1
|
Tong X, Qu N, Kong X, Ni S, Zhou J, Wang K, Zhang L, Wen Y, Shi J, Zhang S, Li X, Zheng M. Deep representation learning of chemical-induced transcriptional profile for phenotype-based drug discovery. Nat Commun 2024; 15:5378. [PMID: 38918369 PMCID: PMC11199551 DOI: 10.1038/s41467-024-49620-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Artificial intelligence transforms drug discovery, with phenotype-based approaches emerging as a promising alternative to target-based methods, overcoming limitations like lack of well-defined targets. While chemical-induced transcriptional profiles offer a comprehensive view of drug mechanisms, inherent noise often obscures the true signal, hindering their potential for meaningful insights. Here, we highlight the development of TranSiGen, a deep generative model employing self-supervised representation learning. TranSiGen analyzes basal cell gene expression and molecular structures to reconstruct chemical-induced transcriptional profiles with high accuracy. By capturing both cellular and compound information, TranSiGen-derived representations demonstrate efficacy in diverse downstream tasks like ligand-based virtual screening, drug response prediction, and phenotype-based drug repurposing. Notably, in vitro validation of TranSiGen's application in pancreatic cancer drug discovery highlights its potential for identifying effective compounds. We envisage that integrating TranSiGen into the drug discovery and mechanism research holds significant promise for advancing biomedicine.
Collapse
Affiliation(s)
- Xiaochu Tong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Ning Qu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xiangtai Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Shengkun Ni
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jingyi Zhou
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Kun Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Lehan Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yiming Wen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Jiangshan Shi
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| |
Collapse
|
2
|
Saleh O, Shihadeh H, Yousef A, Erekat H, Abdallh F, Al-Leimon A, Elsalhy R, Altiti A, Dajani M, AlBarakat MM. The Effect of Intratumor Heterogeneity in Pancreatic Ductal Adenocarcinoma Progression and Treatment. Pancreas 2024; 53:e450-e465. [PMID: 38728212 DOI: 10.1097/mpa.0000000000002342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
BACKGROUND AND OBJECTIVES Pancreatic cancer is one of the most lethal malignancies. Even though many substantial improvements in the survival rates for other major cancer forms were made, pancreatic cancer survival rates have remained relatively unchanged since the 1960s. Even more, no standard classification system for pancreatic cancer is based on cellular biomarkers. This review will discuss and provide updates about the role of stem cells in the progression of PC, the genetic changes associated with it, and the promising biomarkers for diagnosis. MATERIALS AND METHODS The search process used PubMed, Cochrane Library, and Scopus databases to identify the relevant and related articles. Articles had to be published in English to be considered. RESULTS The increasing number of studies in recent years has revealed that the diversity of cancer-associated fibroblasts is far greater than previously acknowledged, which highlights the need for further research to better understand the various cancer-associated fibroblast subpopulations. Despite the huge diversity in pancreatic cancer, some common features can be noted to be shared among patients. Mutations involving CDKN2, P53, and K-RAS can be seen in a big number of patients, for example. Similarly, some patterns of genes and biomarkers expression and the level of their expression can help in predicting cancer behavior such as metastasis and drug resistance. The current trend in cancer research, especially with the advancement in technology, is to sequence everything in hopes of finding disease-related mutations. CONCLUSION Optimizing pancreatic cancer treatment requires clear classification, understanding CAF roles, and exploring stroma reshaping approaches.
Collapse
Affiliation(s)
- Othman Saleh
- From the Faculty of Medicine, The Hashemite University, Zarqa
| | | | | | - Hana Erekat
- School of medicine, University of Jordan, Amman
| | - Fatima Abdallh
- From the Faculty of Medicine, The Hashemite University, Zarqa
| | | | | | | | - Majd Dajani
- From the Faculty of Medicine, The Hashemite University, Zarqa
| | - Majd M AlBarakat
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| |
Collapse
|
3
|
Terracina S, Tarani L, Ceccanti M, Vitali M, Francati S, Lucarelli M, Venditti S, Verdone L, Ferraguti G, Fiore M. The Impact of Oxidative Stress on the Epigenetics of Fetal Alcohol Spectrum Disorders. Antioxidants (Basel) 2024; 13:410. [PMID: 38671857 PMCID: PMC11047541 DOI: 10.3390/antiox13040410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Fetal alcohol spectrum disorders (FASD) represent a continuum of lifelong impairments resulting from prenatal exposure to alcohol, with significant global impact. The "spectrum" of disorders includes a continuum of physical, cognitive, behavioral, and developmental impairments which can have profound and lasting effects on individuals throughout their lives, impacting their health, social interactions, psychological well-being, and every aspect of their lives. This narrative paper explores the intricate relationship between oxidative stress and epigenetics in FASD pathogenesis and its therapeutic implications. Oxidative stress, induced by alcohol metabolism, disrupts cellular components, particularly in the vulnerable fetal brain, leading to aberrant development. Furthermore, oxidative stress is implicated in epigenetic changes, including alterations in DNA methylation, histone modifications, and microRNA expression, which influence gene regulation in FASD patients. Moreover, mitochondrial dysfunction and neuroinflammation contribute to epigenetic changes associated with FASD. Understanding these mechanisms holds promise for targeted therapeutic interventions. This includes antioxidant supplementation and lifestyle modifications to mitigate FASD-related impairments. While preclinical studies show promise, further clinical trials are needed to validate these interventions' efficacy in improving clinical outcomes for individuals affected by FASD. This comprehensive understanding of the role of oxidative stress in epigenetics in FASD underscores the importance of multidisciplinary approaches for diagnosis, management, and prevention strategies. Continued research in this field is crucial for advancing our knowledge and developing effective interventions to address this significant public health concern.
Collapse
Affiliation(s)
- Sergio Terracina
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
| | - Luigi Tarani
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, 00185 Roma, Italy
| | - Mauro Ceccanti
- SITAC, Società Italiana per il Trattamento dell’Alcolismo e le sue Complicanze, 00185 Rome, Italy;
| | | | - Silvia Francati
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
- Pasteur Institute Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Sabrina Venditti
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University, 00185 Rome, Italy
| | - Loredana Verdone
- Institute of Molecular Biology and Pathology (IBPM-CNR), 00185 Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
| | - Marco Fiore
- Institute of Biochemistry and Cell Biology (IBBC-CNR), Department of Sensory Organs, Sapienza University of Rome, 00185 Roma, Italy
| |
Collapse
|
4
|
Bahado‐Singh RO, Turkoglu O, Aydas B, Vishweswaraiah S. Precision oncology: Artificial intelligence, circulating cell-free DNA, and the minimally invasive detection of pancreatic cancer-A pilot study. Cancer Med 2023; 12:19644-19655. [PMID: 37787018 PMCID: PMC10587955 DOI: 10.1002/cam4.6604] [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] [Received: 05/23/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is among the most lethal cancers. The lack of effective tools for early detection results in late tumor detection and, consequently, high mortality rate. Precision oncology aims to develop targeted individual treatments based on advanced computational approaches of omics data. Biomarkers, such as global alteration of cytosine (CpG) methylation, can be pivotal for these objectives. In this study, we performed DNA methylation profiling of pancreatic cancer patients using circulating cell-free DNA (cfDNA) and artificial intelligence (AI) including Deep Learning (DL) for minimally invasive detection to elucidate the epigenetic pathogenesis of PC. METHODS The Illumina Infinium HD Assay was used for genome-wide DNA methylation profiling of cfDNA in treatment-naïve patients. Six AI algorithms were used to determine PC detection accuracy based on cytosine (CpG) methylation markers. Additional strategies for minimizing overfitting were employed. The molecular pathogenesis was interrogated using enrichment analysis. RESULTS In total, we identified 4556 significantly differentially methylated CpGs (q-value < 0.05; Bonferroni correction) in PC versus controls. Highly accurate PC detection was achieved with all 6 AI platforms (Area under the receiver operator characteristics curve [0.90-1.00]). For example, DL achieved AUC (95% CI): 1.00 (0.95-1.00), with a sensitivity and specificity of 100%. A separate modeling approach based on logistic regression-based yielded an AUC (95% CI) 1.0 (1.0-1.0) with a sensitivity and specificity of 100% for PC detection. The top four biological pathways that were epigenetically altered in PC and are known to be linked with cancer are discussed. CONCLUSION Using a minimally invasive approach, AI, and epigenetic analysis of circulating cfDNA, high predictive accuracy for PC was achieved. From a clinical perspective, our findings suggest that that early detection leading to improved overall survival may be achievable in the future.
