (PSGR2)] and OR51E2 (PSGR) in human PCa tissue by RNA-Seq analysis and RT-PCR and elucidated the subcellular localization of both receptor proteins in human prostate tissue. The OR51E1 agonist nonanoic acid (NA) leads to the phosphorylation of various protein kinases and growth suppression of the PCa cell line LNCaP. Furthermore, treatment with NA causes reduction of androgen-mediated AR target gene expression. Interestingly, NA induces cellular senescence, which coincides with reduced E2F1 mRNA levels. In contrast, treatment with the structurally related compound 1-nonanol or the OR2AG1 agonist amyl butyrate, neither of which activates OR51E1, did not lead to reduced cell growth or an induction of cellular senescence. However, decanoic acid, another OR51E1 agonist, also induces cellular senescence. Thus, our results suggest the involvement of OR51E1 in growth processes of PCa cells and its impact on AR-mediated signaling. These findings provide novel evidences to support the functional importance of ORs in PCa pathogenesis.
Collapse
Affiliation(s)
- Désirée Maßberg
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | | | - Anne Offermann
- Pathology of the University Hospital of Luebeck and the Leibniz Research Center Borstel, Luebeck and Borstel, Germany
| | - Annika Simon
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Sven Perner
- Pathology of the University Hospital of Luebeck and the Leibniz Research Center Borstel, Luebeck and Borstel, Germany
| | | | - Katarina Luko
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Stathis Philippou
- Institute for Pathology und Cytology, Augusta-Kranken-Anstalt gGmbH Bochum, Bochum, Germany
| | - Burkhard Ubrig
- Clinic for Urology, Augusta-Kranken-Anstalt gGmbH Bochum, Bochum, Germany
| | - Markus Heiland
- Clinic for Urology, Augusta-Kranken-Anstalt gGmbH Bochum, Bochum, Germany
| | - Lea Weber
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | | | | | - Günter Gisselmann
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Lian Gelis
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany.,Present address: Global Drug Discovery - Clinical Sciences, Bayer Pharma AG, Wuppertal, Germany
| | - Hanns Hatt
- Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany
| |
Collapse
|
16
|
Yachie-Kinoshita A, Onishi K, Ostblom J, Langley MA, Posfai E, Rossant J, Zandstra PW. Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions. Mol Syst Biol 2018; 14:e7952. [PMID: 29378814 PMCID: PMC5787708 DOI: 10.15252/msb.20177952] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or that cause its destabilization to initiate development, are complex and incompletely understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) to simulate single-cell fate transitions and strongly connected components (SCCs) strategy to represent population heterogeneity. This framework was applied to a reverse-engineered and curated core GRN for mouse embryonic stem cells (mESCs) and used to simulate cellular responses to combinations of five signaling pathways. Our simulations predicted experimentally verified cell population compositions and input signal combinations controlling specific cell fate transitions. Extending the model to PSC differentiation, we predicted a combination of signaling activators and inhibitors that efficiently and robustly generated a Cdx2+Oct4- cells from naïve mESCs. Overall, this platform provides new strategies to simulate cell fate transitions and the heterogeneity that typically occurs during development and differentiation.
Collapse
Affiliation(s)
- Ayako Yachie-Kinoshita
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,The Systems Biology Institute, Minato, Tokyo, Japan
| | - Kento Onishi
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Matthew A Langley
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Eszter Posfai
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada .,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Medicine by Design, A Canada First Research Excellence Program at the University of Toronto, Toronto, ON, Canada
| |
Collapse
|
17
|
Abstract
One of the major challenges in the cancer treatment is the development of drug resistance. It represents a major obstacle to curing cancer with constrained efficacy of both conventional chemotherapy and targeted therapies, even recent immune checkpoint blockade therapy. Deciphering the mechanisms of resistance is critical to further understanding the multifactorial pathways involved, and developing more specific targeted treatments. To date, numerous studies have reported the potential role of microRNAs (miRNAs) in the resistance to various cancer treatments. MicroRNAs are a family of small noncoding RNAs that regulate gene expression by sequence-specific targeting of mRNAs causing translational repression or mRNA degradation. More than 1200 validated human miRNAs have been identified in human genome. While one miRNA can regulate hundreds of targets, a single target can also be affected by multiple miRNAs. Evidence suggests that dysregulation of specific miRNAs may be involved in the acquisition of resistance, thereby modulating the sensitivity of cancer cells to treatment. Therefore, manipulation of miRNAs may be an attractive strategy for more effective individualized therapies through reprograming resistant network in cancer cells.
Collapse
Affiliation(s)
- Jun Zhu
- Jiangsu Cancer Hospital, 42 Baiziting, Nanjing, Jiangsu, 210009, China.
| | - Wei Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Wei Wu
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California in San Francisco, 600 16th Street Mission Bay/Genentech Hall, Room N212, San Francisco, CA, 94143, USA
| |
Collapse
|
18
|
Soozangar N, Sadeghi MR, Jeddi F, Somi MH, Shirmohamadi M, Samadi N. Comparison of genome‐wide analysis techniques to DNA methylation analysis in human cancer. J Cell Physiol 2017; 233:3968-3981. [DOI: 10.1002/jcp.26176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Narges Soozangar
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Molecular Medicine Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad R. Sadeghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Farhad Jeddi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Mohammad H. Somi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Department of Biochemistry, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
| |
Collapse
|
19
|
Basanta D, Anderson ARA. Homeostasis Back and Forth: An Ecoevolutionary Perspective of Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a028332. [PMID: 28289244 DOI: 10.1101/cshperspect.a028332] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The role of genetic mutations in cancer is indisputable: They are a key source of tumor heterogeneity and drive its evolution to malignancy. But, the success of these new mutant cells relies on their ability to disrupt the homeostasis that characterizes healthy tissues. Mutated clones unable to break free from intrinsic and extrinsic homeostatic controls will fail to establish a tumor. Here, we will discuss, through the lens of mathematical and computational modeling, why an evolutionary view of cancer needs to be complemented by an ecological perspective to understand why cancer cells invade and subsequently transform their environment during progression. Importantly, this ecological perspective needs to account for tissue homeostasis in the organs that tumors invade, because they perturb the normal regulatory dynamics of these tissues, often coopting them for its own gain. Furthermore, given our current lack of success in treating advanced metastatic cancers through tumor-centric therapeutic strategies, we propose that treatments that aim to restore homeostasis could become a promising venue of clinical research. This ecoevolutionary view of cancer requires mechanistic mathematical models to both integrate clinical with biological data from different scales but also to detangle the dynamic feedback between the tumor and its environment. Importantly, for these models to be useful, they need to embrace a higher degree of complexity than many mathematical modelers are traditionally comfortable with.
Collapse
Affiliation(s)
- David Basanta
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, Florida 33612
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, Florida 33612
| |
Collapse
|
20
|
Gu Y, Zhang Z, Yin J, Ye J, Song Y, Liu H, Xiong Y, Lu M, Zheng G, He Z. Epigenetic silencing of miR-493 increases the resistance to cisplatin in lung cancer by targeting tongue cancer resistance-related protein 1(TCRP1). JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:114. [PMID: 28859669 PMCID: PMC5580233 DOI: 10.1186/s13046-017-0582-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/16/2017] [Indexed: 02/04/2023]
Abstract
Background The potential mechanisms regarding how methylation of microRNA(miRNA) CpG Island could regulate cancer cell chemo-resistance remains unclear. This study aims to explore the epigenetic dysregulation mechanism of miRNA-493 and the ability to modulate lung cancer cell chemotherapy resistance. Methods Real-time quantitative PCR (qRT-PCR) and In situ hybridization (ISH) were used to analyze the expression of miR-493 in lung cancer cell lines and tumor tissue, respectively. Bisulfite sequencing PCR (BSP) was used to exam the promoter CpG Island of miR-493. The effect of miR-493 on chemosensitivity was evaluated by cell viability assays, apoptosis assays and in vivo experiment. The DNA damage was measured by γ-H2AX immunofluorescence. Luciferase reporter assay was used to assess the target genes of miR-493. Expression of target proteins and downstream molecules were analyzed by Western blot. Results miR-493 is silenced in resistant lung cancer cell due to the aberrant DNA methylation. Enforced expression of miR-493 in lung cancer cells promotes chemotherapy sensitivity to cisplatin through impairing the DNA damage repair and increasing the cells apoptosis in vitro and in vivo. Furthermore, we identify that TCRP1 is a direct functional target of miR-493. Ectopic expression of TCRP1 attenuated increased apoptosis in miR-493-overexpressing lung cancer cells upon cisplatin treatment. Meanwhile, miR-493 level is negatively correlated with TCRP1 expression in lung cancer patients and TCRP1 expression were correlated with poor survival. Conclusions Our results highlight that hyper-methylation of miR-493CpG island might play important roles in the development of lung cancer chemo-resistance by targeting TCRP1, which might be used as a potential therapeutic target in preventing the chemo-resistance of lung cancer.