Collapse
Affiliation(s)
- Ray O. Bahado‐Singh
- Department of Obstetrics and GynecologyCorewell Health – William Beaumont University HospitalRoyal OakMichiganUSA
| | - Onur Turkoglu
- Department of Obstetrics and GynecologyCorewell Health – William Beaumont University HospitalRoyal OakMichiganUSA
| | - Buket Aydas
- Department of Care Management AnalyticsBlue Cross Blue Shield of MichiganDetroitMichiganUSA
| | | |
Collapse
|
5
|
DNA methylome in pancreatic cancer identified novel promoter hyper-methylation in NPY and FAIM2 genes associated with poor prognosis in Indian patient cohort. Cancer Cell Int 2022; 22:334. [PMID: 36329447 PMCID: PMC9635159 DOI: 10.1186/s12935-022-02737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the leading cancers worldwide and has a poor survival, with a 5-year survival rate of only 8.5%. In this study we investigated altered DNA methylation associated with PDAC severity and prognosis. Methods Methylome data, generated using 450 K bead array, was compared between paired PDAC and normal samples in the TCGA cohort (n = 9) and our Indian cohort (n = 7). The total Indian Cohort (n = 75) was split into cohort 1 (n = 7), cohort 2 (n = 22), cohort 3 (n = 26) and cohort 4 (n = 20).Validation of differential methylation (6 selected CpG loci) and associated gene expression for differentially methylated genes (10 selected gDMs) were carried out in separate validation cohorts, using MSP, RT-PCR and IHC correlations between methylation and gene expression were observed in TCGA, GTEx cohorts and in validation cohorts. Kaplan–Meier survival analysis was done to study differential prognosis, during 2–5 years of follow-up. Results We identified 156 DMPs, mapped to 91 genes (gDMs), in PDAC; 68 (43.5%) DMPs were found to be differentially methylated both in TCGA cohort and our cohort, with significant concordance at hypo- and hyper-methylated loci. Enrichments of “regulation of ion transport”, “Interferon alpha/beta signalling”, “morphogenesis and development” and “transcriptional dysregulation” pathways were observed among 91 gDMs. Hyper-methylation of NPY and FAIM2 genes with down-regulated expression in PDAC, were significantly associated with poor prognosis in the Indian patient cohort. Conclusions Ethnic variations among populations may determine the altered epigenetic landscape in the PDAC patients of the Indian cohort. Our study identified novel differentially methylated genes (mainly NPY and FAIM2) and also validated the previously identified differentially methylated CpG sites associated with PDAC cancer patient’s survival. Comparative analysis of our data with TCGA and CPTAC cohorts showed that both NPY and FAIM2 hyper-methylation and down-regulations can be novel epigenetically regulated genes in the Indian patient population, statistically significantly associated with poor survival and advanced tumour stages. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02737-1.
Collapse
|
6
|
Synergistic Antitumoral Effect of Epigenetic Inhibitors and Gemcitabine in Pancreatic Cancer Cells. Pharmaceuticals (Basel) 2022; 15:ph15070824. [PMID: 35890123 PMCID: PMC9323654 DOI: 10.3390/ph15070824] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenetic modifications could drive some of the molecular events implicated in proliferation, drug resistance and metastasis of pancreatic ductal adenocarcinoma (PDAC). Thus, epigenetic enzyme inhibitors could be the key to revert those events and transform PDAC into a drug-sensitive tumor. We performed a systematic study with five different epigenetic enzyme inhibitors (1, UVI5008, MS275, psammaplin A, and BIX01294) targeting either Histone Deacetylase (HDAC) 1 or 1/4, DNA methyltransferase 3a (DNMT3a), Euchromatic histone lysine methyltransferase 2 (EHMT2), or Sirtuin 1 (SIRT1), as well as one drug that restores the p53 function (P53R3), in three different human PDAC cell lines (SKPC-1, MIA PaCa-2, and BxPC-3) using 2D and 3D cell cultures. The synergistic effect of these antitumoral drugs with gemcitabine was tested and the most efficient combinations were characterized by RNA-seq. The inhibition of HDAC1/4 (MS275), HDAC1/4/SIRT1/DNMT3a (UVI5008) or EHMT2 (BIX01294) induced a significant reduction on the cell viability, even in gemcitabine-resistance cells. The combination of UVI5008 or MS275 with gemcitabine induced a synergistic effect at low concentration and the RNA-Seq analysis revealed some synergy candidate genes as potential biomarkers. Reverting aberrant epigenetic modifications in combination with gemcitabine offers an alternative treatment for PDAC patients, with an important reduction of the therapeutic dose.
Collapse
|
7
|
Mathison AJ, Kerketta R, de Assuncao TM, Leverence E, Zeighami A, Urrutia G, Stodola TJ, di Magliano MP, Iovanna JL, Zimmermann MT, Lomberk G, Urrutia R. Kras G12D induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells. Genome Biol 2021; 22:289. [PMID: 34649604 PMCID: PMC8518179 DOI: 10.1186/s13059-021-02498-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations. RESULTS Here, we apply biological, biochemical, and network biology methods to validate GEMM-derived cell models using inducible KrasG12D expression. We describe the time-dependent, chromatin remodeling program that impacts function during early oncogenic signaling. We find that the KrasG12D-induced transcriptional response is dominated by downregulated expression concordant with layers of epigenetic events. More open chromatin characterizes the ATAC-seq profile associated with a smaller group of upregulated genes and epigenetic marks. RRBS demonstrates that promoter hypermethylation does not account for the silencing of the extensive gene promoter network. Moreover, ChIP-Seq reveals that heterochromatin reorganization plays little role in this early transcriptional program. Notably, both gene activation and silencing primarily depend on the marking of genes with a combination of H3K27ac, H3K4me3, and H3K36me3. Indeed, integrated modeling of all these datasets shows that KrasG12D regulates its transcriptional program primarily through unique super-enhancers and enhancers, and marking specific gene promoters and bodies. We also report chromatin remodeling across genomic areas that, although not contributing directly to cis-gene transcription, are likely important for KrasG12D functions. CONCLUSIONS In summary, we report a comprehensive, time-dependent, and coordinated early epigenomic program for KrasG12D in pancreatic cells, which is mechanistically relevant to understanding chromatin remodeling events underlying transcriptional outcomes needed for the function of this oncogene.
Collapse
Affiliation(s)
- Angela J Mathison
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Romica Kerketta
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Elise Leverence
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Atefeh Zeighami
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Guillermo Urrutia
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy J Stodola
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Michael T Zimmermann
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gwen Lomberk
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Raul Urrutia
- Genomic Science and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA.
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
| |
Collapse
|
8
|
Xiang F, Zhu Z, Zhang M, Wang J, Chen Z, Li X, Zhang T, Gu Q, Wu R, Kang X. 3,3'-Diindolylmethane Enhances Paclitaxel Sensitivity by Suppressing DNMT1-Mediated KLF4 Methylation in Breast Cancer. Front Oncol 2021; 11:627856. [PMID: 34150611 PMCID: PMC8209418 DOI: 10.3389/fonc.2021.627856] [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: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Paclitaxel (PTX) is a first-line chemotherapeutic drug for the treatment of breast cancer, but drug resistance seriously limits its clinical use. The aim of the present work was to explore the effect of 3,3’-diindolylmethane (DIM) on PTX sensitivity and its possible mechanism in breast cancer. The expression of Krüppel-like factor 4 (KLF4) and DNA-methyltransferase 1 (DNMT1) in breast cancer tissues were assessed by immunohistochemistry and Western blotting. The methylation of KLF4 was evaluated by the MassARRAY platform. The lentivirus carrying KLF4 and DNMT1 gene or shRNA targeting DNMT1 were used to overexpress KLF4 or knockdown DNMT1 in MCF-7 and T47D breast cancer cells and the role of KLF4 and DNMT1 in regulation of PTX sensitivity was investigated. The effect of PTX on inhibiting the proliferation of MCF-7 and T47D cells was measured by CCK-8 assay. Flow cytometry was used to examine cell apoptosis. The expression of mRNA and protein was evaluated by qRT-PCR and Western blotting analysis, respectively. Our data showed that the expression of DNMT1 was increased, and the methylation level of CpG sites (−148 bp) in the KLF4 promoter was increased while the KLF4 expression was significantly decreased in breast cancer tissues. Overexpression of KLF4 increased the sensitivity of MCF-7 and T47D cells to PTX. DNMT1 increased the methylation of the KLF4 promoter and decrease the expression of KLF4. Knockdown of DNMT1 increased the sensitivity of MCF-7 and T47D cells to PTX. DIM enhanced the PTX sensitivity of MCF-7 and T47D cells, decreased the expression of DNMT1 and the methylation level of KLF4 promoter, thus increasing the level of KLF4. Furthermore, overexpression of DNMT1 attenuated the effect of DIM on the regulation of PTX sensitivity. Collectively, our data indicated that DNMT1-mediated hypermethylation of KLF4 promoter leads to downregulation of KLF4 in breast cancer. The level of KLF4 is correlated with the sensitivity of MCF-7 and T47D cells to PTX. DIM could enhance the antitumor efficacy of PTX on MCF-7 and T47D cells by regulating DNMT1 and KLF4.
Collapse
Affiliation(s)
- Fenfen Xiang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaowei Zhu
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengzhe Zhang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Wang
- General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zixi Chen
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxiao Li
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tao Zhang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Gu
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Wu
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiangdong Kang
- Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
9
|
Wu W, Cao X, Mo L. Overexpression of KDM4D promotes acute myeloid leukemia cell development by activating MCL-1. Am J Transl Res 2021; 13:2308-2319. [PMID: 34017391 PMCID: PMC8129427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Acute myeloid leukemia (AML) is regarded as a fatal cancer in the world. The overall survival in adult patients with AML is still poor. As lysine demethylases, the KDM4 family is found highly expressed in many kinds of tumors. In this study, we demonstrate that KDM4D is overexpressed in AML and knockdown of KDM4D not only inhibits the proliferation of AML cells, but also induces cell cycle arrest and apoptosis. Furthermore, our research shows that KDM4D can regulate the expression of MCL-1 by demethylating H3K9me3 at the promoter region in AML cells. Besides, we find that high expression of KDM4D is correlated with poor overall survival in AML patients. Taken together, our study demonstrated that KDM4D can promote MCL-1 expression in AML and may serve as a novel target for the treatment of AML.
Collapse
Affiliation(s)
- Wei Wu
- Department of Hepatopancreatobiliary Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and TechnologyGusao Tree Road No. 16 of Jianghan District, Wuhan 430000, Hubei Province, China
| | - Xiaonian Cao
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430040, China
| | - Luxia Mo
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & TechnologyWuhan, China
| |
Collapse
|
10
|
Yang D, Chen T, Zhan M, Xu S, Yin X, Liu Q, Chen W, Zhang Y, Liu D, Yan J, Huang Q, Wang J. Modulation of mTOR and epigenetic pathways as therapeutics in gallbladder cancer. MOLECULAR THERAPY-ONCOLYTICS 2020; 20:59-70. [PMID: 33575471 PMCID: PMC7851494 DOI: 10.1016/j.omto.2020.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/24/2020] [Indexed: 02/05/2023]
Abstract
Gallbladder cancer (GBC) is the most common malignancy of the biliary tract, with extremely dismal prognosis. Limited therapeutic options are available for GBC patients. We used whole-exome sequencing of human GBC to identify the ErbB and epigenetic pathways as two vulnerabilities in GBC. We screened two focused small-molecule libraries that target these two pathways using GBC cell lines and identified the mTOR inhibitor INK-128 and the histone deacetylase (HDAC) inhibitor JNJ-26481585 as compounds that inhibited proliferation at low concentrations. Both significantly suppressed tumor growth and metastases in mouse models. Both synergized with the standard of care chemotherapeutic agent gemcitabine in cell lines and in mouse models. Furthermore, the activation of the mTOR pathway, measured by immunostaining for phosphorylated mTOR and downstream effector S6K1, is correlated with poor prognosis in GBC. Phosphorylated mTOR or p-S6K1 in clinical samples is an independent indicator for overall survival in GBC patients. Taken together, our findings suggest that mTOR inhibitors and HDAC inhibitors can serve as potential therapeutics for GBC, and the phosphorylation of mTOR and S6K1 may serve as biomarkers for GBC.
Collapse
Affiliation(s)
- Dong Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Zhan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sunwang Xu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangfan Yin
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, USA
| | - Qin Liu
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, USA
| | - Wei Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yunhe Zhang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dejun Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinchun Yan
- Department of Radiation Oncology, Cancer Hospital of Fudan University, 270 Dong An Road, Shanghai, China
| | - Qihong Huang
- Shanghai Respiratory Research Institute, Shanghai, China.,Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.,Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China.,The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, USA
| | - Jian Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
11
|
Yang T, Tang H, Risch HA, Olson SH, Petersen G, Bracci PM, Gallinger S, Hung R, Neale RE, Scelo G, Duell EJ, Kurtz RC, Khaw KT, Severi G, Sund M, Wareham N, Amos CI, Li D, Wei P. Incorporating multiple sets of eQTL weights into gene-by-environment interaction analysis identifies novel susceptibility loci for pancreatic cancer. Genet Epidemiol 2020; 44:880-892. [PMID: 32779232 PMCID: PMC7657998 DOI: 10.1002/gepi.22348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 11/11/2022]
Abstract
It is of great scientific interest to identify interactions between genetic variants and environmental exposures that may modify the risk of complex diseases. However, larger sample sizes are usually required to detect gene-by-environment interaction (G × E) than required to detect genetic main association effects. To boost the statistical power and improve the understanding of the underlying molecular mechanisms, we incorporate functional genomics information, specifically, expression quantitative trait loci (eQTLs), into a data-adaptive G × E test, called aGEw. This test adaptively chooses the best eQTL weights from multiple tissues and provides an extra layer of weighting at the genetic variant level. Extensive simulations show that the aGEw test can control the Type 1 error rate, and the power is resilient to the inclusion of neutral variants and noninformative external weights. We applied the proposed aGEw test to the Pancreatic Cancer Case-Control Consortium (discovery cohort of 3,585 cases and 3,482 controls) and the PanScan II genome-wide association study data (replication cohort of 2,021 cases and 2,105 controls) with smoking as the exposure of interest. Two novel putative smoking-related pancreatic cancer susceptibility genes, TRIP10 and KDM3A, were identified. The aGEw test is implemented in an R package aGE.