Collapse
Affiliation(s)
- Yixue Gu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Zhijie Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Jiang Yin
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Jiahui Ye
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Yin Song
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Hao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Yan Xiong
- Department of Pharmacology, Guangzhou Institute of Snake Venom Research, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.
| | - Minying Lu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Guopei Zheng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China
| | - Zhimin He
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China.
| |
Collapse
|
21
|
Reher D, Klink B, Deutsch A, Voss-Böhme A. Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model. Biol Direct 2017; 12:18. [PMID: 28800767 PMCID: PMC5553611 DOI: 10.1186/s13062-017-0188-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/17/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated and the decrease of cell-cell adhesion allows tumour cells to dissociate from the primary tumour mass. This complex process depends on intracellular cues that are subject to genetic and epigenetic variability, as well as extrinsic cues from the local environment resulting in a spatial heterogeneity in the adhesive phenotype of individual tumour cells. Here, we use a novel mathematical model to study how adhesion heterogeneity, influenced by intrinsic and extrinsic factors, affects the dissemination of tumour cells from an epithelial cell population. The model is a multiscale cellular automaton that couples intracellular adhesion receptor regulation with cell-cell adhesion. RESULTS Simulations of our mathematical model indicate profound effects of adhesion heterogeneity on tumour cell dissemination. In particular, we show that a large variation of intracellular adhesion receptor concentrations in a cell population reinforces cell dissemination, regardless of extrinsic cues mediated through the local cell density. However, additional control of adhesion receptor concentration through the local cell density, which can be assumed in healthy cells, weakens the effect. Furthermore, we provide evidence that adhesion heterogeneity can explain the remarkable differences in adhesion receptor concentrations of epithelial and mesenchymal phenotypes observed during EMT and might drive early dissemination of tumour cells. CONCLUSIONS Our results suggest that adhesion heterogeneity may be a universal trigger to reinforce cell dissemination in epithelial cell populations. This effect can be at least partially compensated by a control of adhesion receptor regulation through neighbouring cells. Accordingly, our findings explain how both an increase in intra-tumour adhesion heterogeneity and the loss of control through the local environment can promote tumour cell dissemination. REVIEWERS This article was reviewed by Hanspeter Herzel, Thomas Dandekar and Marek Kimmel.
Collapse
Affiliation(s)
- David Reher
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany.
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Str. 46, Dresden, 01062, Germany.
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, Dresden, 01307, Germany
- German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Center for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Andreas Deutsch
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Str. 46, Dresden, 01062, Germany
| | - Anja Voss-Böhme
- Center for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Str. 46, Dresden, 01062, Germany
- Hochschule für Technik und Wirtschaft Dresden, Fakultät Informatik/Mathematik, Friedrich-List-Platz 1, Dresden, 01069, Germany
| |
Collapse
|
22
|
Huang YQ, Ling XH, Yuan RQ, Chen ZY, Yang SB, Huang HX, Zhong WD, Qiu SP. miR‑30c suppresses prostate cancer survival by targeting the ASF/SF2 splicing factor oncoprotein. Mol Med Rep 2017; 16:2431-2438. [PMID: 28677791 PMCID: PMC5548014 DOI: 10.3892/mmr.2017.6910] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 04/13/2017] [Indexed: 12/29/2022] Open
Abstract
Our previous study revealed that microRNA (miR) −30c represents a potential tumor suppressor gene, the expression of which is associated with decreased oncogenic potential in prostate cancer (PCa) cell lines. However, the functional role and underlying mechanisms of miR-30c in PCa remain to be fully elucidated. Reverse transcription-quantitative polymerase chain reaction and immunohistochemical analysis were used to detect the expression levels of alternative splicing factor/splicing factor 2 (ASF/SF2) in PCa tissues. A luciferase reporter assay was used to investigate whether ASF/SF2 may be a direct target gene of miR-30c. In addition, the effects of miR-30c on the proliferation and apoptosis of PCa cell lines were examined, following transfection with miR-30c mimics. Furthermore, correlation analysis was performed to investigate the relationship between the expression of miR-30c and ASF/SF2 and various clinicopathological parameters of patients with PCa. The present results demonstrated that PCa tissues exhibited higher levels of alternative splicing factor/splicing factor 2 (ASF/SF2), compared with normal tissues. In addition, miR-30c was revealed to targete the 3′-untranslated region of the ASF/SF2 gene, causing a decrease in the mRNA and protein levels of ASF/SF2. Furthermore, miR-30c was reported to decrease cell proliferation, increase the percentage of cells in the G1 cell cycle phase, and promote apoptosis through the inhibition of ASF/SF2. Following correlation analysis using patient samples, the expression of ASF/SF2 was revealed to be tightly correlated with the pathological stage of PCa and biochemical recurrence (BCR). In addition, patients with PCa exhibiting low expression levels of miR-30c and high expression of ASF/SF2 had significantly lower rates of BCR-free survival. In conclusion, the present study suggested that the tumor suppressor miR-30c may be involved in PCa tumorigenesis, possibly via targeting ASF/SF2. The combined analysis of the expression of ASF/SF2 and miR-30c may be a valuable tool for early prediction of BCR in patients with PCa following radical prostatectomy.
Collapse
Affiliation(s)
- Ya-Qiang Huang
- Department of Urology, Zhongshan Hospital of Sun Yat‑sen University, Zhongshan, Guangdong 528400, P.R. China
| | - Xiao-Hui Ling
- Reproductive Medicine Centre, Huizhou Municipal Central People's Hospital, Huizhou, Guangdong 516001, P.R. China
| | - Run-Qiang Yuan
- Department of Urology, Zhongshan Hospital of Sun Yat‑sen University, Zhongshan, Guangdong 528400, P.R. China
| | - Zhi-Yun Chen
- Reproductive Medicine Centre, Huizhou Municipal Central People's Hospital, Huizhou, Guangdong 516001, P.R. China
| | - Sheng-Bang Yang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Hong-Xing Huang
- Department of Urology, Zhongshan Hospital of Sun Yat‑sen University, Zhongshan, Guangdong 528400, P.R. China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Shao-Peng Qiu
- Department of Urology, First Affiliated Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| |
Collapse
|
23
|
Heng HH. Heterogeneity-mediated cellular adaptation and its trade-off: searching for the general principles of diseases. J Eval Clin Pract 2017; 23:233-237. [PMID: 27421676 DOI: 10.1111/jep.12598] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/14/2016] [Indexed: 12/18/2022]
Abstract
Big-data-omics have promised the success of precision medicine. However, most common diseases belong to adaptive systems where the precision is all but difficult to achieve. In this commentary, I propose a heterogeneity-mediated cellular adaptive model to search for the general model of diseases, which also illustrates why in most non-infectious non-Mendelian diseases the involvement of cellular evolution is less predictable when gene profiles are used. This synthesis is based on the following new observations/concepts: 1) the gene only codes "parts inheritance" while the genome codes "system inheritance" or the entire blueprint; 2) the nature of somatic genetic coding is fuzzy rather than precise, and genetic alterations are not just the results of genetic error but are in fact generated from internal adaptive mechanisms in response to environmental dynamics; 3) stress-response is less specific within cellular evolutionary context when compared to known biochemical specificities; and 4) most medical interventions have their unavoidable uncertainties and often can function as negative harmful stresses as trade-offs. The acknowledgment of diseases as adaptive systems calls for the action to integrate genome- (not simply individual gene-) mediated cellular evolution into molecular medicine.