Collapse
Affiliation(s)
- Tianzhong Yang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Divison of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Hongwei Tang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Gloria Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Paige M. Bracci
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Rayjean Hung
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Rachel E. Neale
- Cancer Aetiology and Prevention Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Eric J. Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program Catalan Institute of Oncology - Bellvitge Biomedical Research Institute (ICO-IDIBELL) Avda. Gran Via 199-203 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Robert C. Kurtz
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, UK
| | - Gianluca Severi
- Gustave Roussy, F-94805, Villejuif, France
- CESP, Fac. de médecine - Univ. Paris-Sud, Fac. de médecine - UVSQ, INSERM, Université Paris-Saclay, 94805, Villejuif, France
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, Sweden
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
12
|
Leite ML, Oliveira KBS, Cunha VA, Dias SC, da Cunha NB, Costa FF. Epigenetic Therapies in the Precision Medicine Era. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Michel Lopes Leite
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | | | - Victor Albuquerque Cunha
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | - Simoni Campos Dias
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
- Animal Biology DepartmentUniversidade de Brasília UnB, Campus Darcy Ribeiro. Brasilia DF 70910‐900 Brazil
| | - Nicolau Brito da Cunha
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | - Fabricio F. Costa
- Cancer Biology and Epigenomics ProgramAnn & Robert H Lurie Children's Hospital of Chicago Research Center, Northwestern University's Feinberg School of Medicine 2430 N. Halsted St., Box 220 Chicago IL 60611 USA
- Northwestern University's Feinberg School of Medicine 2430 N. Halsted St., Box 220 Chicago IL 60611 USA
- MATTER Chicago 222 W. Merchandise Mart Plaza, Suite 12th Floor Chicago IL 60654 USA
- Genomic Enterprise (www.genomicenterprise.com) San Diego, CA 92008 and New York NY 11581 USA
| |
Collapse
|
13
|
Zhou J, Qie S, Fang H, Xi J. MiR-487a-3p suppresses the malignant development of pancreatic cancer by targeting SMAD7. Exp Mol Pathol 2020; 116:104489. [PMID: 32622014 DOI: 10.1016/j.yexmp.2020.104489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To uncover the role of microRNA-487a-3p (miR-487a-3p) in influencing the malignant development of pancreatic cancer and the involvement of its downstream target SMAD7. METHODS MiR-487a-3p level in 40 pancreatic cancer and paracancerous tissues was detected by quantitative real-time polymerase chain reaction (qRT-PCR). The relationship between miR-487a-3p level and clinical indicators in pancreatic cancer patients was analyzed. Regulatory effects of miR-487a-3p on biological phenotypes of pancreatic cancer cells were assessed. At last, the involvement of miR-487a-3p and its downstream target SMAD7 in pancreatic cancer was determined. RESULTS MiR-487a-3p was lowly expressed in pancreatic cancer tissues. Pancreatic cancer patients expressing a low level of miR-487a-3p suffered high metastasis rate and poor prognosis. Overexpression of miR-487a-3p markedly attenuated proliferative and migratory capacities in pancreatic cancer cells. SMAD7 was the downstream target of miR-487a-3p, which was highly expressed in pancreatic cancer samples. Overexpression of SMAD7 reversed the regulatory effects of miR-487a-3p on pancreatic cancer cell phenotypes. CONCLUSIONS MiR-487a-3p is downregulated in pancreatic cancer samples, which is linked to metastasis and prognosis in pancreatic cancer. It inhibits the malignant development of pancreatic cancer by negatively regulating SMAD7.
Collapse
Affiliation(s)
- Jing Zhou
- Medical Care Clinic, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Shuyan Qie
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Hongjuan Fang
- Department of Endocrinology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jianing Xi
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
14
|
Ciernikova S, Earl J, García Bermejo ML, Stevurkova V, Carrato A, Smolkova B. Epigenetic Landscape in Pancreatic Ductal Adenocarcinoma: On the Way to Overcoming Drug Resistance? Int J Mol Sci 2020; 21:ijms21114091. [PMID: 32521716 PMCID: PMC7311973 DOI: 10.3390/ijms21114091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/02/2020] [Accepted: 06/06/2020] [Indexed: 12/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive solid malignancies due to the rapid rate of metastasis and high resistance to currently applied cancer therapies. The complex mechanism underlying the development and progression of PDAC includes interactions between genomic, epigenomic, and signaling pathway alterations. In this review, we summarize the current research findings on the deregulation of epigenetic mechanisms in PDAC and the influence of the epigenome on the dynamics of the gene expression changes underlying epithelial–mesenchymal transition (EMT), which is responsible for the invasive phenotype of cancer cells and, therefore, their metastatic potential. More importantly, we provide an overview of the studies that uncover potentially actionable pathways. These studies provide a scientific basis to test epigenetic drug efficacy in synergy with other anticancer therapies in future clinical trials, in order to reverse acquired therapy resistance. Thus, epigenomics has the potential to generate relevant new knowledge of both a biological and clinical impact. Moreover, the potential, hurdles, and challenges of predictive biomarker discoveries will be discussed, with a special focus on the promise of liquid biopsies.
Collapse
Affiliation(s)
- Sona Ciernikova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia;
- Correspondence: ; Tel.: +421-2-3229-5198
| | - Julie Earl
- Molecular Epidemiology and Predictive Tumor Markers Group, Medical Oncology Research Laboratory, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, 28034 Madrid, Spain; (J.E.); (A.C.)
| | - María Laura García Bermejo
- Biomarkers and Therapeutic Targets Group, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, 28034 Madrid, Spain;
| | - Viola Stevurkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia;
| | - Alfredo Carrato
- Molecular Epidemiology and Predictive Tumor Markers Group, Medical Oncology Research Laboratory, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, 28034 Madrid, Spain; (J.E.); (A.C.)
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia;
| |
Collapse
|
15
|
Differential methylation landscape of pancreatic ductal adenocarcinoma and its precancerous lesions. Hepatobiliary Pancreat Dis Int 2020; 19:205-217. [PMID: 32312637 DOI: 10.1016/j.hbpd.2020.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/18/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pancreatic cancer is one of the most lethal diseases with an incidence almost equal to the mortality. In addition to having genetic causes, cancer can also be considered an epigenetic disease. DNA methylation is the premier epigenetic modification and patterns of aberrant DNA methylation are recognized to be a common hallmark of human tumor. In the multistage carcinogenesis of pancreas starting from precancerous lesions to pancreatic ductal adenocarcinoma (PDAC), the epigenetic changes play a significant role. DATA SOURCES Relevant studies for this review were derived via an extensive literature search in PubMed via using various keywords such as pancreatic ductal adenocarcinoma, precancerous lesions, methylation profile, epigenetic biomarkers that are relevant directly or closely associated with the concerned area of our interest. The literature search was intensively done considering a time frame of 20 years (1998-2018). RESULT In this review we have highlighted the hypermethylation and hypomethylation of the precancerous PDAC lesions (pancreatic intra-epithelial neoplasia, intraductal papillary mucinous neoplasm, mucinous cystic neoplasm and chronic pancreatitis) and PDAC along with the potential biomarkers. We have also achieved the early epigenetic driver that leads to progression from precancerous lesions to PDAC. A bunch of epigenetic driver genes leads to progression of precancerous lesions to PDAC (ppENK, APC, p14/5/16/17, hMLH1 and MGMT) are also documented. We summarized the importance of these observations in therapeutics and diagnosis of PDAC hence identifying the potential use of epigenetic biomarkers in epigenetic targeted therapy. Epigenetic inactivation occurs by hypermethylation of CpG islands in the promoter regions of tumor suppressor genes. We listed all hyper- and hypomethylation of CpG islands of several genes in PDAC including its precancerous lesions. CONCLUSIONS The concept of the review would help to understand their biological effects, and to determine whether they may be successfully combined with other epigenetic drugs. However, we need to continue our research to develop more specific DNA-demethylating agents, which are the targets for hypermethylated CpG methylation sites.
Collapse
|
16
|
Miller AL, Garcia PL, Yoon KJ. Developing effective combination therapy for pancreatic cancer: An overview. Pharmacol Res 2020; 155:104740. [PMID: 32135247 DOI: 10.1016/j.phrs.2020.104740] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 02/08/2023]
Abstract
Pancreatic cancer is a fatal disease. The five-year survival for patients with all stages of this tumor type is less than 10%, with a majority of patients dying from drug resistant, metastatic disease. Gemcitabine has been a standard of care for the treatment of pancreatic cancer for over 20 years, but as a single agent gemcitabine is not curative. Since the only therapeutic option for the over 80 percent of pancreatic cancer patients ineligible for surgical resection is chemotherapy with or without radiation, the last few decades have seen a significant effort to develop effective therapy for this disease. This review addresses preclinical and clinical efforts to identify agents that target molecular characteristics common to pancreatic tumors and to develop mechanism-based combination approaches to therapy. Some of the most promising combinations include agents that inhibit transcription dependent on BET proteins (BET bromodomain inhibitors) or that inhibit DNA repair mediated by PARP (PARP inhibitors).
Collapse
Affiliation(s)
- Aubrey L Miller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham AL, 35294 USA
| | - Patrick L Garcia
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham AL, 35294 USA
| | - Karina J Yoon
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham AL, 35294 USA.
| |
Collapse
|
17
|
Mathison A, Milech De Assuncao T, Dsouza NR, Williams M, Zimmermann MT, Urrutia R, Lomberk G. Discovery, expression, cellular localization, and molecular properties of a novel, alternative spliced HP1γ isoform, lacking the chromoshadow domain. PLoS One 2020; 15:e0217452. [PMID: 32027651 PMCID: PMC7004349 DOI: 10.1371/journal.pone.0217452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
By reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we used a combination of bioinformatics-based methodologies, as well as experimentally-derived datasets, that reveal the existence of a novel short HP1γ (CBX3) isoform, named here sHP1γ, generated by alternative splicing of the CBX3 locus. The sHP1γ mRNA encodes a protein composed of 101 residues and lacks the C-terminal chromoshadow domain (CSD) that is required for dimerization and heterodimerization in the previously described 183 a. a HP1γ protein. Fold recognition, order-to-disorder calculations, threading, homology-based molecular modeling, docking, and molecular dynamic simulations show that the sHP1γ is comprised of a CD flanked by intrinsically disordered regions (IDRs) with an IDR-CD-IDR domain organization and likely retains the ability to bind to the H3K9Me3. Both qPCR analyses and mRNA-seq data derived from large-scale studies confirmed that sHP1γ mRNA is expressed in the majority of human tissues at approximately constant ratios with the chromoshadow domain containing isoform. However, sHP1γ mRNA levels appear to be dysregulated in different cancer types. Thus, our data supports the notion that, due to the existence of functionally different isoforms, the regulation of HP1γ-mediated functions is more complex than previously anticipated.
Collapse
Affiliation(s)
- Angela Mathison
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Thiago Milech De Assuncao
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Monique Williams
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Raul Urrutia
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Gwen Lomberk
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| |
Collapse
|
18
|
Mohammadi M, Irani S, Salahshourifar I, Hosseini J, Moradi A, Pouresmaeili F. Investigation of GSTP1 and epigenetic regulators expression pattern in a population of Iranian patients with prostate cancer. Hum Antibodies 2020; 28:327-334. [PMID: 32831196 DOI: 10.3233/hab-200424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIM Prostate cancer is the leading cause of death in many countries. It is important to diagnose the disease in the early stages. Current methods detect the disease with low specificity. Examining the expression of genes responsible for disease and their epigenetic regulators are good tools in this regard. MATERIAL AND METHODS In this prospective case-control study, 40 Iranian patients with cancer, 40 Iranian patients with prostate hyperplasia, and 40 control samples were examined. After blood sampling from each individual, RNA extraction and cDNA synthesis, GSTP1, HDAC, DNMT3A, and DNMT3B expressions were measured in three understudy groups using specific primers and Real-Time PCR method. RESULTS A reverse correlation was identified between loss of GSTP1 expression and overexpression of HDAC, DNMT3A, and DNMT3B (P value < 0.0001) with a beneficial pattern of cancer development with high efficiency. The significant decrease of GSTP1 expression in patients in comparison to the healthy controls and the elevated expression levels of the studied epigenetic regulators in PCA and BPH samples indicate the impact of the regulators on GSTP1 expression activity. CONCLUSION This study showed that the measurement of combined GSTP1 and its epigenetic regulators' expression could be used as suitable genetic markers for the detection and separation of healthy individuals from prostatic patient groups in the Iranian population. However, a similar study in a larger population of case and control could help us to distinguish between normal, benign, and malignant conditions.
Collapse
Affiliation(s)
- Mahan Mohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iman Salahshourifar
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Jalil Hosseini
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Moradi
- Department of Pathology, Shohadaye Tajrish Hospital, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
19
|
Emerging epigenomic landscapes of pancreatic cancer in the era of precision medicine. Nat Commun 2019; 10:3875. [PMID: 31462645 PMCID: PMC6713756 DOI: 10.1038/s41467-019-11812-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 08/06/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic studies have advanced our understanding of pancreatic cancer at a mechanistic and translational level. Genetic concepts and tools are increasingly starting to be applied to clinical practice, in particular for precision medicine efforts. However, epigenomics is rapidly emerging as a promising conceptual and methodological paradigm for advancing the knowledge of this disease. More importantly, recent studies have uncovered potentially actionable pathways, which support the prediction that future trials for pancreatic cancer will involve the vigorous testing of epigenomic therapeutics. Thus, epigenomics promises to generate a significant amount of new knowledge of both biological and medical importance. In pancreatic cancer, the epigenomic landscape can strongly impact the disease phenotype. Here, the authors discuss recent advances in our understanding of pancreatic cancer epigenomics, and how this knowledge can integrate with precision medicine approaches in this lethal disease.
Collapse
|
20
|
Abstract
PURPOSE OF REVIEW The goal of this manuscript is to review the current literature related to fibrogenesis in the pancreatobiliary system and how this process contributes to pancreatic and biliary diseases. In particular, we seek to define the current state of knowledge regarding the epigenetic mechanisms that govern and regulate tissue fibrosis in these organs. A better understanding of these underlying molecular events will set the stage for future epigenetic therapeutics. RECENT FINDINGS We highlight the significant advances that have been made in defining the pathogenesis of pancreatobiliary fibrosis as it relates to chronic pancreatitis, pancreatic cancer, and the fibro-obliterative cholangiopathies. We also review the cell types involved as well as concepts related to epithelial-mesenchymal crosstalk. Furthermore, we outline important signaling pathways (e.g., TGFβ) and diverse epigenetic processes (i.e., DNA methylation, non-coding RNAs, histone modifications, and 3D chromatin remodeling) that regulate fibrogenic gene networks in these conditions. We review a growing body of scientific evidence linking epigenetic regulatory events to fibrotic disease states in the pancreas and biliary system. Advances in this understudied area will be critical toward developing epigenetic pharmacological approaches that may lead to more effective treatments for these devastating and difficult to treat disorders.
Collapse
Affiliation(s)
- Sayed Obaidullah Aseem
- Division of Gastroenterology and Hepatology, Rochester, FL, USA
- Gastroenterology Research Unit, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Robert C Huebert
- Division of Gastroenterology and Hepatology, Rochester, FL, USA.
- Gastroenterology Research Unit, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Mayo Clinic Foundation, Rochester, MN, USA.
| |
Collapse
|
21
|
Adams CR, Htwe HH, Marsh T, Wang AL, Montoya ML, Subbaraj L, Tward AD, Bardeesy N, Perera RM. Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer. eLife 2019; 8:45313. [PMID: 31134896 PMCID: PMC6538376 DOI: 10.7554/elife.45313] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/02/2019] [Indexed: 12/17/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a heterogeneous disease comprised of a basal-like subtype with mesenchymal gene signatures, undifferentiated histopathology and worse prognosis compared to the classical subtype. Despite their prognostic and therapeutic value, the key drivers that establish and control subtype identity remain unknown. Here, we demonstrate that PDA subtypes are not permanently encoded, and identify the GLI2 transcription factor as a master regulator of subtype inter-conversion. GLI2 is elevated in basal-like PDA lines and patient specimens, and forced GLI2 activation is sufficient to convert classical PDA cells to basal-like. Mechanistically, GLI2 upregulates expression of the pro-tumorigenic secreted protein, Osteopontin (OPN), which is especially critical for metastatic growth in vivo and adaptation to oncogenic KRAS ablation. Accordingly, elevated GLI2 and OPN levels predict shortened overall survival of PDA patients. Thus, the GLI2-OPN circuit is a driver of PDA cell plasticity that establishes and maintains an aggressive variant of this disease.