Collapse
Affiliation(s)
- Henry H Heng
- Center for Molecular Medicine and Genetics, and Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| |
Collapse
|
24
|
Izgi K, Canatan H, Iskender B. Current status in cancer cell reprogramming and its clinical implications. J Cancer Res Clin Oncol 2016; 143:371-383. [DOI: 10.1007/s00432-016-2258-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
|
25
|
Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. BMC Cancer 2016; 16:680. [PMID: 27558259 PMCID: PMC4997669 DOI: 10.1186/s12885-016-2700-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 08/09/2016] [Indexed: 12/20/2022] Open
Abstract
Background Galectin-7 (Gal-7) is negatively regulated in cervical cancer, and appears to be a link between the apoptotic response triggered by cancer and the anti-tumoral activity of the immune system. Our understanding of how cervical cancer cells and their molecular networks adapt in response to the expression of Gal-7 remains limited. Methods Meta-analysis of Gal-7 expression was conducted in three cervical cancer cohort studies and TCGA. In silico prediction and bisulfite sequencing were performed to inquire epigenetic alterations. To study the effect of Gal-7 on cervical cancer, we ectopically re-expressed it in the HeLa and SiHa cervical cancer cell lines, and analyzed their transcriptome and SILAC-based proteome. We also examined the tumor and microenvironment host cell transcriptomes after xenotransplantation into immunocompromised mice. Differences between samples were assessed with the Kruskall-Wallis, Dunn’s Multiple Comparison and T tests. Kaplan–Meier and log-rank tests were used to determine overall survival. Results Gal-7 was constantly downregulated in our meta-analysis (p < 0.0001). Tumors with combined high Gal-7 and low galectin-1 expression (p = 0.0001) presented significantly better prognoses (p = 0.005). In silico and bisulfite sequencing assays showed de novo methylation in the Gal-7 promoter and first intron. Cells re-expressing Gal-7 showed a high apoptosis ratio (p < 0.05) and their xenografts displayed strong growth retardation (p < 0.001). Multiple gene modules and transcriptional regulators were modulated in response to Gal-7 reconstitution, both in cervical cancer cells and their microenvironments (FDR < 0.05 %). Most of these genes and modules were associated with tissue morphogenesis, metabolism, transport, chemokine activity, and immune response. These functional modules could exert the same effects in vitro and in vivo, even despite different compositions between HeLa and SiHa samples. Conclusions Gal-7 re-expression affects the regulation of molecular networks in cervical cancer that are involved in diverse cancer hallmarks, such as metabolism, growth control, invasion and evasion of apoptosis. The effect of Gal-7 extends to the microenvironment, where networks involved in its configuration and in immune surveillance are particularly affected. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2700-8) contains supplementary material, which is available to authorized users.
Collapse
|
26
|
Alekseenko IV, Pleshkan VV, Monastyrskaya GS, Kuzmich AI, Snezhkov EV, Didych DA, Sverdlov ED. Fundamentally low reproducibility in molecular genetic cancer research. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416070036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
27
|
Kim MC, Kim NY, Seo YR, Kim Y. An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line. J Cancer 2016; 7:1668-1679. [PMID: 27698904 PMCID: PMC5039388 DOI: 10.7150/jca.15423] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022] Open
Abstract
Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology. The RNA-seq data were analyzed with the MeDIP-seq data in an integrated way to identify the epigenetically modified genes that defined the SP. Concomitant changes in mRNA expression and DNA methylation were found in 122 genes, including 118 down-regulated genes with hypermethylation and 4 up-regulated genes with hypomethylation. Gene ontology revealed that a large portion of the genes belonged to the groups of biological processes such as stem cell maintenance, stem cell development, stem cell differentiation, and the negative regulation of the developmental process. Among these genes, BNC1, RPS6KA3, TWSG1 and DUSP15 contained aberrant methylation in the CpG islands of the promoter region, indicating that the genes regulated by DNA methylation characterized a distinct subpopulation of HMM cells. The present study provided valuable information to shed light on the epigenetic contributions to the generation and maintenance of tumor cell heterogeneity.
Collapse
Affiliation(s)
- Myung-Chul Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea.; BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea
| | - Na-Yon Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea.; BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea
| | - Yu-Ri Seo
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea
| | - Yongbaek Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea.; Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea
| |
Collapse
|
28
|
Reprogramming bladder cancer cells for studying cancer initiation and progression. Tumour Biol 2016; 37:13237-13245. [DOI: 10.1007/s13277-016-5226-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022] Open
|
29
|
Now H, Yoo JY. AG490 and PF431396 Sensitive Tyrosine Kinase Control the Population Heterogeneity of Basal STAT1 Activity in Ube1l Deficient Cells. PLoS One 2016; 11:e0159453. [PMID: 27427993 PMCID: PMC4948911 DOI: 10.1371/journal.pone.0159453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022] Open
Abstract
A population often contains distinct sub-populations, thereby increasing the complexity of the overall heterogeneity. However, the cellular origin and biological relevance of sub-populations in cell population have not been clearly identified. Here we demonstrated the novel roles of ISGylation, which is an IFN-induced post-translational modification, controlling heterogeneity at the population level in cultured adherent cells. Without UBE1L, an E1 enzyme of ISGylation, mouse embryonic fibroblasts (MEF) exhibited low viral resistance despite high STAT1 and ISG expression compared with the wild-type MEF. We observe that Ube1l−/− MEF populations consist of two behaviorally distinguishable sub-populations with distinct basal STAT1 activity, while wild-type MEF populations are unimodal. This population heterogeneity in Ube1l knock-out cells was perturbed by tyrosine kinase inhibitors, AG490 and PF431396. In contrast, the neutralization of type I IFN did not affect population heterogeneity. Based on these results, we concluded that UBE1L functions to adjust basal immunological states with the regulation of population heterogeneity.
Collapse
Affiliation(s)
- Hesung Now
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- * E-mail:
| |
Collapse
|
30
|
Chisholm RH, Lorenzi T, Clairambault J. Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation. Biochim Biophys Acta Gen Subj 2016; 1860:2627-45. [PMID: 27339473 DOI: 10.1016/j.bbagen.2016.06.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/25/2016] [Accepted: 06/05/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level. SCOPE OF REVIEW We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies. MAJOR CONCLUSIONS Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies. GENERAL SIGNIFICANCE Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
Collapse
Affiliation(s)
- Rebecca H Chisholm
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Tommaso Lorenzi
- School of Mathematics and Statistics, University of St Andrews, North Haugh, KY16 9SS, St Andrews, Scotland, United Kingdom. http://www.tommasolorenzi.com
| | - Jean Clairambault
- INRIA Paris, MAMBA team, 2, rue Simone Iff, CS 42112, 75589 Paris Cedex 12, France; Sorbonne Universités, UPMC Univ. Paris 6, UMR 7598, Laboratoire Jacques-Louis Lions, Boîte courrier 187, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| |
Collapse
|
31
|
Tellez CS, Juri DE, Do K, Picchi MA, Wang T, Liu G, Spira A, Belinsky SA. miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis. Cancer Res 2016; 76:4741-51. [PMID: 27302168 DOI: 10.1158/0008-5472.can-15-3367] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/16/2016] [Indexed: 02/06/2023]
Abstract
miRNA silencing by promoter hypermethylation may represent a mechanism by which lung cancer develops and progresses, but the miRNAs involved during malignant transformation are unknown. We previously established a model of premalignant lung cancer wherein we treated human bronchial epithelial cells (HBEC) with low doses of tobacco carcinogens. Here, we demonstrate that next-generation sequencing of carcinogen-transformed HBECs treated with the demethylating agent 5-aza-2'deoxycytidine revealed miR-196b and miR-34c-5p to be epigenetic targets. Bisulfite sequencing confirmed dense promoter hypermethylation indicative of silencing in multiple malignant cell lines and primary tumors. Chromatin immunoprecipitation studies further demonstrated an enrichment in repressive histone marks on the miR-196b promoter during HBEC transformation. Restoration of miR-196b expression by transfecting transformed HBECs with specific mimics led to cell-cycle arrest mediated in part through transcriptional regulation of the FOS oncogene, and miR-196b reexpression also significantly reduced the growth of tumor xenografts. Luciferase assays demonstrated that forced expression of miR-196b inhibited the FOS promoter and AP-1 reporter activity. Finally, a case-control study revealed that methylation of miR-196b in sputum was strongly associated with lung cancer (OR = 4.7, P < 0.001). Collectively, these studies highlight miR-196b as a tumor suppressor whose silencing early in lung carcinogenesis may provide a selective growth advantage to premalignant cells. Targeted delivery of miR-196b could therefore serve as a preventive or therapeutic strategy for the management of lung cancer. Cancer Res; 76(16); 4741-51. ©2016 AACR.