Collapse
Affiliation(s)
- Christina R Adams
- Department of Anatomy, University of California, San Francisco, San Francisco, United States
| | - Htet Htwe Htwe
- Department of Anatomy, University of California, San Francisco, San Francisco, United States
| | - Timothy Marsh
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Aprilgate L Wang
- Department of Anatomy, University of California, San Francisco, San Francisco, United States
| | - Megan L Montoya
- Department of Anatomy, University of California, San Francisco, San Francisco, United States
| | - Lakshmipriya Subbaraj
- Department of Otolaryngology, University of California, San Francisco, San Francisco, United States
| | - Aaron D Tward
- Department of Otolaryngology, University of California, San Francisco, San Francisco, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, United States
| | - Rushika M Perera
- Department of Anatomy, University of California, San Francisco, San Francisco, United States.,Department of Pathology, University of California, San Francisco, San Francisco, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
22
|
Ettel M, Zhao L, Schechter S, Shi J. Expression and prognostic value of NSD1 and SETD2 in pancreatic ductal adenocarcinoma and its precursor lesions. Pathology 2019; 51:392-398. [PMID: 31060750 DOI: 10.1016/j.pathol.2019.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic regulation is emerging as a critical mechanism for pancreatic ductal adenocarcinoma (PDA) development. Histone methylation is an important regulatory mechanism, altering chromatin structure and promoter accessibility and causing aberrant gene expression. NSD1 and SETD2 genes encoding two histone H3K36 methyltransferases, are mutated or altered in 8-10% of PDA cases. However, whether there is altered protein expression of NSD1 or SETD2 in PDA and its precursors, and whether they have diagnostic or prognostic utility is unknown. Tissue microarrays composed of a total of 190 and 192 duplicated cases of PDA (n=74 and 75), metastatic PDA (n=17 and 18), pancreatic intraepithelial neoplasia (PanIN; n=19 and 24), intraductal papillary mucinous neoplasm (IPMN; n=36), mucinous cystic neoplasm (MCN; n=12) and benign pancreatic tissues (n=27 and 32) were analysed for expression of NSD1 and SETD2 by immunohistochemistry. We assessed intensity and percentage of positive cells. NSD1 expression was significantly increased in metastatic PDA compared to benign ducts, primary PDA, and all other lesions combined (p=0.03, 0.02, and 0.03 respectively). Additionally, significantly decreased SETD2 protein expression was found in metastatic PDA and PanIN lesions compared to benign ducts (p=0.04 and 0.007, respectively). High NSD1 expression was associated with clinical stage III/IV disease (p=0.026), tumour grade 2 (p=0.022), use of neoadjuvant therapy (p=0.037), and overall higher clinical stage (p=0.022). There is no significant difference in overall and progression-free survival between NSD1/SETD2 high and low PDA. Expression of NSD1 and SETD2 is specifically altered in metastatic PDA and some of the PDA precursor lesions, supporting their important role in PDA development and metastasis. In addition, increased NSD1 expression is significantly associated with higher clinical stage and neoadjuvant therapy, suggesting that NSD1 may be a useful prognostic marker.
Collapse
Affiliation(s)
- Mark Ettel
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Shula Schechter
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jiaqi Shi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
23
|
Abstract
Several challenges present themselves when discussing current approaches to the prevention or treatment of pancreatic cancer. Up to 45% of the risk of pancreatic cancer is attributed to unknown causes, making effective prevention programs difficult to design. The most common type of pancreatic cancer, pancreatic ductal adenocarcinoma (PDAC), is generally diagnosed at a late stage, leading to a poor prognosis and 5-year survival estimate. PDAC tumors are heterogeneous, leading to many identified cell subtypes within one patient’s primary tumor. This explains why there is a high frequency of tumors that are resistant to standard treatments, leading to high relapse rates. This review will discuss how epigenetic technologies and epigenome-wide association studies have been used to address some of these challenges and the future promises these approaches hold.
Collapse
Affiliation(s)
- Rahul R Singh
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA; (R.R.S.); (K.M.R.)
| | - Katie M Reindl
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA; (R.R.S.); (K.M.R.)
| | - Rick J Jansen
- Department of Public Health, North Dakota State University, Fargo, ND 58102, USA
- Biostatistics Core Facility, North Dakota State University, Fargo, ND 58102, USA
- Center for Immunization Research and Education, North Dakota State University, Fargo, ND 58102, USA
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58102, USA
| |
Collapse
|
24
|
Abstract
Pancreatic cancer is a devastating disease with poor prognosis in the modern era. Inflammatory processes have emerged as key mediators of pancreatic cancer development and progression. Recently, studies have been carried out to investigate the underlying mechanisms that contribute to tumorigenesis induced by inflammation. In this review, the role of inflammation in the initiation and progression of pancreatic cancer is discussed.
Collapse
Affiliation(s)
- Kamleshsingh Shadhu
- Pancreas Center of The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
- Pancreas Institute of Nanjing Medical University, Nanjing, P.R. China
- School of International Education of Nanjing Medical University, Nanjing, P.R. China
| | - Chunhua Xi
- Pancreas Center of The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
- Pancreas Institute of Nanjing Medical University, Nanjing, P.R. China
| |
Collapse
|
25
|
|
26
|
Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nat Commun 2018; 9:1978. [PMID: 29773832 PMCID: PMC5958058 DOI: 10.1038/s41467-018-04383-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival. Moreover, we describe the state of promoters, enhancers, super-enhancers, euchromatic, and heterochromatic regions for each subtype. Further analyses indicate that the distinct epigenomic landscapes are regulated by different membrane-to-nucleus pathways. Inactivation of a basal-specific super-enhancer associated pathway reveals the existence of plasticity between subtypes. Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets. Pancreatic ductal adenocarcinoma (PDAC) is a complex disease and its underlying epigenomic heterogeneity is not fully understood. Here, the authors utilize patient-derived PDAC xenografts to define the epigenomic landscape of PDAC, highlighting chromatin states linked to differing disease aggressiveness and survival.
Collapse
|
27
|
Epigenetic inhibition of miR-663b by long non-coding RNA HOTAIR promotes pancreatic cancer cell proliferation via up-regulation of insulin-like growth factor 2. Oncotarget 2018; 7:86857-86870. [PMID: 27895308 PMCID: PMC5349959 DOI: 10.18632/oncotarget.13490] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/06/2016] [Indexed: 01/06/2023] Open
Abstract
Pancreatic cancer is one of the most deadly cancers with a poor prognosis. Although microRNAs are involving in the carcinogenesis and development of pancreatic cancer, little information is known regarding the role of miR-663b in pancreatic cancer. In this study, the expression of miR-663b in pancreatic cancer cells was down-regulated by hypermethylation in its putative promoter region, and overexpression of miR-663b repressed cell proliferation, invasion and migration, and induced apoptosis in pancreatic cancer cells. Bioinformatics analysis, luciferase report assay and rescue experiments showed that insulin-like growth factor 2 (IGF2) was a direct target of miR-663b. Results from clinical samples showed that the expression level of miR-663b correlated with the pathological grading, and the expression of miR-663b was down-regulated and was inversely correlated with IGF2 expression level in pancreatic cancer tissues. More importantly, the long non-coding RNA, HOX transcript antisense RNA (HOTAIR), was up-regulated in both pancreatic cancer cells and tissues, and HOTAIR suppressed the expression of miR-663b in pancreatic cancer by histone modification on H3K4me3 and H3K27me3 on miR-663b promoter. Further in vivo studies demonstrated that the stable overexpression of miR-663b or knock-down of HOTAIR inhibited tumor growth and was associated with IGF2 expression. In summary, our studies demonstrated that miR-663b is epigenetically repressed by HOTAIR and exerts its tumor-suppressive function via targeting IGF2 in pancreatic cancer.
Collapse
|
28
|
Next Generation Immunotherapy for Pancreatic Cancer: DNA Vaccination is Seeking New Combo Partners. Cancers (Basel) 2018; 10:cancers10020051. [PMID: 29462900 PMCID: PMC5836083 DOI: 10.3390/cancers10020051] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/07/2018] [Accepted: 02/14/2018] [Indexed: 12/21/2022] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDA) is an almost incurable radio- and chemo-resistant tumor, and its microenvironment is characterized by a strong desmoplastic reaction associated with a significant infiltration of T regulatory lymphocytes and myeloid-derived suppressor cells (Tregs, MDSC). Investigating immunological targets has identified a number of metabolic and cytoskeletal related molecules, which are typically recognized by circulating antibodies. Among these molecules we have investigated alpha-enolase (ENO1), a glycolytic enzyme that also acts a plasminogen receptor. ENO1 is also recognized by T cells in PDA patients, so we developed a DNA vaccine that targets ENO1. This efficiently induces many immunological processes (antibody formation and complement-dependent cytotoxicity (CDC)-mediated tumor killing, infiltration of effector T cells, reduction of infiltration of myeloid and Treg suppressor cells), which significantly increase the survival of genetically engineered mice that spontaneously develop pancreatic cancer. Although promising, the ENO1 DNA vaccine does not completely eradicate the tumor, which, after an initial growth inhibition, returns to proliferate again, especially when Tregs and MDSC ensue in the tumor mass. This led us to develop possible strategies for combinatorial treatments aimed to broaden and sustain the antitumor immune response elicited by DNA vaccination. Based on the data we have obtained in recent years, this review will discuss the biological bases of possible combinatorial treatments (chemotherapy, PI3K inhibitors, tumor-associated macrophages, ENO1 inhibitors) that could be effective in amplifying the response induced by the immune vaccination in PDA.
Collapse
|
29
|
Borgoni S, Iannello A, Cutrupi S, Allavena P, D'Incalci M, Novelli F, Cappello P. Depletion of tumor-associated macrophages switches the epigenetic profile of pancreatic cancer infiltrating T cells and restores their anti-tumor phenotype. Oncoimmunology 2017; 7:e1393596. [PMID: 29308326 DOI: 10.1080/2162402x.2017.1393596] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/11/2017] [Accepted: 10/13/2017] [Indexed: 12/30/2022] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDA) is characterized by a complex tumor microenvironment that supports its progression, aggressiveness and resistance to therapies. The delicate interplay between cancer and immune cells creates the conditions for PDA development, particularly due to the functional suppression of T cell anti-tumor effector activity. However, some of the mechanisms involved in this process are still poorly understood. In this study, we analyze whether the functional and epigenetic profile of T cells that infiltrate PDA is modulated by the microenvironment, and in particular by tumor-associated macrophages (TAMs). CD4 and CD8 T cells obtained from mice orthotopically injected with syngeneic PDA cells, and untreated or treated with Trabectedin, a cytotoxic drug that specifically targets TAMs, were sorted and analyzed by flow cytometry and characterized for their epigenetic profile. Assessment of cytokine production and the epigenetic profile of genes coding for IL10, T-bet and PD1 revealed that T cells that infiltrated PDA displayed activated Il10 promoter and repressed T-bet activity, in agreement with their regulatory phenotype (IL10high/IFNγlow, PD1high). By contrast, in Trabectedin-treated mice, PDA-infiltrating T cells displayed repressed Il10 and Pdcd1 and activated T-bet promoter activity, in accordance with their anti-tumor effector phenotype (IL10low/IFNγhigh), indicating a key role of TAMs in orchestrating functions of PDA-infiltrating T cells by modulating their epigenetic profile towards a pro-tumoral phenotype. These results suggest the targeting of TAMs as an efficient strategy to obtain an appropriate T cell anti-tumor immune response and open new potential combinations for PDA treatment.
Collapse
Affiliation(s)
- Simone Borgoni
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, via Nizza 52, Torino, Italy.,Center for Experimental Research and Medical Studies, University Hospital Città della Salute e della Scienza di Torino, via Santena 5, Torino, Italy
| | - Andrea Iannello
- Center for Molecular Systems Biology, University of Turin, Orbassano, Turin, Italy.,Dept. of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Santina Cutrupi
- Center for Molecular Systems Biology, University of Turin, Orbassano, Turin, Italy.,Dept. of Clinical and Biological Sciences, University of Turin, Orbassano, Turin, Italy
| | - Paola Allavena
- Dept. Immunology and Inflammation, IRCCS-Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (Milano), Italy
| | - Maurizio D'Incalci
- Dept. of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, Milan, Italy
| | - Francesco Novelli
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, via Nizza 52, Torino, Italy.,Center for Experimental Research and Medical Studies, University Hospital Città della Salute e della Scienza di Torino, via Santena 5, Torino, Italy.,Transplant Immunology Service, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy.,Molecular Biotechnology Center, via Nizza 52, Torino, Italy
| | - Paola Cappello
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, via Nizza 52, Torino, Italy.,Center for Experimental Research and Medical Studies, University Hospital Città della Salute e della Scienza di Torino, via Santena 5, Torino, Italy.,Molecular Biotechnology Center, via Nizza 52, Torino, Italy
| |
Collapse
|
30
|
Azizi M, Fard-Esfahani P, Mahmoodzadeh H, Fazeli MS, Azadmanesh K, Zeinali S, Teimoori-Toolabi L. MiR-377 reverses cancerous phenotypes of pancreatic cells via suppressing DNMT1 and demethylating tumor suppressor genes. Epigenomics 2017; 9:1059-1075. [PMID: 28758420 DOI: 10.2217/epi-2016-0175] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AIM The aim was to investigate the effect of miR-377 on DNMT1 expression and cancer phenotype in pancreatic cancer cells. MATERIALS & METHODS Real-time PCR, luciferase assay, MTT and Annexin-PI staining were used. RESULTS Decreased miR-377 and increased DNMT1 (verified as a target for mir-377) levels in pancreatic cancer tissues and cell lines in comparison with normal tissues was confirmed to be influenced by promoter methylation. Also hypermethylation of BNIP3, SPARC, TFPI2 and PENK promoters was observed in tumor samples but not in normal tissues which negatively correlated with their expression. Restoration of miR-377 resulted in a reduction of the expression of DNMT1 and reactivation of BNIP3 and SPARC genes via promoter demethylation. Furthermore, enhanced expression of miR-377 could significantly inhibit cell proliferation and induce apoptosis. CONCLUSION Our findings showed that miR-377 through targeting DNMT1 could reduce DNA methylation of some tumor suppressor genes and restore their expression in pancreatic cancer cells.
Collapse
Affiliation(s)
- Masoumeh Azizi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Habibollah Mahmoodzadeh
- Cancer Institute of Iran, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Division of Colo-Rectal Surgery, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sirous Zeinali
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
31
|
Xie VK, Li Z, Yan Y, Jia Z, Zuo X, Ju Z, Wang J, Du J, Xie D, Xie K, Wei D. DNA-Methyltransferase 1 Induces Dedifferentiation of Pancreatic Cancer Cells through Silencing of Krüppel-Like Factor 4 Expression. Clin Cancer Res 2017; 23:5585-5597. [PMID: 28659310 DOI: 10.1158/1078-0432.ccr-17-0387] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/19/2017] [Accepted: 06/19/2017] [Indexed: 01/22/2023]
Abstract
Purpose: The dismal prognosis of pancreatic cancer has been linked to poor tumor differentiation. However, molecular basis of pancreatic cancer differentiation and potential therapeutic value of the underlying molecules remain unknown. We investigated the mechanistic underexpression of Krüppel-like factor 4 (KLF4) in pancreatic cancer and defined a novel epigenetic pathway of its activation for pancreatic cancer differentiation and treatment.Experimental Design: Expressions of KLF4 and DNMT1 in pancreatic cancer tissues were determined by IHC and the genetic and epigenetic alterations of KLF4 in and KLF4's impact on differentiation of pancreatic cancer were examined using molecular biology techniques. The function of dietary 3,3'-diindolylmethane (DIM) on miR-152/DNMT1/KLF4 signaling in pancreatic cancer was evaluated using both cell culture and animal models.Results: Overexpression of DNMT1 and promoter hypermethylation contributed to decreased KLF4 expression in and associated with poor differentiation of pancreatic cancer. Manipulation of KLF4 expression significantly affected differentiation marker expressions in pancreatic cancer cells. DIM treatment significantly induced miR-152 expression, which blocked DNMT1 protein expression and its binding to KLF4 promoter region, and consequently reduced promoter DNA methylation and activated KLF4 expression in pancreatic cancer cells. In addition, DIM treatment caused significant inhibition of cell growth in vitro and tumorigenesis in animal models of pancreatic cancer.Conclusions: This is the first demonstration that dysregulated KLF4 expression associates with poor differentiation of pancreatic cancer. Epigenetic activation of miR-152/DNMT1/KLF4 signaling pathway by dietary DIM causes differentiation and significant growth inhibition of pancreatic cancer cells, highlighting its translational implications for pancreatic and other cancers. Clin Cancer Res; 23(18); 5585-97. ©2017 AACR.