Collapse
Affiliation(s)
- Carmen S Tellez
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
| | - Daniel E Juri
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Kieu Do
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Teresa Wang
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Gang Liu
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Avrum Spira
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
| |
Collapse
|
32
|
Stepanenko AA, Andreieva SV, Korets KV, Mykytenko DO, Baklaushev VP, Huleyuk NL, Kovalova OA, Kotsarenko KV, Chekhonin VP, Vassetzky YS, Avdieiev SS, Dmitrenko VV. Temozolomide promotes genomic and phenotypic changes in glioblastoma cells. Cancer Cell Int 2016; 16:36. [PMID: 27158244 PMCID: PMC4858898 DOI: 10.1186/s12935-016-0311-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Temozolomide (TMZ) is a first-line drug for the treatment of glioblastoma. Long-term TMZ-treated tumour cells acquire TMZ resistance by profound reprogramming of the transcriptome, proteome, kinome, metabolism, and demonstrate versatile and opposite changes in proliferation, invasion, in vivo growth, and drug cross-resistance. We hypothesized that chromosomal instability (CIN) may be implicated in the generation of TMZ-driven molecular and phenotype diversity. CIN refers to the rate (cell-to-cell variability) with which whole chromosomes or portions of chromosomes are gained or lost. METHODS The long-term TMZ-treated cell lines were established in vitro (U251TMZ1, U251TMZ2, T98GTMZ and C6TMZ) and in vivo (C6R2TMZ). A glioma model was achieved by the intracerebral stereotactic implantation of C6 cells into the striatum region of rats. Genomic and phenotypic changes were analyzed by conventional cytogenetics, array CGH, trypan blue exclusion assay, soft agar colony formation assay, scratch wound healing assay, transwell invasion assay, quantitative polymerase chain reaction, and Western blotting. RESULTS Long-term TMZ treatment increased CIN-mediated genomic diversity in U251TMZ1, U251TMZ2 and T98GTMZ cells but reduced it in C6TMZ and C6R2TMZ cells. U251TMZ1 and U251TMZ2 cell lines, established in parallel with a similar treatment procedure with the only difference in the duration of treatment, underwent individual phenotypic changes. U251TMZ1 had a reduced proliferation and invasion but increased migration, whereas U251TMZ2 had an enhanced proliferation and invasion but no changes in migration. U251TMZ1 and U251TMZ2 cells demonstrated individual patterns in expression/activation of signal transduction proteins (e.g., MDM2, p53, ERK, AKT, and ASK). C6TMZ and C6R2TMZ cells had lower proliferation, colony formation efficiency and migration, whereas T98GTMZ cells had increased colony formation efficiency without any changes in proliferation, migration, and invasion. TMZ-treated lines demonstrated a differential response to a reduction in glucose concentration and an increased resistance to TMZ re-challenge but not temsirolimus (mTOR inhibitor) or U0126 (MEK1/2 inhibitor) treatment. CONCLUSION Long-term TMZ treatment selected resistant genotype-phenotype variants or generated novel versatile phenotypes by increasing CIN. An increase of resistance to TMZ re-challenge seems to be the only predictable trait intrinsic to all long-term TMZ-treated tumour cells. Changes in genomic diversity may be responsible for heterogeneous phenotypes of TMZ-treated cell lines.
Collapse
Affiliation(s)
- Aleksei A Stepanenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| | - Svitlana V Andreieva
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| | - Kateryna V Korets
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| | - Dmytro O Mykytenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| | - Vladimir P Baklaushev
- Department of Medicinal Nanobiotechnology, Pirogov Russian State Medical University, Ostrovitianov str. 1, Moscow, 117997 Russia ; Federal Research and Clinical Centre, FMBA of Russia, Orekhoviy Bulvar str. 28, Moscow, 115682 Russia
| | - Nataliya L Huleyuk
- Department of Diagnostic of Hereditary Pathology, Institute of Hereditary Pathology, National Academy of Medical Sciences of Ukraine, Lysenko str. 31A, Lviv, 79008 Ukraine
| | - Oksana A Kovalova
- Department of Experimental Cell System, R.E.Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Science of Ukraine, Vasylkivska str. 45, Kiev, 03022 Ukraine
| | - Kateryna V Kotsarenko
- Department of Human Genetics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| | - Vladimir P Chekhonin
- Department of Medicinal Nanobiotechnology, Pirogov Russian State Medical University, Ostrovitianov str. 1, Moscow, 117997 Russia
| | - Yegor S Vassetzky
- CNRS UMR8126, Institut de Cancérologie Gustave Roussy, Université Paris-Sud 11, Camille-Desmoulins str. 39, Villejuif, 94805 France
| | - Stanislav S Avdieiev
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| | - Vladimir V Dmitrenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Zabolotnogo str. 150, Kiev, 03680 Ukraine
| |
Collapse
|
33
|
Heng HHQ, Regan SM, Liu G, Ye CJ. Why it is crucial to analyze non clonal chromosome aberrations or NCCAs? Mol Cytogenet 2016; 9:15. [PMID: 26877768 PMCID: PMC4752783 DOI: 10.1186/s13039-016-0223-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/03/2016] [Indexed: 12/28/2022] Open
Abstract
Current cytogenetics has largely focused its efforts on the identification of recurrent karyotypic alterations, also known as clonal chromosomal aberrations (CCAs). The rationale of doing so seems simple: recurrent genetic changes are relevant for diseases or specific physiological conditions, while non clonal chromosome aberrations (NCCAs) are insignificant genetic background or noise. However, in reality, the vast majority of chromosomal alterations are NCCAs, and it is challenging to identify commonly shared CCAs in most solid tumors. Furthermore, the karyotype, rather than genes, represents the system inheritance, or blueprint, and each NCCA represents an altered genome system. These realizations underscore the importance of the re-evaluation of NCCAs in cytogenetic analyses. In this concept article, we briefly review the definition of NCCAs, some historical misconceptions about them, and why NCCAs are not insignificant "noise," but rather a highly significant feature of the cellular population for providing genome heterogeneity and complexity, representing one important form of fuzzy inheritance. The frequencies of NCCAs also represent an index to measure both internally- and environmentally-induced genome instability. Additionally, the NCCA/CCA cycle is associated with macro- and micro-cellular evolution. Lastly, elevated NCCAs are observed in many disease/illness conditions. Considering all of these factors, we call for the immediate action of studying and reporting NCCAs. Specifically, effort is needed to characterize and compare different types of NCCAs, to define their baseline in various tissues, to develop methods to access mitotic cells, to re-examine/interpret the NCCAs data, and to develop an NCCA database.
Collapse
Affiliation(s)
- Henry H. Q. Heng
- />Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- />Department of Pathology, Wayne State University School of Medicine, 3226 Scott Hall, 540 E. Canfield, Detroit, MI 48201 USA
| | - Sarah M. Regan
- />Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
- />Division of Graduate Medical Sciences, Boston University School of Medicine, Boston, MA 02118 USA
| | - Guo Liu
- />Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201 USA
| | - Christine J. Ye
- />The Division of Hematology/Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI USA
| |
Collapse
|
34
|
Ling XH, Chen ZY, Luo HW, Liu ZZ, Liang YK, Chen GX, Jiang FN, Zhong WDE. BCL9, a coactivator for Wnt/β-catenin transcription, is targeted by miR-30c and is associated with prostate cancer progression. Oncol Lett 2016; 11:2001-2008. [PMID: 26998113 PMCID: PMC4774446 DOI: 10.3892/ol.2016.4161] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 11/11/2015] [Indexed: 12/30/2022] Open
Abstract
B-cell lymphoma 9 (BCL9), a component of aberrantly activated Wnt signaling, is an important contributing factor to tumor progression. Our previous data indicated that downregulation of the tumor suppressor microRNA-30c (miR-30c) was a frequent pathogenetic event in prostate cancer (PCa). However, a functional link between miR-30c and BCL9/Wnt signaling, and their clinical and pathological significance in PCa, have not been well established. The present study demonstrated that miR-30c serves as a key negative regulator targeting BCL9 transcription in PCa cells. Ectopic expression of miR-30c was associated with reduced expression of Wnt pathway downstream targets, including c-Myc, cluster of differentiation 44 and sex determining region Y-box 9 in DU145 human PCa cells. Examination of clinical prostate specimens revealed higher levels of BCL9 expression in PCa compared with that in benign prostate tissues. After substantiating this finding by patient sample analysis, BCL9 expression or activity was observed to be closely correlated with PCa biochemical recurrence (BCR) and disease progression, whereas it was inversely associated with miR-30c. Furthermore, overexpression of BCL9 in PCa acted cooperatively with miR-30c low expression to predict earlier BCR in PCa. These findings indicate that inhibition of BCL9/Wnt signaling by miR-30c is important in the progression of PCa. Furthermore, the combined analysis of miR-30c and BCL9 may be valuable tool for prediction of BCR in PCa patients following radical prostatectomy.
Collapse
Affiliation(s)
- Xiao-Hui Ling
- Reproductive Medicine Centre, Huizhou Municipal Central People's Hospital, Huizhou, Guangdong 516001, P.R. China
| | - Zhi-Yun Chen
- Reproductive Medicine Centre, Huizhou Municipal Central People's Hospital, Huizhou, Guangdong 516001, P.R. China
| | - Hong-Wei Luo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China; Guangdong Provincial Institute of Nephrology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Ze-Zhen Liu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Ying-Ke Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Guan-Xing Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Fu-Neng Jiang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Wei-DE Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China; Guangdong Provincial Institute of Nephrology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| |
Collapse
|
35
|
Chang L, Li C, Guo T, Wang H, Ma W, Yuan Y, Liu Q, Ye Q, Liu Z. The human RNA surveillance factor UPF1 regulates tumorigenesis by targeting Smad7 in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:8. [PMID: 26759305 PMCID: PMC4711019 DOI: 10.1186/s13046-016-0286-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 01/07/2016] [Indexed: 01/08/2023]
Abstract
Background In spite of progress in diagnostics and treatment of Hepatocellular Carcinoma (HCC), its prognosis remains poor, and improved treatment strategies for HCC require detailed understanding of the underlying mechanism. In this investigation we studied the role of Up-frameshift 1 (UPF1) in the tumorigenesis of HCC. Methods We determined the expression level of UPF1 in HCC tissues with quantitative real-time PCR and western blotting and then studied its clinical significance. Sodium bisulfite sequencing was used to investigate the regulation of UPF1. We explored the biological significance of UPF1 with gain-and-loss-of-function analyses both in vitro and in vivo. The relationship between UPF1 and SMAD7 was also investigated by western blotting and immunofluorescence. Results A great downregulation of UPF1 due to promoter hypermethylation was observed in tumor tissues compared to their adjacent normal tissues. Meanwhile, patients with low UPF1 expression have significantly poorer prognosis than those with high expression. Functionally, UPF1 regulated HCC tumorigenesis both in vitro and in vivo. Moreover, the decreased UPF1 level in HCC reduces NMD efficiency and leads to up-regulation of Smad7, then affects the TGF-β pathway. Conclusion Our findings revealed that UPF1 is a potential tumor suppressive gene and may be a potential therapeutic target for HCC.
Collapse
Affiliation(s)
- Lei Chang
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Cuicui Li
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation Donghu Road 169, Wuhan, 430071, China.
| | - Tao Guo
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Haitao Wang
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Weijie Ma
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Yufeng Yuan
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Quanyan Liu
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Qifa Ye
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation Donghu Road 169, Wuhan, 430071, China.
| | - Zhisu Liu
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| |
Collapse
|
36
|
Stepanenko AA, Andreieva SV, Korets KV, Mykytenko DO, Baklaushev VP, Chekhonin VP, Dmitrenko VV. mTOR inhibitor temsirolimus and MEK1/2 inhibitor U0126 promote chromosomal instability and cell type-dependent phenotype changes of glioblastoma cells. Gene 2015; 579:58-68. [PMID: 26748241 DOI: 10.1016/j.gene.2015.12.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/14/2015] [Accepted: 12/26/2015] [Indexed: 01/22/2023]
Abstract
The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) and the RAF/mitogen-activated and extracellular signal-regulated kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathways are frequently deregulated in cancer. Temsirolimus (TEM) and its primary active metabolite rapamycin allosterically block mTOR complex 1 substrate recruitment. The context-/experimental setup-dependent opposite effects of rapamycin on the multiple centrosome formation, aneuploidy, DNA damage/repair, proliferation, and invasion were reported. Similarly, the context-dependent either tumor-promoting or suppressing effects of RAF-MEK-ERK pathway and its inhibitors were demonstrated. Drug treatment-mediated stress may promote chromosomal instability (CIN), accelerating changes in the genomic landscape and phenotype diversity. Here, we characterized the genomic and phenotypic changes of U251 and T98G glioblastoma cell lines long-term treated with TEM or U0126, an inhibitor of MEK1/2. TEM significantly increased clonal and non-clonal chromosome aberrations. Both TEM and U0126 affected copy number alterations (CNAs) pattern. A proliferation rate of U251TEM and U251U0126 cells was lower and higher, respectively, than control cells. Colony formation efficiency of U251TEM significantly decreased, whereas U251U0126 did not change. U251TEM and U251U0126 cells decreased migration. In contrast, T98GTEM and T98GU0126 cells did not change proliferation, colony formation efficiency, and migration. Changes in the sensitivity of inhibitor-treated cells to the reduction of the glucose concentration were observed. Our results suggest that CIN and adaptive reprogramming of signal transduction pathways may be responsible for the cell type-dependent phenotype changes of long-term TEM- or U0126-treated tumor cells.