Collapse
Affiliation(s)
- Victoria K Xie
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhiwei Li
- Department Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yongmin Yan
- Department Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhiliang Jia
- Department Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiangsheng Zuo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiawei Du
- Department of Oncology, Shanghai Tongji University East Hospital, Shanghai, P.R. China
| | - Dacheng Xie
- Department of Oncology, Shanghai Tongji University East Hospital, Shanghai, P.R. China
| | - Keping Xie
- Department Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Daoyan Wei
- Department Gastroenterology Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
32
|
Abstract
The pancreatic adenocarcinoma initiation results from the interaction of genetic events combined with multiple other factors. Among the genetic alterations that contribute to the pathogenesis of this disease, the mutation of the KRAS oncogene is required but not sufficient to trigger this cancer. Pancreatitis, an inflammatory disease, facilitates and accelerates the transformation of pancreatic cells when the KRAS oncogene is mutated. Of note, the repertoire of molecular mediators of pancreatitis which are responsible of the promotion of KRAS-mediated transformation is not completely defined. Importantly, autophagy has been proposed as one of the cellular mechanisms contributing to pancreatic carcinogenesis, especially in the initial phases, in which the oncogene KRAS appears to play its leading role. In addition, autophagy is strongly induced during pancreatitis. Although some aspects of autophagy in pancreatic cancer development are not completely established, we can affirm that overexpression of VMP1, an inducer of autophagy which is specifically activated in pancreas during pancreatitis, improves the development of pancreatic precancerous lesions PanINs when the oncogene KRAS is mutated. In addition, inhibition of the autophagic flux with chloroquine inhibits the KRAS pro-tumor effect in the pancreas. In conclusion, activation of expression of VMP1 improves the pro-tumor role of KRAS in pancreas.
Collapse
Affiliation(s)
- Juan L Iovanna
- Centre de recherche en cancérologie de Marseille (CRCM), Inserm U1068, CNRS UMR 7258, Aix-Marseille Université et Institut Paoli-Calmettes, Parc scientifique et technologique de Luminy, 163, avenue de Luminy, 13288 Marseille, France
| |
Collapse
|
33
|
Borazanci E, Dang CV, Robey RW, Bates SE, Chabot JA, Von Hoff DD. Pancreatic Cancer: “A Riddle Wrapped in a Mystery inside an Enigma”. Clin Cancer Res 2017; 23:1629-1637. [DOI: 10.1158/1078-0432.ccr-16-2070] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/27/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most difficult-to-treat cancers. With an increasing incidence and inability to make major progress, it represents the very definition of unmet medical need. Progress has been made in understanding the basic biology—systematic genomic sequencing has led to the recognition that PDAC is not typically a heavily mutated tumor, although there are exceptions. The most consistently mutated genes are KRAS, CDKN2A, TP53, and SMAD4/DPC4. Study of familial PDAC has led to the recognition that a variety of defects in DNA repair genes can be associated with the emergence of pancreatic cancer. Recent studies suggest that epigenetics may play a larger role than previously recognized. A major new understanding is the recognition that PDAC should be considered a composite of tumor cells, as well as pancreatic stellate cells, immune cells, and extracellular matrix. The individual components contribute to metabolic aberration, immune dysfunction, and chemotherapy resistance, and therapeutic innovations may be needed to address them individually. It has also been recognized that metastatic seeding from PDAC occurs very early in the disease course—in an estimated 73% of cases, once the tumor reaches 2 cm. The implication of this is that therapies directed toward micrometastatic disease and increasing fractional cell kill are most needed. Neoadjuvant approaches have been taken to increase resectability and improve outcome. So much work remains, and most critical is the need to understand how this tumor originates and develops. Clin Cancer Res; 23(7); 1629–37. ©2017 AACR.
See all articles in this CCR Focus section, “Pancreatic Cancer: Challenge and Inspiration.”
Collapse
Affiliation(s)
- Erkut Borazanci
- 1HonorHealth, Scottsdale, Arizona and TGen, Phoenix, Arizona
| | - Chi V. Dang
- 2Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Susan E. Bates
- 4Columbia University Medical Center, New York, New York
- 5James J. Peters Bronx VA Medical Center, Bronx, New York
| | | | | |
Collapse
|
34
|
Alterations of Epigenetic Regulators in Pancreatic Cancer and Their Clinical Implications. Int J Mol Sci 2016; 17:ijms17122138. [PMID: 27999365 PMCID: PMC5187938 DOI: 10.3390/ijms17122138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/08/2016] [Accepted: 12/14/2016] [Indexed: 12/11/2022] Open
Abstract
Pancreatic cancer is one of the most aggressive human cancer types with a five-year survival less than 7%. Emerging evidence revealed that many genetic alterations in pancreatic cancer target epigenetic regulators. Some of these mutations are driver mutations in cancer development. Several most important mechanisms of epigenetic regulations include DNA methylation, histone modifications (methylation, acetylation, and ubiquitination), chromatin remodeling, and non-coding ribonucleic acids (RNAs). These modifications can alter chromatin structure and promoter accessibility, and thus lead to aberrant gene expression. However, exactly how these alterations affect epigenetic reprogramming in pancreatic cancer cells and in different stages of tumor development is still not clear. This mini-review summarizes the current knowledge of epigenetic alterations in pancreatic cancer development and progression, and discusses the clinical applications of epigenetic regulators as diagnostic biomarkers and therapeutic targets in pancreatic cancer.
Collapse
|
35
|
Demir IE, Ceyhan GO, Friess H. Epigenomic therapies: the potential of targeting SIRT6 for the treatment of pancreatic cancer. Expert Opin Ther Targets 2016; 21:1-3. [PMID: 27885875 DOI: 10.1080/14728222.2017.1265507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ihsan Ekin Demir
- a Department of Surgery, Klinikum rechts der Isar , Technische Universität München , Munich , Germany
| | - Güralp O Ceyhan
- a Department of Surgery, Klinikum rechts der Isar , Technische Universität München , Munich , Germany
| | - Helmut Friess
- a Department of Surgery, Klinikum rechts der Isar , Technische Universität München , Munich , Germany
| |
Collapse
|
36
|
Iovanna JL. Autophagy Induced during Pancreatitis Promotes KRAS-Dependent Transformation in the Pancreas. Front Oncol 2016; 6:226. [PMID: 27833900 PMCID: PMC5080356 DOI: 10.3389/fonc.2016.00226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/10/2016] [Indexed: 12/18/2022] Open
Abstract
Pancreatitis is an inflammatory disease that both facilitates and accelerates the transformation of pancreatic cells upon activation of the KRAS oncogene. Autophagy is proposed to be one of the cellular mechanisms contributing to pancreatic carcinogenesis, especially during initial stages in which the KRAS oncogene appears to play a key role. Autophagy is also strongly induced during pancreatitis by the overexpression of VMP1. We recently developed a genetically engineered mouse model in which the VMP1 protein is induced simultaneously with the activation of the oncogene KrasG12D specifically in the pancreas, by the addition of doxycycline to a water drink. Using this sophisticated animal model, we can affirm that pancreatic autophagy, induced during pancreatitis by the overexpression of VMP1, promotes the development of precancerous lesions when induced by the mutated KRAS. In addition, the treatment of these mice with chloroquine, an inhibitor of autophagic flux, reverses the effects of VMP1 in pancreatic cancer induced by the KRAS oncogene. Overall, these results bear both mechanistic and biomedical relevance for further understanding and potentially targeting pathways that are critical for initiating pancreatic carcinogenesis, particularly if associated with pancreatitis.
Collapse
Affiliation(s)
- Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université et Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy , Marseille , France
| |
Collapse
|
37
|
Baines A, Martin P, Rorie C. Current and Emerging Targeting Strategies for Treatment of Pancreatic Cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 144:277-320. [DOI: 10.1016/bs.pmbts.2016.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|