Collapse
Affiliation(s)
- A A Stepanenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Zabolotnogo Str. 150, Kyiv 03680, Ukraine.
| | - S V Andreieva
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Zabolotnogo Str. 150, Kyiv 03680, Ukraine
| | - K V Korets
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Zabolotnogo Str. 150, Kyiv 03680, Ukraine
| | - D O Mykytenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Zabolotnogo Str. 150, Kyiv 03680, Ukraine
| | - V P Baklaushev
- Department of Medicinal Nanobiotechnology, Pirogov Russian State Medical University, Ostrovitianov str. 1, Moscow 117997, Russia; Federal Research and Clinical Centre, FMBA of Russia, Orekhoviy bulvar str. 28, Moscow 115682, Russia
| | - V P Chekhonin
- Department of Medicinal Nanobiotechnology, Pirogov Russian State Medical University, Ostrovitianov str. 1, Moscow 117997, Russia
| | - V V Dmitrenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, Zabolotnogo Str. 150, Kyiv 03680, Ukraine
| |
Collapse
|
37
|
Rida PCG, Cantuaria G, Reid MD, Kucuk O, Aneja R. How to be good at being bad: centrosome amplification and mitotic propensity drive intratumoral heterogeneity. Cancer Metastasis Rev 2015; 34:703-13. [PMID: 26358854 PMCID: PMC4778553 DOI: 10.1007/s10555-015-9590-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cancer is truly an iconic disease--a tour de force whose multiple formidable strengths can be attributed to the bewildering heterogeneity that a tumor can manifest both spatially and temporally. A Darwinian evolutionary process is believed to undergird, at least in part, the generation of this heterogeneity that contributes to poor clinical outcomes. Risk assessment in clinical oncology is currently based on a small number of clinicopathologic factors (like stage, histological grade, receptor status, and serum tumor markers) and offers limited accuracy in predicting disease course as evidenced by the prognostic heterogeneity that persists in risk segments produced by present-day models. We posit that this insufficiency stems from the exclusion of key risk contributors from such models, especially the omission of certain factors implicated in generating intratumoral heterogeneity. The extent of centrosome amplification and the mitotic propensity inherent in a tumor are two such vital factors whose contributions to poor prognosis are presently overlooked in risk prognostication. Supernumerary centrosomes occur widely in tumors and are potent drivers of chromosomal instability that fosters intratumoral heterogeneity. The mitotic propensity of a proliferating population of tumor cells reflects the cell cycling kinetics of that population. Since frequent passage through improperly regulated mitotic divisions accelerates production of diverse genotypes, the mitotic propensity inherent in a tumor serves as a powerful beacon of risk. In this review, we highlight how centrosome amplification and error-prone mitoses contribute to poor clinical outcomes and urge the need to develop these cancer-specific traits as much-needed clinically-facile prognostic biomarkers with immense potential value for individualized cancer treatment in the clinic.
Collapse
Affiliation(s)
- Padmashree C G Rida
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
- Novazoi Theranostics Inc., Plano, TX, 75025, USA
| | - Guilherme Cantuaria
- Department of Gynecologic Oncology, Northside Hospital Cancer Institute, Atlanta, GA, 30342, USA
| | - Michelle D Reid
- Deparment of Pathology, Emory Univ Hospital, Atlanta, GA, 30033, USA
| | - Omer Kucuk
- Winship Cancer Institute of Emory University, Atlanta, GA, 30322, USA
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
- Institute of Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA.
| |
Collapse
|
38
|
Identification of the specific epigenetic alterations associated with chemo-resistance via reprogramming of cancer cells. Med Hypotheses 2015; 85:710-4. [PMID: 26527497 DOI: 10.1016/j.mehy.2015.10.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/11/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022]
Abstract
BACKGROUND Chemo-resistance is the main obstacle in cancer therapy, limiting the effectiveness of drug treatment. Epigenetics-mediated changes are suggested as a critical factor paying the chemo-resistance phenotype. Since epigenetic modulations are a reversible phenomenon, reversion of epigenetic changes represents a promising therapeutic approach for cancer. However, heterogeneity in epigenetic marks in tumor cells makes it difficult to identify the specific epigenetic aberrations contributing to chemo-resistance. Our hypothesis aimed to explore this issue to add therapeutic options for cancer. PRESENTATION OF THE HYPOTHESIS Epigenetic alterations, the main mediator of cellular reprogramming, occur rapidly upon exposure to chemotherapy. Recent studies have demonstrated that reprogramming resets/erases the epigenetic marks established during differentiation to specific somatic cell types. To overcome the heterogeneous nature of cancer cells, we will attempt to make homogenous cancer cell colonies by reprogramming. Comparison of the drug-resistant cancer cells obtained from these colonies to parent cancer cells and reprogrammed cancer cells is an effective way to determine the precise epigenetic alterations underlying specific chemo-resistance. TESTING THE HYPOTHESIS Cellular reprogramming of cancer cells led to generation of homogenous colonies. Following lineage specification and long term drug treatment, the obtained drug resistance cells will be compared with parent cancer cells for whole genome epigenetic signature. IMPLICATIONS OF THE HYPOTHESIS A key implication of this hypothesis is that determination of the usefulness of cellular reprogramming of cancer cells enabling the identification of specific epigenetic modulation associated with particular drug resistance will enable exploration of new research avenues for cancer treatment.
Collapse
|
39
|
Stepanenko A, Dmitrenko V. HEK293 in cell biology and cancer research: phenotype, karyotype, tumorigenicity, and stress-induced genome-phenotype evolution. Gene 2015; 569:182-90. [DOI: 10.1016/j.gene.2015.05.065] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/11/2015] [Accepted: 05/26/2015] [Indexed: 01/18/2023]
|
40
|
Talukder AK, Ravishankar S, Sasmal K, Gandham S, Prabhukumar J, Achutharao PH, Barh D, Blasi F. XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine. PLoS One 2015; 10:e0123569. [PMID: 25905921 PMCID: PMC4408095 DOI: 10.1371/journal.pone.0123569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
In translational cancer medicine, implicated pathways and the relevant master genes are of focus. Exome's specificity, processing-time, and cost advantage makes it a compelling tool for this purpose. However, analysis of exome lacks reliable combinatory analysis tools and techniques. In this paper we present XomAnnotate – a meta- and functional-analysis software for exome. We compared UnifiedGenotyper, Freebayes, Delly, and Lumpy algorithms that were designed for whole-genome and combined their strengths in XomAnnotate for exome data through meta-analysis to identify comprehensive mutation profile (SNPs/SNVs, short inserts/deletes, and SVs) of patients. The mutation profile is annotated followed by functional analysis through pathway enrichment and network analysis to identify most critical genes and pathways implicated in the disease genesis. The efficacy of the software is verified through MDS and clustering and tested with available 11 familial non-BRCA1/BRCA2 breast cancer exome data. The results showed that the most significantly affected pathways across all samples are cell communication and antigen processing and presentation. ESCO1, HYAL1, RAF1 and PRKCA emerged as the key genes. Network analysis further showed the purine and propanotate metabolism pathways along with RAF1 and PRKCA genes to be master regulators in these patients. Therefore, XomAnnotate is able to use exome data to identify entire mutation landscape, pathways, and the master genes accurately with wide concordance from earlier microarray and whole-genome studies -- making it a suitable biomedical software for using exome in next-generation translational medicine.
Collapse
Affiliation(s)
- Asoke K. Talukder
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
- * E-mail:
| | - Shashidhar Ravishankar
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Krittika Sasmal
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Santhosh Gandham
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Jyothsna Prabhukumar
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Prahalad H. Achutharao
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Debmalya Barh
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, 721172, India
| | - Francesco Blasi
- Laboratory of Transcriptional Regulation in Development and Cancer, IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milano, Italy
| |
Collapse
|
41
|
Yamamoto Y, Hyodo I, Koga Y, Tsumura R, Sato R, Obonai T, Fuchigami H, Furuya F, Yasunaga M, Harada M, Kato Y, Ohtsu A, Matsumura Y. Enhanced antitumor effect of anti-tissue factor antibody-conjugated epirubicin-incorporating micelles in xenograft models. Cancer Sci 2015; 106:627-34. [PMID: 25711681 PMCID: PMC4452165 DOI: 10.1111/cas.12645] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/07/2015] [Accepted: 02/20/2015] [Indexed: 12/23/2022] Open
Abstract
For the creation of a successful antibody–drug conjugate (ADC), both scientific and clinical evidence has indicated that highly toxic anticancer agents (ACA) should be conjugated to a monoclonal antibody (mAb) to administer a reasonable amount of ADC to patients without compromising the affinity of the mAb. For ordinary ACA, the conjugation of a mAb to ACA-loaded micellar nanoparticles is clinically applicable. Tissue factor (TF) is often overexpressed in various cancer cells and tumor vascular endothelium. Accordingly, anti-TF-NC-6300, consisting of epirubicin-incorporating micelles (NC-6300) conjugated with the F(ab')2 of anti-TF mAb was developed. The in vitro and in vivo efficacy and pharmacokinetics of anti-TF-NC-6300 were compared to NC-6300 using two human pancreatic cancer cell lines, BxPC3 (high TF expression) and SUIT2 (low TF expression), and a gastric cancer cell line, 44As3 (high TF expression). The intracellular uptake of epirubicin was faster and greater in BxPC3 cells treated with anti-TF-NC-6300, compared with NC-6300. Anti-TF-NC-6300 showed a superior antitumor activity in BxPC3 and 44As3 xenografts, compared with NC-6300, while the activities of both micelles were similar in the SUIT2 xenograft. A higher tumor accumulation of anti-TF-NC-6300 compared to NC-6300 was seen, regardless of the TF expression levels. However, anti-TF-NC-6300 appeared to be localized to the tumor cells with high TF expression. These results indicated that the enhanced antitumor effect of anti-TF-NC6300 may be independent of the tumor accumulation but may depend on the selective intratumor localization and the preferential internalization of anti-TF-NC-6300 into high TF tumor cells.
Collapse
Affiliation(s)
- Yoshiyuki Yamamoto
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan.,Department of Gastroenterology and Hepatology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ichinosuke Hyodo
- Department of Gastroenterology and Hepatology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshikatsu Koga
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Ryo Tsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Ryuta Sato
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Toshihumi Obonai
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hirobumi Fuchigami
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Fumiaki Furuya
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Masahiro Yasunaga
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | | | - Yasuki Kato
- Research Division, NanoCarrier Co. Ltd., Kashiwa, Japan
| | - Atsushi Ohtsu
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| |
Collapse
|
42
|
Detection and Automated Scoring of Dicentric Chromosomes in Nonstimulated Lymphocyte Prematurely Condensed Chromosomes After Telomere and Centromere Staining. Int J Radiat Oncol Biol Phys 2015; 91:640-9. [DOI: 10.1016/j.ijrobp.2014.10.048] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/27/2014] [Accepted: 10/24/2014] [Indexed: 12/24/2022]
|
43
|
Wnuk M, Miedziak B, Kulak K, Panek A, Golec E, Deregowska A, Adamczyk J, Lewinska A. Single-cell analysis of aneuploidy events using yeast whole chromosome painting probes (WCPPs). J Microbiol Methods 2015; 111:40-9. [PMID: 25639739 DOI: 10.1016/j.mimet.2015.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 01/27/2015] [Accepted: 01/27/2015] [Indexed: 11/18/2022]
Abstract
Aneuploidy is considered a widespread genetic variation in such cell populations as yeast strains, cell lines and cancer cells, and spontaneous changes in the chromosomal copy number may have implications for data interpretation. Thus, aneuploidy monitoring is essential during routine laboratory practice, especially while conducting biochemical and/or gene expression analyses. In the present study, we constructed a panel of whole chromosome painting probes (WCPPs) to monitor aneuploidy in a single yeast Saccharomyces cerevisiae cell. The WCPP-based system was validated using "normal" haploid and diploid cells, as well as disomic cells both with and without cell synchronisation. FISH that utilised WCPPs was combined with DNA cell cycle analysis (imaging cytometry) to provide a detailed analysis of signal variability during the cell cycle. Chromosome painting can be utilised to detect spontaneously formed disomic chromosomes and study aneuploidy-promoting conditions. For example, the frequency of disomic chromosomes was increased in cells lacking NAD(+)-dependent histone deacetylase Sir2p compared with wild-type cells (p<0.05). In conclusion, WCPPs may be considered to be a powerful molecular tool to identify individual genomic differences. Moreover, the WCPP-based system may be used at the single-cell level of analysis to supplement array-based techniques and high-throughput analyses at the population scale.
Collapse
Affiliation(s)
- Maciej Wnuk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland.
| | - Beata Miedziak
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Klaudia Kulak
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Anita Panek
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Ewelina Golec
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Anna Deregowska
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Jagoda Adamczyk
- Department of Genetics, University of Rzeszow, Rejtana 16C, 35-959 Rzeszow, Poland
| | - Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Poland
| |
Collapse
|
44
|
Stepanenko A, Andreieva S, Korets K, Mykytenko D, Huleyuk N, Vassetzky Y, Kavsan V. Step-wise and punctuated genome evolution drive phenotype changes of tumor cells. Mutat Res 2015; 771:56-69. [PMID: 25771981 DOI: 10.1016/j.mrfmmm.2014.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
The pattern of genome evolution can be divided into two phases: the step-wise continuous phase (step-wise clonal evolution, stable dominant clonal chromosome aberrations (CCAs), and low frequency of non-CCAs, NCCAs) and punctuated phase (marked by elevated NCCAs and transitional CCAs). Depending on the phase, system stresses (the diverse CIN promoting factors) may lead to the very different phenotype responses. To address the contribution of chromosome instability (CIN) to phenotype changes of tumor cells, we characterized CCAs/NCCAs of HeLa and HEK293 cells, and their derivatives after genotoxic stresses (a stable plasmid transfection, ectopic expression of cancer-associated CHI3L1 gene or treatment with temozolomide) by conventional cytogenetics, copy number alterations (CNAs) by array comparative genome hybridization, and phenotype changes by cell viability and soft agar assays. Transfection of either the empty vector pcDNA3.1 or pcDNA3.1_CHI3L1 into 293 cells initiated the punctuated genome changes. In contrast, HeLa_CHI3L1 cells demonstrated the step-wise genome changes. Increased CIN correlated with lower viability of 293_pcDNA3.1 cells but higher colony formation efficiency (CFE). Artificial CHI3L1 production in 293_CHI3L1 cells increased viability and further contributed to CFE. The opposite growth characteristics of 293_CHI3L1 and HeLa_CHI3L1 cells were revealed. The effect and function of a (trans)gene can be opposite and versatile in cells with different genetic network, which is defined by genome context. Temozolomide treatment of 293_pcDNA3.1 cells intensified the stochastic punctuated genome changes and CNAs, and significantly reduced viability and CFE. In contrast, temozolomide treatment of HeLa_CHI3L1 cells promoted the step-wise genome changes, CNAs, and increased viability and CFE, which did not correlate with the ectopic CHI3L1 production. Thus, consistent coevolution of karyotypes and phenotypes was observed. CIN as a driving force of genome evolution significantly influences growth characteristics of tumor cells and should be always taken into consideration during the different experimental manipulations.
Collapse
Affiliation(s)
- Aleksei Stepanenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine.
| | - Svitlana Andreieva
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Kateryna Korets
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Dmytro Mykytenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Nataliya Huleyuk
- Institute of Hereditary Pathology, National Academy of Medical Sciences of Ukraine, Lviv 79008, Ukraine
| | - Yegor Vassetzky
- CNRS UMR8126, Université Paris-Sud 11, Institut de Cancérologie Gustave Roussy, Villejuif 94805, France
| | - Vadym Kavsan
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| |
Collapse
|
45
|
Shi M, Wang S, Yao Y, Li Y, Zhang H, Han F, Nie H, Su J, Wang Z, Yue L, Cao J, Li Y. Biological and clinical significance of epigenetic silencing of MARVELD1 gene in lung cancer. Sci Rep 2014; 4:7545. [PMID: 25520033 PMCID: PMC4269892 DOI: 10.1038/srep07545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/01/2014] [Indexed: 01/20/2023] Open
Abstract
Epigenetic silence in cancer frequently altered signal-transduction pathways during the early stages of tumor development. Recent progress in the field of cancer epigenetics has led to new opportunities for diagnosis and treatment of cancer. We previously demonstrated that novel identified nuclear factor MARVELD1 was widely expressed in human tissues, but down-regulated by promoter methylation in multiple cancers. This study was carried out to determine the biological and clinical significance of MARVELD1 gene silencing in lung cancer. Here, we found the reduced MARVELD1 expression significantly correlated with diagnostic histopathology and malignant degree of lung cancers. DNA hypermethylation and histone deacetylation synergistically inactivated MARVELD1 gene in lung cancer cells. Moreover, MARVELD1 modulated the efficiency of nonsense-mediated mRNA decay (NMD) through interaction with NMD core factor SMG1. The decreased MARVELD1 level in lung cancer reduces NMD efficiency through diminishing the association between NMD complex component UPF1/SMG1 and premature termination codons containing mRNA (PTC-mRNA). The results suggested that MARVELD1 silencing is an appealing diagnostic biomarker for lung cancer and epigenetic silencing of MARVELD1 gene links with the regulatory mechanism of NMD pathway in lung cancer, which may be required for tumorigenesis.
Collapse
Affiliation(s)
- Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Shan Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yuanfei Yao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yiqun Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Hao Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jie Su
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zeyu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Yue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jingyan Cao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| |
Collapse
|
46
|
Tsuchiya M, Nakajima Y, Waku T, Hiyoshi H, Morishita T, Furumai R, Hayashi Y, Kishimoto H, Kimura K, Yanagisawa J. CHIP buffers heterogeneous Bcl-2 expression levels to prevent augmentation of anticancer drug-resistant cell population. Oncogene 2014; 34:4656-63. [DOI: 10.1038/onc.2014.387] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 09/25/2014] [Accepted: 10/14/2014] [Indexed: 01/12/2023]
|
47
|
Heng HH, Bremer SW, Stevens JB, Horne SD, Liu G, Abdallah BY, Ye KJ, Ye CJ. Chromosomal instability (CIN): what it is and why it is crucial to cancer evolution. Cancer Metastasis Rev 2014; 32:325-40. [PMID: 23605440 DOI: 10.1007/s10555-013-9427-7] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Results of various cancer genome sequencing projects have "unexpectedly" challenged the framework of the current somatic gene mutation theory of cancer. The prevalence of diverse genetic heterogeneity observed in cancer questions the strategy of focusing on contributions of individual gene mutations. Much of the genetic heterogeneity in tumors is due to chromosomal instability (CIN), a predominant hallmark of cancer. Multiple molecular mechanisms have been attributed to CIN but unifying these often conflicting mechanisms into one general mechanism has been challenging. In this review, we discuss multiple aspects of CIN including its definitions, methods of measuring, and some common misconceptions. We then apply the genome-based evolutionary theory to propose a general mechanism for CIN to unify the diverse molecular causes. In this new evolutionary framework, CIN represents a system behavior of a stress response with adaptive advantages but also serves as a new potential cause of further destabilization of the genome. Following a brief review about the newly realized functions of chromosomes that defines system inheritance and creates new genomes, we discuss the ultimate importance of CIN in cancer evolution. Finally, a number of confusing issues regarding CIN are explained in light of the evolutionary function of CIN.
Collapse
Affiliation(s)
- Henry H Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA,
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Epigenetic dynamics: role of epimarks and underlying machinery in plants exposed to abiotic stress. Int J Genomics 2014; 2014:187146. [PMID: 25313351 PMCID: PMC4182684 DOI: 10.1155/2014/187146] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/28/2014] [Accepted: 08/07/2014] [Indexed: 12/21/2022] Open
Abstract
Abiotic stress induces several changes in plants at physiological and molecular level. Plants have evolved regulatory mechanisms guided towards establishment of stress tolerance in which epigenetic modifications play a pivotal role. We provide examples of gene expression changes that are brought about by conversion of active chromatin to silent heterochromatin and vice versa. Methylation of CG sites and specific modification of histone tail determine whether a particular locus is transcriptionally active or silent. We present a lucid review of epigenetic machinery and epigenetic alterations involving DNA methylation, histone tail modifications, chromatin remodeling, and RNA directed epigenetic changes.
Collapse
|
49
|
Anchang B, Do MT, Zhao X, Plevritis SK. CCAST: a model-based gating strategy to isolate homogeneous subpopulations in a heterogeneous population of single cells. PLoS Comput Biol 2014; 10:e1003664. [PMID: 25078380 PMCID: PMC4117418 DOI: 10.1371/journal.pcbi.1003664] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 04/25/2014] [Indexed: 12/12/2022] Open
Abstract
A model-based gating strategy is developed for sorting cells and analyzing populations of single cells. The strategy, named CCAST, for Clustering, Classification and Sorting Tree, identifies a gating strategy for isolating homogeneous subpopulations from a heterogeneous population of single cells using a data-derived decision tree representation that can be applied to cell sorting. Because CCAST does not rely on expert knowledge, it removes human bias and variability when determining the gating strategy. It combines any clustering algorithm with silhouette measures to identify underlying homogeneous subpopulations, then applies recursive partitioning techniques to generate a decision tree that defines the gating strategy. CCAST produces an optimal strategy for cell sorting by automating the selection of gating markers, the corresponding gating thresholds and gating sequence; all of these parameters are typically manually defined. Even though CCAST is optimized for cell sorting, it can be applied for the identification and analysis of homogeneous subpopulations among heterogeneous single cell data. We apply CCAST on single cell data from both breast cancer cell lines and normal human bone marrow. On the SUM159 breast cancer cell line data, CCAST indicates at least five distinct cell states based on two surface markers (CD24 and EPCAM) and provides a gating sorting strategy that produces more homogeneous subpopulations than previously reported. When applied to normal bone marrow data, CCAST reveals an efficient strategy for gating T-cells without prior knowledge of the major T-cell subtypes and the markers that best define them. On the normal bone marrow data, CCAST also reveals two major mature B-cell subtypes, namely CD123+ and CD123- cells, which were not revealed by manual gating but show distinct intracellular signaling responses. More generally, the CCAST framework could be used on other biological and non-biological high dimensional data types that are mixtures of unknown homogeneous subpopulations.
Collapse
Affiliation(s)
- Benedict Anchang
- Department of Radiology, Center for Cancer Systems Biology, Stanford University, Stanford, California, United States of America
| | - Mary T. Do
- Department of Radiology, Center for Cancer Systems Biology, Stanford University, Stanford, California, United States of America
| | - Xi Zhao
- Department of Radiology, Center for Cancer Systems Biology, Stanford University, Stanford, California, United States of America
| | - Sylvia K. Plevritis
- Department of Radiology, Center for Cancer Systems Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
50
|
Horne SD, Pollick SA, Heng HHQ. Evolutionary mechanism unifies the hallmarks of cancer. Int J Cancer 2014; 136:2012-21. [PMID: 24957955 DOI: 10.1002/ijc.29031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/13/2014] [Indexed: 12/15/2022]
Abstract
The basis for the gene mutation theory of cancer that dominates current molecular cancer research consists of: the belief that gene-level aberrations such as mutations are the main cause of cancers, the concept that stepwise gene mutation accumulation drives cancer progression, and the hallmarks of cancer. The research community swiftly embraced the hallmarks of cancer, as such synthesis has supported the notions that common cancer genes are responsible for the majority of cancers and the complexity of cancer can be dissected into simplified molecular principles. The gene/pathway classification based on individual hallmarks provides explanation for the large number of diverse gene mutations, which is in contrast to the original estimation that only a handful of gene mutations would be discovered. Further, these hallmarks have been highly influential as they also provide the rationale and research direction for continued gene-based cancer research. While the molecular knowledge of these hallmarks is drastically increasing, the clinical implication remains limited, as cancer dynamics cannot be summarized by a few isolated/fixed molecular principles. Furthermore, the highly heterogeneous genetic signature of cancers, including massive stochastic genome alterations, challenges the utility of continuously studying each individual gene mutation under the framework of these hallmarks. It is therefore necessary to re-evaluate the concept of cancer hallmarks through the lens of cancer evolution. In this analysis, the evolutionary basis for the hallmarks of cancer will be discussed and the evolutionary mechanism of cancer suggested by the genome theory will be employed to unify the diverse molecular mechanisms of cancer.
Collapse
Affiliation(s)
- Steven D Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
| | | | | |
Collapse
|